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@tonyd33 tonyd33 commented Mar 15, 2026

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How the feature works? / How did you fix the issue?

(Screenshots, videos, or GIFs, if applicable)

Check list

  • unit-tests written
  • e2e-tests written
  • documentation updated
  • PR name follows the pattern #1234 – issue name
  • branch name doesn't contain '#'
  • PR is linked with the issue
  • base branch (master or release/xx) is correct
  • task status changed to "Code review"
  • reviewers are notified about the pull request

svvald and others added 30 commits November 19, 2025 12:42
@svvald @rrodionov91
epam#8254 – Allow for stereo bonds up and down to be a bond between A…
84bd398 
…A and LGA (epam#8491)

* epam#8254 – Support having stereo bonds as bonds between AA and LGA

* epam#8254 – Support stereo bonds for automatically assigned leaving atoms

* epam#8254 – Convert bonds between monomers to stereo when expanding monomers

* epam#8254 – Some refactoring

* epam#8254 – Implement proper handling of cases when monomer bond goes TO stereo bonded LGA

* epam#8254 – Implement stereo bonds support in between monomers when loading/switching modes

* epam#8254 – Update autotests

* - updated screenshots

* - updated tests

---------

Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
@AlexeyGirin
epam#8544 Refactor: This assertion is unnecessary since it does not c…
ff4c77f 
…hange the type of the expression (part 10) (epam#8545)

* Initial plan

* Remove redundant non-null assertions in struct.ts

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.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
epam#8576 Refactor: Array-mutating methods should not be used mislead…
2c7d392 
…ingly (epam#8577)

* Initial plan

* Fix array mutation issue by using spread syntax before reverse()

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.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
epam#7588 Refactor rxnMerge(mols, nReactants, nProducts, nAgents, sho…
4902fcf 
…uldReactionRelayout) function to reduce its Cognitive Complexity from 53 to the 15 allowed. (epam#8570)

* Initial plan

* Refactor rxnMerge function to reduce cognitive complexity

- Extract bond length calculation into calculateAverageBondLength()
- Extract molecule rescaling into rescaleMolecules()
- Extract fragment type determination into getFragmentType()
- Extract molecule categorization into categorizeMolecules()
- Move shiftMol helper to module level
- Extract layout logic into layoutReactionFragments()
- Extract merge logic into mergeWithoutLayout()
- Extract plus sign addition into addPlusSigns()
- Extract bounding box aggregation into aggregateBoundingBoxes()
- Extract arrow creation logic into createReactionArrow()

The main rxnMerge function now orchestrates these helper functions,
making the code flow easier to read and reducing cognitive complexity.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.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
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
epam#6731 Ambiguous phosphates (alternatives and mixed) in sequence s…
cc917c2 
…hown as % symbol instead of @ symbol (epam#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>

---------

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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: 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: 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

---------

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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

---------

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>

* #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>

---------

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+ivanmasl…
@AlexeyGirin
first (epam#8586)
015e5f2
@AlexeyGirin
epam#8584 Tooltip for attachment points appears too far from attachme…
f74eb0c 
…nt point (epam#8585)

* Initial plan

* Fix tooltip positioning for attachment points using getShiftedSegmentPosition

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

* Fix tooltip positioning to account for canvas offset in popup mode

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

* Revert reatom.ts changes - keep only InfoTooltip fix for popup mode

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

* Fix tooltip positioning for attachment points in popup mode

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

* epam#8544 Refactor: This assertion is unnecessary since it does not change the type of the expression (part 10) (epam#8545)

* Initial plan

* Remove redundant non-null assertions in struct.ts

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

---------

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

* Initial plan

* Fix tooltip positioning for attachment points using getShiftedSegmentPosition

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

* Fix tooltip positioning to account for canvas offset in popup mode

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>
@KristinaKasyanovskaya
epam#8363 - Include 'Arrange as a Ring' button for Flex mode (epam#8535)
09f8e64 
* feat: Include 'Arrange as a Ring' button for Flex mode

* fix: fix position Arrange as a Ring in context menu

* fix: add 'Arrange as a Ring' button only in flex mode

* test: update snapshots

* fix: fix data attribute

* fix: fix selected monomer function

* test: update snapshots
@AlexeyGirin
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
epam#8509 Refactor: Variables are missing in props validation (let's …
1fa8e7c 
…rewrite JS to TS) 12 (epam#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>

