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Refactor: #8093 - Unexpected unknown property "user-focus" - #8094

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Oct 13, 2025
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Refactor: #8093 - Unexpected unknown property "user-focus" #8094
AlexeyGirin merged 3 commits into
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copilot/refactor-invalid-css-properties

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Copilot AI commented Oct 8, 2025 •
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  • Explore repository structure and understand the issue
  • Locate the problematic file: packages/ketcher-macromolecules/src/components/Ruler/RulerArea.module.less
  • Identify the invalid CSS property user-focus: none on line 36
  • Understand the context - the property is in .rulerInputDragging class which is used during drag operations
  • Remove the invalid user-focus: none property from line 36
  • Verify the fix with stylelint
  • Build and test the changes
  • Apply prettier formatting fixes

Summary

Fixed the issue by removing the invalid CSS property user-focus: none from line 36 in packages/ketcher-macromolecules/src/components/Ruler/RulerArea.module.less.

Changes made:

  1. Removed the non-standard user-focus: none CSS property which is not part of W3C specifications
  2. Applied prettier formatting to the file (selector split and newline at EOF)

Why this is correct:

  • The user-focus property does not exist in CSS specifications and causes validation warnings
  • The intended functionality (preventing focus during drag) is already achieved through the disabled={isDragging} attribute on the input element in RulerInput.tsx
  • The user-select: none property (which is valid) remains to prevent text selection during drag

Testing:

  • ✅ Stylelint passes
  • ✅ Prettier formatting passes
  • ✅ Package builds successfully
  • ✅ No functional changes expected - the behavior is already handled by the disabled attribute
Original prompt

This section details on the original issue you should resolve

<issue_title>Refactor: Unexpected unknown property "user-focus"</issue_title>
<issue_description>Problem:
Unexpected unknown property "user-focus"

Why is this an issue?
The W3C specifications define the valid CSS properties. Only the official and browser-specific properties should be used to get the expected impact in the final rendering.

Noncompliant code example

a {
  colour: blue; /* Noncompliant; colour is not part of the specifications */
}

Compliant solution

a {
  color: blue;
}

Problem locations:
packages/ketcher-macromolecules/src/components/Ruler/RulerArea.module.less:36</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes #8093

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

Copilot AI and others added 2 commits October 8, 2025 20:14
@AlexeyGirin
Remove invalid CSS property 'user-focus' from RulerArea.module.less
8988544 
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
@AlexeyGirin
Apply prettier formatting to RulerArea.module.less
f3914c3 
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Copilot AI requested a review from AlexeyGirin October 8, 2025 20:32
@AlexeyGirin
AlexeyGirin marked this pull request as ready for review October 8, 2025 21:27
@AlexeyGirin AlexeyGirin changed the title [WIP] Refactor invalid CSS properties for compliance Refactor: #8093 - Unexpected unknown property "user-focus" Oct 8, 2025
@AlexeyGirin

AlexeyGirin commented Oct 10, 2025

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Check ruler behaviour

@AlexeyGirin
AlexeyGirin merged commit c6af0da into master Oct 13, 2025
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@AlexeyGirin
AlexeyGirin deleted the copilot/refactor-invalid-css-properties branch October 13, 2025 19:36
AlexeyGirin added a commit that referenced this pull request Nov 5, 2025
@AlexeyGirin
Refactor: #8093 - Unexpected unknown property "user-focus" (#8094)
237d4d2 
* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
AlexeyGirin added a commit that referenced this pull request Nov 5, 2025
@AlexeyGirin
Refactor: #8093 - Unexpected unknown property "user-focus" (#8094)
0e531df 
* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
AlexeyGirin added a commit that referenced this pull request Nov 7, 2025
@AlexeyGirin
@KristinaKasyanovskaya @rrodionov91 @ivanmaslow @Zhirnoff @svvald @ViktoriaTkacheva @ljubica-milovic @KukushkinDmi1riy
#7735 - System shows inner circles of aromatized benzene rings from c…
ddf9b22 
…ollapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f73)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Initial plan

* f2

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* Initial plan

* Initial plan

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>
Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: ViktoriaTkacheva <139227567+ViktoriaTkacheva@users.noreply.github.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
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AlexeyGirin added a commit that referenced this pull request Nov 7, 2025
@AlexeyGirin
@KristinaKasyanovskaya @rrodionov91 @ivanmaslow @Zhirnoff @svvald @ViktoriaTkacheva @ljubica-milovic @KukushkinDmi1riy
#7735 - System shows inner circles of aromatized benzene rings from c…
bff96e8 
…ollapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f73)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
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* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Initial plan

* f2

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* Initial plan

* Initial plan

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>
Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: ViktoriaTkacheva <139227567+ViktoriaTkacheva@users.noreply.github.com>
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AlexeyGirin added a commit that referenced this pull request Nov 7, 2025
@AlexeyGirin
@KristinaKasyanovskaya @rrodionov91 @ivanmaslow @Zhirnoff @svvald @ViktoriaTkacheva @ljubica-milovic @KukushkinDmi1riy
#7735 - System shows inner circles of aromatized benzene rings from c…
6e4f70d 
…ollapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f73)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Initial plan

* f2

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

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* f1

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* Initial plan

* Initial plan

---------

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Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
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AlexeyGirin added a commit that referenced this pull request Nov 7, 2025
@AlexeyGirin
@KristinaKasyanovskaya @rrodionov91 @ivanmaslow @Zhirnoff @svvald @ViktoriaTkacheva @ljubica-milovic @KukushkinDmi1riy
#7735 - System shows inner circles of aromatized benzene rings from c…
613c1b4 
…ollapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* fixes

---------

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* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

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---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f73)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Initial plan

* f2

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* Initial plan

* Initial plan

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>
Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: ViktoriaTkacheva <139227567+ViktoriaTkacheva@users.noreply.github.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
AlexeyGirin added a commit that referenced this pull request Nov 7, 2025
@AlexeyGirin
@KristinaKasyanovskaya @svvald @ViktoriaTkacheva @ivanmaslow @Zhirnoff @rrodionov91 @ljubica-milovic @KukushkinDmi1riy
#5578 - Peptide section for ambiguous monomers should have "Ambiguous…
a297100 
… Amino Acids" name (#8263)

* Initial plan

* Fix: Change "Amino acids" to "Amino Acids" in MonomerGroups enum

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support und…
AlexeyGirin added a commit that referenced this pull request Nov 7, 2025
@AlexeyGirin
@KristinaKasyanovskaya @svvald @ViktoriaTkacheva @ivanmaslow @Zhirnoff @rrodionov91 @ljubica-milovic @KukushkinDmi1riy
#5580 - Order of sections for ambiguous bases is wrong - Ambiguous Ba…
1947482 
…ses should come first (#8264)

* Initial plan

* Fix order of ambiguous bases sections to match requirements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/…
AlexeyGirin added a commit that referenced this pull request Nov 7, 2025
@AlexeyGirin
@svvald @ViktoriaTkacheva @ivanmaslow @Zhirnoff @KristinaKasyanovskaya @rrodionov91 @ljubica-milovic @KukushkinDmi1riy
#5927 - Font size and label position should be corrected at "Open str…
9206769 
…ucture" dialog (#8286)

* Initial plan

* Fix font size and label alignment in Open structure dialog dropdowns

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGi…
AlexeyGirin added a commit that referenced this pull request Nov 19, 2025
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
#7372 "Ghost image" doesn't satisfy the UX design (#8309)
9ed2a83 
* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Initial plan

* f2

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* Initial plan

* Initial plan

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>
Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: ViktoriaTkacheva <139227567+ViktoriaTkacheva@users.noreply.github.com>
Co-authored-by…
AlexeyGirin added a commit that referenced this pull request Nov 19, 2025
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
#6731 Ambiguous phosphates (alternatives and mixed) in sequence shown…
cc917c2 
… as % symbol instead of @ symbol (#8580)

* Initial plan

* Fix: Add Phosphate class to ambiguous monomer @ symbol check

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
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Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

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---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Initial plan

* f2

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* Initial plan

* Initial plan

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>
Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
Co-authored-by: Ivan Maslov <165396466+ivanmasl…
AlexeyGirin added a commit that referenced this pull request Nov 20, 2025
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
#8509 Refactor: Variables are missing in props validation (let's rewr…
1fa8e7c 
…ite JS to TS) 12 (#8550)

* Initial plan

* Convert Check.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8556 System losts Modification types values while save it KET (#8557)

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGir…
AlexeyGirin added a commit that referenced this pull request Nov 20, 2025
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
Disable "Change direction" and "Attach S-Group..." for bonds between …
073b33b 
…monomers (#8604)

* Initial plan

* Disable Change direction and Attach S-Group for bonds between monomers

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8509 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 12 (#8550)

* Initial plan

* Convert Check.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8556 System losts Modification types values while save it KET (#8557)

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to …
AlexeyGirin added a commit that referenced this pull request Nov 20, 2025
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
#7566 Autotests: Refactor fileFormats.ts (get rid of it) (#8598)
7637fbd 
* Initial plan

* Create file structure and update first batch of test files

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Update remaining test files and remove fileFormats.ts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove extraneous quotes from mol file

* Clean up quotation marks in mol file

Removed unnecessary quotation marks from the file.