---------

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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>

---------

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>

---------

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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>

---------

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>

---------

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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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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>

---------

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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>

---------

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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: 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

---------

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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>

---------

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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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* #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>

---------

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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

---------

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

---------

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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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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 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
epam#8459 – Refactor: Variables are missing in props validation (let'…
1043e77 
…s rewrite JS to TS) 10 (epam#8519)

* Initial plan

* Convert Analyse.jsx to TypeScript with proper type definitions

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

* Fix: Display values in Decimal places dropdowns

Changed from `.toString()` to pass numeric values directly to Select component. The Select component expects values that match the option values, which are numbers (0-7), not strings. Converting to string caused a type mismatch preventing the selected value from being displayed.

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

---------

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Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>
@AlexeyGirin
epam#8501 Refactor: Variables are missing in props validation (let's …
f55384d 
…rewrite JS to TS) 4 (epam#8514)

* Initial plan

* Convert ElementsTable.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>
@AlexeyGirin
epam#8499 Refactor: Variables are missing in props validation (let's …
9c002ee 
…rewrite JS to TS) 2 (epam#8512)

* Initial plan

* Convert PeriodTable.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>
@rrodionov91 @AlexeyGirin
Fixed build (epam#8607)
9760d33 
* - fixed build

* fixes

* f2

* f3

---------

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

---------

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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>

---------

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>

---------

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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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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>

---------

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

---------

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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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>

---------

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>

---------

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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* #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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* 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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* #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

---------

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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

---------

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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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
@svvald @KristinaKasyanovskaya @Zhirnoff @rrodionov91 @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
epam#7566 Autotests: Refactor fileFormats.ts (get rid of it) (epam#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>

---------

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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>

---------

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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>

---------

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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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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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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>

---------

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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>

---------

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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>

* 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

---------

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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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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>

---------

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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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>

---------

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>

---------

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

---------

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>

---------

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: impl…
@rrodionov91
Backmerge: epam#8599 - Correct the stereo-bonds of sugars (epam#8606)
8001872
@AlexeyGirin
epam#8590 Refactor: Remove all methods from SmilesFormatter class exc…
fafeb2d 
…ept one - isContainsCoordinates (epam#8610)

* Initial plan

* Refactor SmilesFormatter: remove all methods except isContainsCoordinates

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

* Remove unused SmiSerializer and Smiles serialization code

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

---------

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@AlexeyGirin
@rrodionov91 @svvald @KristinaKasyanovskaya @Zhirnoff @ViktoriaTkacheva @ivanmaslow @ljubica-milovic @KukushkinDmi1riy @lmhs @cx-luo @OliverDudgeon
epam#8567 Refactor: Deprecated APIs should not be used (part 5) (epam…
5fc4e5a 
…#8569)

* 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>

---------

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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* #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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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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* 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: 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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* #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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* #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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* #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>

* 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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* 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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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

---------

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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

---------

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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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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

---------

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 m…
@KristinaKasyanovskaya
fix: Context menu remains visible after creating cyclic structure via…
63da604 
… right-click menu (epam#8601)
@KristinaKasyanovskaya
epam#7326 - Preview: Delete option is unavailable when right-clicking…
3aebd8d 
… on a bond in macro mode (epam#8636)

* fix: Delete option is available when right-clicking on a bond in macro mode

* test: update snapshots
@KristinaKasyanovskaya
fix: Selection tool icon open dropdown menu as in Micro mode (epam#8621)
96793cb
@AlexeyGirin
epam#8612 Refactor: Prefer tag over ARIA role (part 4) (epam#8615)
59319f2 
* Initial plan

* Replace div role="button" with semantic button elements

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

* Remove redundant aria-disabled attribute in favor of native disabled

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

* f1

* 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>
@AlexeyGirin
epam#8504 Refactor: Variables are missing in props validation (let's …
3be80d7 
…rewrite JS to TS) 7 (epam#8616)

* Initial plan

* Convert TypeChoice.jsx to TypeScript with proper type definitions

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

* Add explanatory comments for type compatibility and required props

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.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
epam#8619 Refactor: Expected a for-of loop instead of a for loop with…
5aa657c 
… this simple iteration (part 4) (epam#8620)

* Initial plan

* Refactor for loops to for-of loops in utils.js

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.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
epam#8563 Refactor: Mark the props of the component as read-only (epa…
10d97e3 
…m#8622)