* Remove unnecessary characters from MOL file

* Update one-unknown-superatom-contracted.mol

* Update one-unknown-superatom-expanded.mol

* Remove unnecessary quotes from mol file

* Update functional-groups-expanded-contracted.mol

* Clean up quotation marks in mol file

Removed unnecessary quotation marks from the file.

* Remove extra quotes from one-functional-group-expanded.mol

* Remove extraneous quotes from mol file

* Clean up quotation marks in mol file

Removed unnecessary quotation marks at the beginning and end of the file.

* Update unknown-superatom-expanded-contracted.mol

* #8509 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 12 (#8550)

* Initial plan

* Convert Check.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8556 System losts Modification types values while save it KET (#8557)

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: impl…
AlexeyGirin added a commit that referenced this pull request Nov 20, 2025
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#8509 Refactor: Variables are missing in props validation (let's rewr…
d36153e 
…ite JS to TS) 12 (#8550)

* Initial plan

* Convert Check.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8556 System losts Modification types values while save it KET (#8557)

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

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---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGir…
AlexeyGirin added a commit that referenced this pull request Nov 20, 2025
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
Disable "Change direction" and "Attach S-Group..." for bonds between …
3958d0e 
…monomers (#8604)

* Initial plan

* Disable Change direction and Attach S-Group for bonds between monomers

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8509 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 12 (#8550)

* Initial plan

* Convert Check.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8556 System losts Modification types values while save it KET (#8557)

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to …
AlexeyGirin added a commit that referenced this pull request Nov 20, 2025
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
#7566 Autotests: Refactor fileFormats.ts (get rid of it) (#8598)
e8c05e8 
* Initial plan

* Create file structure and update first batch of test files

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Update remaining test files and remove fileFormats.ts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove extraneous quotes from mol file

* Clean up quotation marks in mol file

Removed unnecessary quotation marks from the file.

* Remove unnecessary characters from MOL file

* Update one-unknown-superatom-contracted.mol

* Update one-unknown-superatom-expanded.mol

* Remove unnecessary quotes from mol file

* Update functional-groups-expanded-contracted.mol

* Clean up quotation marks in mol file

Removed unnecessary quotation marks from the file.

* Remove extra quotes from one-functional-group-expanded.mol

* Remove extraneous quotes from mol file

* Clean up quotation marks in mol file

Removed unnecessary quotation marks at the beginning and end of the file.

* Update unknown-superatom-expanded-contracted.mol

* #8509 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 12 (#8550)

* Initial plan

* Convert Check.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8556 System losts Modification types values while save it KET (#8557)

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* fixes

* f2

* f3

* f4

* f5

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Ivan Maslov <165396466+ivanmaslow@users.noreply.github.com>
Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: impl…
AlexeyGirin added a commit that referenced this pull request Nov 21, 2025
@AlexeyGirin
@rrodionov91 @svvald @KristinaKasyanovskaya @Zhirnoff @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
#8567 Refactor: Deprecated APIs should not be used (part 5) (#8569)
5fc4e5a 
* Initial plan

* Fix deprecated event global usage in templatePreview.ts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* Initial plan

* Fix deprecated event global usage in templatePreview.ts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f2

* Fixed build (#8607)

* - fixed build

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* Disable "Change direction" and "Attach S-Group..." for bonds between monomers (#8604)

* Initial plan

* Disable Change direction and Attach S-Group for bonds between monomers

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8509 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 12 (#8550)

* Initial plan

* Convert Check.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8556 System losts Modification types values while save it KET (#8557)

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8500 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 3 (#8513)

* Initial plan

* Refactor AtomInfo from JSX to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8503 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 6 (#8515)

* Initial plan

* Refactor OutinerRow.jsx to TypeScript with proper props validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Complete OutinerRow TypeScript migration

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8506 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 9 (#8518)

* Initial plan

* Convert About.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8508 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 11 (#8520)

* Initial plan

* Convert FrozenInput from JSX to TSX with proper TypeScript types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: Variables are missing in props validation (let's rewrite JS to TS) 14 (#8522)