* Initial plan

* Mark component props as read-only using Readonly utility type

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.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
epam#8626 Refactor: Variables are missing in props validation (let's …
9df1913 
…rewrite JS to TS) 18 (epam#8632)

* Initial plan

* Refactor buttonlist.jsx to TypeScript with proper type definitions

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

* Fix parameter naming: rename 'multipl' to 'multiple' in oneOrMore 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>
@AlexeyGirin
epam#8627 Refactor: Variables are missing in props validation (let's …
42709cb 
…rewrite JS to TS) 19 (epam#8633)

* Initial plan

* Convert ComboBox component from JSX to TypeScript with proper prop types

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

* Address code review feedback - improve type safety and JSX rendering

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.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
epam#8628 Refactor: Variables are missing in props validation (let's …
e637436 
…rewrite JS to TS) 20 (epam#8634)

* Initial plan

* Convert errorPopover.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>
@AlexeyGirin @KristinaKasyanovskaya
epam#8624 Refactor: Variables are missing in props validation (let's …
9cdb6ef 
…rewrite JS to TS) 16 (epam#8630)

* Initial plan

* Refactor cliparea.jsx to TypeScript with proper prop type validation

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

* fix: Context menu remains visible after creating cyclic structure via right-click menu (epam#8601)

* epam#7326 - Preview: Delete option is unavailable when right-clicking on a bond in macro mode (epam#8636)

* fix: Delete option is available when right-clicking on a bond in macro mode

* test: update snapshots

* fix: Selection tool icon open dropdown menu as in Micro mode (epam#8621)

* epam#8612 Refactor: Prefer tag over ARIA role (part 4) (epam#8615)

* Initial plan

* Replace div role="button" with semantic button elements

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

* Remove redundant aria-disabled attribute in favor of native disabled

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

* f1

* 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>

* epam#8504 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 7 (epam#8616)

* Initial plan

* Convert TypeChoice.jsx to TypeScript with proper type definitions

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

* Add explanatory comments for type compatibility and required props

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

---------

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

* epam#8619 Refactor: Expected a for-of loop instead of a for loop with this simple iteration (part 4) (epam#8620)

* Initial plan

* Refactor for loops to for-of loops in utils.js

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

---------

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

* epam#8563 Refactor: Mark the props of the component as read-only (epam#8622)

* Initial plan

* Mark component props as read-only using Readonly utility type

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

---------

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

* epam#8626 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 18 (epam#8632)

* Initial plan

* Refactor buttonlist.jsx to TypeScript with proper type definitions

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

* Fix parameter naming: rename 'multipl' to 'multiple' in oneOrMore 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>

* epam#8627 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 19 (epam#8633)

* Initial plan

* Convert ComboBox component from JSX to TypeScript with proper prop types

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

* Address code review feedback - improve type safety and JSX rendering

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

---------

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

* epam#8628 Refactor: Variables are missing in props validation (let's rewrite JS to TS) 20 (epam#8634)

* Initial plan

* Convert errorPopover.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>

* Initial plan

* f1

* 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: Kristina <kristina_kasyanovskaya@epam.com>
Co-authored-by: Alexey Girin <agirin@mail.ru>
@KristinaKasyanovskaya
epam#4645 - In the “Modify RNA Builder” mode, when hovering over the …
bbdd7ae 
…buttons “Yes” and “Cancel” in the “Update Sequence” window, tooltips are displayed (epam#8714)

* fix: in the “Modify RNA Builder” mode, when hovering over the buttons “Yes” and “Cancel” in the “Update Sequence” window, tooltips are displayed

* test: update test logic & add data test-id
umutzd-alt and others added 21 commits February 24, 2026 18:07
umutzd-alt
epam#9209 - Refactor: (JavaScript) Loop counters should not be assign…
29431c7 
…ed within the loop body (epam#9237)

* Refactor loop structures to use while instead of for for improved readability in utils.js and v3000.js

* Refactor spacebarsplit function for improved readability and maintainability
umutzd-alt
refactor: update according to Sonar errors (epam#9272)
3df8e0d
@guliaisaeva
epam#9160-(TypeScript) Unused assignments should be removed (epam#9226)
dfa9ebf 
* 9160/refactor:remove unused assignments