* Initial plan

* Refactor: Convert Recognize.jsx to TypeScript with proper prop types validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8510 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 13 (#8523)

* Initial plan

* Convert ErrorsCheck.jsx to TypeScript with proper type definitions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8502 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 5 (#8524)

* Initial plan

* Refactor MainRow.jsx to TypeScript with prop type validation

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8538 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 7) (#8539)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8540 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 8) (#8541)

* Initial plan

* Remove redundant type assertions and casts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8542 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 9) (#8543)

* Initial plan

* Remove redundant type assertions from DrawingEntitiesManager and sgroup

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8546 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 11) (#8547)

* Initial plan

* Remove redundant type assertions and non-null assertions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Autotests: 8553 autotests update the monomer preview (#8558)

* draft

* Final

* f2

* #8554 System losts AxoLabs alias while save it KET (#8555)

* Initial plan

* Add aliasAxoLabs to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* Create page object for Abbreviation Preview Tooltip (#8552)

* Initial plan

* Create AbbreviationPreviewTooltip page object and refactor tests

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

---------

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Co-authored-by: Alexey Girin <agirin@mail.ru>

* Initial plan

* Add modificationTypes and naturalAnalog to KET serialization

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Remove naturalAnalog assignment for CHEM monomers

Remove naturalAnalog property assignment for non-CHEM monomers.

* fixes

* f2

* f3

* f4

* f5

---------

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* #7372 "Ghost image" doesn't satisfy the UX design (#8309)

* Initial plan

* Fix ghost image styling to match UX design

- Changed GhostMonomer and GhostRnaPreset components to use white fill with stroke instead of solid gray fill
- Updated all monomer shapes (sugar, phosphate, base) to have white background with #CAD3DD border
- Added strokeWidth of 2px to maintain proper visibility
- All tests pass and linting is clean

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review feedback - use numeric strokeWidth

Changed strokeWidth from string "2" to numeric 2 for better SVG attribute handling

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

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* Simplify empty name check using optional chaining

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #8351 Autotests for Ketcher 3.9.0 bugs (#8391)

* First draft

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* f7

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388)

* #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module

* fixes

* f2

* f3

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>

* draft

* 2

* 3

* 4

* 5

* 6

* 7

* #8281 - Adjust subscription to library update event of Ketcher API  (#8382)

* #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225)

* Initial plan

* Refactor nested ternary in Analyse.jsx into separate method

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224)

* Initial plan

* Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223)

* Initial plan

* Refactor: Extract nested ternary operations into independent functions

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222)

* Initial plan

* Refactor nested ternary operations into if-else statements

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371)

* #7905 – Change selection logic

* #7905 – Enable Indigo functions

* #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point

* #7905 – Support undo/redo for reassign attachment point operation

* #7905 – Support undo/redo for reassign leaving atom operation

* #7905 – Support undo/redo for assign attachment atom operation

* #7905 – Fix build failure

* #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard

* #7905 – Enable layout and clenaup tools, add label to HELM alias input

* #7905 – Revert initial notification change

* #7905 – Update screenshots

* #7905 – Update screenshots

* #7905 – Remove outdated test cases

* #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288)

* Initial plan

* Fix sorting of mixed base percentages in tooltip

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336)

* #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode

* #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure”

* #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements

* #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met

* #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors 

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>

* #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233)

* Initial plan

* Fix bond direction change in context menu for stereo bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify bond type check logic

* Fix return statement formatting in useBondTypeChange

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* fixes

* f2

* f3

* f4

---------

Co-authored-by: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: KukushkinDmi1riy <42671583+KukushkinDmi1riy@users.noreply.github.com>
Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

* Refactor: #8153 - Deprecated APIs should not be used (part 2)  (#8154)

* Initial plan

* Replace deprecated APIs with modern alternatives

- Replace all substr() calls with slice() in v3000.js
- Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js
- Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* f1

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409)

* The function clickOnBond is replaced with getBondLocator.click()
The function declaration of clickOnBond is removed

* The BondType and getBondByIndex are removed from import

* #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317)

* Initial plan

* Fix selection count for sense/antisense chains

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix ESLint error in test

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Address code review: Use proper type assertion instead of any

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197)

* Initial plan

* Fix aromatic circle rendering for collapsed monomers

Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* #7500 - Update the monomer preview   (#8134)