* 9160/refactor:remove unused assignments

* 9160/refactor:try to pass test in github

* remove ubused assignments

* fix:remove unnnessacary changes from structeditor

* fix:revert

* remove  unused assigments

* refactor:use lodash for form and structeditor
@AlexeyGirin
epam#8187 It is possible to create preset with empty name (epam#9075)
ca52a10 
* Initial plan

* fix: reject empty monomer group template names

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

* fix: keep preset template updates while validating names

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

* test: cover whitespace-only preset names

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

* fix: clarify empty preset name error text

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

---------

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@oguzhanduran
epam#9276- Literals should not be used for promise rejection #9276ite…
adf4dca 
…rals should not be used for promise rejection (epam#9277)

* 9276: fix promise rejection for literal usage

* normalizeError utility added

* added normalizeError utility into all necessary files
@Gyv4ik
epam#9269: add anput references to labels for iframe in examples (epa…
1705083 
…m#9275)
@Gyv4ik
refactor: simplify async handling in cut and keydown event methods (e…
e5edab4 
…pam#9305)
@AlexeyGirin @aproskurnov
Support for enhanced stereochemistry markings in macromolecules mode (e…
cca4216 
…pam#9095)

* Initial plan

* Add stereoLabel support to CoreAtom and AtomRenderer for macromolecules mode

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

* Fix magic number in positionStereoLabel method

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

* fixed size of stereolabel

* fixed displaying abs stereoflags

* fixed moving stereolabel after moving second bonds atom

---------

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: Aleksei Proskurnov <proskurn@gmail.com>
@azamatalt
epam#9282 - Empty collections should not be accessed or iterated (epa…
2bfd94d 
…m#9284)

* Fix empty collection access in sequence tests and sgroup action

* Fix: Always initialize `attachmentPoints` as an empty array, disregarding `attrs.attachmentPoints`.
@azamatalt
epam#9218 - Unused methods of React components should be removed (epa…
87fa956 
…m#9221)

* refactor analyse dialog to remove unused class methods

* refactor: move analyseItems constant outside of Analyse component to prevent re-declaration
@azamatalt
epam#9202 - Make EditorHistory constructor private and add getInstanc…
8403a4f 
…e accessor (epam#9213)

* Fix EditorHistory constructor return by using static accessor

* fix: Disable `no-use-before-define` ESLint rule for the `_instance` property.

* style: format EditorHistory.update arguments for improved readability.

* refactor: improve type safety of EditorHistory singleton by adding an instance type guard.
@AlexeyGirin
Update auto_assign.yml to simplify assignee groups (epam#9270)
3299766 
Removed developers and QA groups from auto assign configuration.
@beyzaevcen
epam#8896- fix assertion error when adding ket file to canvas (epam#9315
88c7fdf 
)
@beyzaevcen
epam#9260 - Refactor: Constructors should not contain asynchronous op…
a7f6a74 
…erations (epam#9296)

* Initial plan

* refactor: move async monomers library init out of CoreEditor constructor

Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com>

* epam#9260 - undo the changes on package-lock

---------

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Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com>
@AlexeyGirin @rrodionov91
Introducing rotation of monomers in Macromolecules mode (epam#9094)
f0b070e 
* Initial plan

* Add rotation and flip functionality for monomers in Macromolecules mode

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

* Add interactive rotation handle functionality with 15° snapping

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

* Address code review feedback: extract constants, improve comments

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


---------

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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
@AlexeyGirin @IevaBendikiene
@rrodionov91 @github-advanced-security @aproskurnov @AnnaKosol @ljubica-milovic @zefiris87 @YatsekTest @SergeiBakirov @Gyv4ik @guliaisaeva @azamatalt @beyzaevcen @oguzhanduran umutzd-alt
epam#8241 - Autotests: Git rid of flacky tests (epam#9322)
beeb976 
* Fixed flaky tests

* fixes

* f2

* Update Node.js baseline to 22 (epam#9026)

* Initial plan

* update node version references

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

---------

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

* epam#8999 Refactor: Polynomial regular expression used on uncontrolled data (epam#9000)

* Initial plan

* Replace regex trimRight with trimEnd

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

---------

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

* epam#9003 Refactor: React Router vulnerable to XSS via Open Redirects (epam#9004)

* Initial plan

* chore: update react-router to 7.13.0

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

---------

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

* epam#9005 Refactor: Next library has a Denial of Service with Server Components - Incomplete Fix Follow-Up (epam#9006)

* Initial plan

* chore: upgrade next/react for example-ssr

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

---------

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

* epam#8987 Labels for monomer natural analog category is missing if filter applied (epam#8992)