* feat: update the monomer preview

* fix: fix code after review

* test:update snapshots

* test:update snapshots

* test:update spanshots

* test:update spanshots

* test:update spanshots

* test: update snapshots

* Refactor: #8130 - Fix for many sonar issues (#8131)

* Fix accessibility and spacing issues from Sonar reports

* fixes

* f2

* f3

* f4

* Fix accessibility and spacing issues from Sonar reports

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* Refactor: #8093 - Unexpected unknown property "user-focus"  (#8094)

* Initial plan

* Remove invalid CSS property 'user-focus' from RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Apply prettier formatting to RulerArea.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8103 - Use 'String#startsWith' method instead (#8119)

* Initial plan

* Refactor: #8103 - Use 'String#startsWith' method instead

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146)

* Initial plan

* Add readonly modifiers to fields that are only assigned in constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152)

* Initial plan

* Fix redundant types in unions and intersections

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8160 - Unnecessary constructors should be removed (#8161)

* Initial plan

* Refactor: Remove unnecessary empty constructors

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8162 - Make this public static property readonly (#8163)

* Initial plan

* Add readonly qualifier to public static viewName properties

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* Refactor: #8164 - Duplicated font names should be removed  (#8165)

* Initial plan

* Remove duplicated font names in globals.css

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8156 - Promises should not be misused (#8170)

* Initial plan

* Fix promise misuse in fullscreen APIs and async event handler

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171)

* Initial plan

* Remove redundant type aliases and replace with underlying types

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #4467 - Macro: Ket label should be renamed to Ket Format (#8191)

* Initial plan

* Rename Ket label to Ket Format in macromolecule editor

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fixes

* f2

* f3

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192)

* Initial plan

* Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Also fix spacing in AmbiguousMonomerPreview ContentLine

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196)

* Initial plan

* Fix CHEM ghost image color issue

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8067 - Do not save added or updated monomer in local storage (#8135) (#8140)

(cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76)

* #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194)

* Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label  (#8266)

* fix: send render-stereo-style per settings; align PNG/SVG with canvas

* fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability

* Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272)

* Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277)

* Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280)

* Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275)

* The function moveOnBond is replaced with getBondLocator.hover() (#8298)

The functions declaration of moveOnBond and waitForElementInCanvas are removed

* #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252)

* First draft

* f22

* f3

* f4

* * Initial plan

* Disable Symbol and Name fields when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Add test to verify Symbol and Name fields are disabled when Type is not selected

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190)

* Initial plan

* Fix: Update tooltip to show 'minimize window' when expanded

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

* f3

* f4

* f5

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8158 - Replace this union type with a type alias (#8159)

* Initial plan

* Refactor: Replace union types with type aliases

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused imports after type alias refactoring

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Fix: Remove unused BackBoneSequenceNode import

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Refactor: #8168 - Selectors should not be duplicated  (#8169)

* Initial plan

* Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* feat(PO): add ReactionAutoMappingDialog page object (#8244)

- Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog.
- Introduced `constants.ts` with `AutoMapModeOption` enum.
- Removed `applyAutoMapMode` function from `index.ts`.
- Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function.
- Updated screenshots accordingly.

* Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238)

* - add test;
- add test file;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add test file;
- add screenshots

* - add tests for API switching from molecules mode to macromolecules;
- add screenshots

* - delete exeptions

* - add test;
- add screenshot

* #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232)

* Initial plan

* Add grabbing cursor when dragging monomers from library

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

---------

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Co-authored-by: Mikhail Zhirnov <62464241+Zhirnoff@users.noreply.github.com>

* Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279)

* #8294 - Do allow to collapse s-groups (superatom type) without name (#8297)

* Initial plan

* Disable Contract Abbreviation for s-groups without name

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Use optional chaining to safely check name property

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Simplify empty name check using optional chaining

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---------

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* #7936 - Add tooltips to some attachment points in the monomer creation wizard

* Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321)

* first

* 2

* 3

* 10

* 11

* 12

* 13

* 14

* 1111

* Final

* f2

* Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320)

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add test files;
- add screenshots

* - add tests;
- add screenshots

* Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271)

* #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module

* Update autotests

* Update more autotests

* Skip failing tests

(cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7)

* fix

---------

Co-authored-by: Nikita Chistousov <nikita_chistousov@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038)

* Autotests: 8322 autotests axolabs format support (#8329)

* first

* Final

* Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278)

* Backmerge: #8005 – Changing name for attachment points works wrong (#8282)

* #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms  (#8343)

* fix: fix buttons logic

* fix: fix primary button logic

* #8296 - Make Create Monomer tool disableable (#8346) (#8348)

- made create-monomer functionality disableable using buttons config
- bumped ketcher to 3.9.0-rc.3

(cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b)

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148)

* Initial plan

* Refactor: Replace logical OR (||) with nullish coalescing (??) operator

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218)

* Initial plan

* Fix Promise rejection to use Error object in FileInputForm

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219)

* Initial plan

* Fix Promise rejections to use Error objects in remoteStructService

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220)

* Initial plan

* Refactor: Wrap FileReader error event in Error object for Promise rejection

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

---------

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* #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349)

* fix: menu option mark as connection point disabled

* test: fix test

* fix: prevent modification list overflow in monomer preview tooltip (#8350)

* #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342)

* fix: fix Modification drop-down list

* fix: fix add-modification-type option

* fix: fix error message

* fix: add limit on the modififcations fields

* #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode

* Autotests: 8345 autotests sdf files for librarymonomer information (#8347)

* getTopBondByAttributes removal

* mapTwoAtoms update

* getBottomBondByAttributes removal

* fix

* Some functions removed

* Removing getBottomAtomByAttributes

* removing getFirstAtomCoordinatesByAttributes

* arrow and plus corrections

* removing clickOnPlus

* f

* f2

* f3

* f4

* Some clean up

* fix

* а2

* f3

* f4

* some clean up

* scu2

* f5

* f6

* f7

* draft

* draft2

* Final

* fix

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* f11

* f12

* f13

* f14

* f15

* f16

* f17

* f18

* f19

* f20

* f21

* f22

* f23

* f24

* f25

* f26

* f27

* f28

* Autotests: 8361 autotests some refactoring (#8362)

* first

* f2

* f3

* f4

* f5

* f6

* f7

* f8

* f9

* f10

* #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360)

* - added helm alias field to monomer wizard

* - added helm alias field validation

* - removed helm alias field from chems

* Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372)

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - add tests;
- add screenshots

* - update tests;
- add test files;
- delete unused 'testData.ts'

* Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1)

* The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2)
The function declaration of doubleClickOnBond is removed

* #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378)

* Initial plan

* Add data-topology and data-reacting-center attributes for bonds

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve error handling in getBondFromMoleculeStruct with descriptive comment

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* Improve code quality based on review feedback - simplify null checks and enhance comments

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

* fixes

* f2

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375)

* Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964)

- Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click)
- Updated tests:
  - `atom-properties.spec.ts`
  - `Template-manipulations.spec.ts`
  - `right-click.spec.ts`
- Replaced direct `getByLabel` usage with `fillLabel` calls:
  - via new `LabelEditDialog` for long-click cases
  - via existing `AtomPropertiesDialog` for double-click or context-menu cases

* autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests

- Implemented longClickOnAtom helper in index.ts
- Added setLabel method in LabelEditDialog
- Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it
- Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review)

* Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im monomer wizart in popup

* fix: fix styles

* Autotests: 8376 autotests some refactoring (#8381)

* First

* f2

* f3

* f4

* f5

* f6

* #8200 - Add parameter to Editor to disable saving new monomers to local storage   (#8364)

* fix: add parameter to Editor to disable saving new monomers to local storage

* fix:make monomer library persistence opt‑in via shouldPersist

* #7971 - Update the help document (3.9.) (#8384)

* Delete documentation/images/FG_chain.gif

* Delete documentation/images/Macro-canvas-3.8..png

* Delete documentation/images/Library-Tabs-3.8..png

* Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png

* Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png

* Delete documentation/images/New-Monomer-Micro-3.7..png

* Delete documentation/images/New-Monomer-Macro-3.7..png

* Delete documentation/images/New-Monomer-Library-3.7..png

* Delete documentation/images/Open-Structure-Macro-2-3.0..png

* Add files via upload

* Update help.md

* Update help.md

typos

* #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892)

* #7553 fix fullscreen mode switching dropdown

* #7553 fex: implement popup fullscreen mode with proper top-layer targeting

* #7553 fix test

* fix test

* #7553 Remove ref to custom class

* #7553 Refactor

* #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons  (#8365)

* fix: add scroll im m…
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@svvald svvald svvald approved these changes
@rrodionov91 rrodionov91 Awaiting requested review from rrodionov91
@Zhirnoff Zhirnoff Awaiting requested review from Zhirnoff

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@AlexeyGirin AlexeyGirin

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Refactor: Unexpected unknown property "user-focus"

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@AlexeyGirin @svvald