* Initial plan

* fix: always show monomer group titles in RNA accordion

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

* limit natural analog titles to relevant monomer groups

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 <alexey_girin@epam.com>

* epam#9011 Refactor: qs arrayLimit bypass mitigation via parent dependency updates (epam#9015)

* Initial plan

* Update qs and body-parser overrides

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

* Update body-parser via parent dependency

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

---------

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

* epam#9016 Refactor: update js-yaml dependencies to patched versions without overrides (epam#9019)

* Initial plan

* chore: override js-yaml to patched versions

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

* chore: bump js-yaml patch versions

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* chore: remove js-yaml overrides and update lock

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* Align S-Group subtype combobox width and default option visibility (epam#8979)

* Initial plan

* Align S-Group subtype combobox width with other selects

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

* fix: show selected empty subtype option

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* fixes

* - fixed non specified value

* - fixed unit tests

* fixes

---------

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* Refactor: Potential fix for code scanning alert no. 22: Unvalidated dynamic method call (epam#9001)

* Potential fix for code scanning alert no. 22: Unvalidated dynamic method call

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

* Fix unvalidated dynamic method call in parseSGroup.js (epam#9002)

* Initial plan

* Fix unvalidated dynamic method call in parseSGroup.js

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

* Optimize security fix by moving constants outside function scope

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* epam#9022 Refactor: PostCSS line return parsing error (epam#9023)

* Initial plan

* chore: fix package.json trailing comma

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

* chore: remove postcss override

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* Update CI to Node.js 22.11 (epam#9037)

* epam#9032 - Flex mode icon is active after ketcher close and open again (epam#9049) (epam#9052)

* epam#9032 - Flex mode icon is active after ketcher close and open again

- added reset mode button state to default on destroy

* - updated ketcher version to 3.12.0-rc.2

(cherry picked from commit d721b77)

* epam#9047 - Leaving group atom position is incorrect for nucleotides created in monomer wizard (epam#9048) (epam#9051)

- fixed leaving group atom position for nucleotides in monomer creation wizard

(cherry picked from commit 34ad31d)

* epam#7153 - Molecule from expanded monomer disappars on switching to Macromolecules mode (epam#8989)

* fix dissapearing molecule from expanded monomer

* fixed build

* create fragment after removing s group

* fixed build

* removed redundant

* added comment

* epam#8974 autotests for ketcher 3110 bugs (epam#9031)

* add cases

* add cases and files

* update code and screenshoots

* remove step about screenshoot

* changes after review

* some changes for wariningMessageDialog

* add changes

* add changes after review

* Autotests: 8331 autotests axolabs format support (epam#8339)

* First

* second

* epam#9065 System shows natural analog category for phosphates (epam#9066)

* Initial plan

* chore: plan phosphate category fix

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

* fix: hide phosphate natural analogue groups

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

* fixes

* f2

* f3

* revert: restore RNA phosphate grouping

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* chore: revert package-lock.json

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* fixes

* f2

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* Add fragment selection tool and rename structure selection tooltip (epam#8973)

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* Backmerge: epam#9078 - Update the help document (3.12.) (epam#9079)

* Delete documentation/images/S-Group-Properties-3.6.png

* Add files via upload

* Update help.md

* epam#9084 - Ketcher saves incorrect attachment points configuration for new nucleotides (epam#9086) (epam#9088)

(cherry picked from commit 5177c79)

* - fixed vulnerability (epam#9100)

* epam#7915 autotests enable flipping of all expanded monomers in a structure (epam#9083)

* add test cases

* add description for tests

* epam#8254 Allow for stereo-bonds (up and down) to be a bond between AA and LGA (epam#9080)

* add test cases

* add changes

* add svg format for macro

* add description for the tests

* Update the layout method

* # 8383 Introduce library searching using HELM aliases, AxoLabs aliases, and modification types (epam#9059)

* add test cases

* update screenshoots

* add description for tests

* update code and screenshot

* epam#9098 autotests alignment of sense and antisense strings in axolabs format (epam#9101)

* add cases

* add screenshots and tests

* Changed call for page to the BeforeAll fixture. Stabled some flacky tests (epam#9107)

* add cases (epam#9112)

* epam#9113 The Copolymer S-Group type should not be displayed unless there are at least two structural repeating units (SRUs) in selection (epam#9117)

* Initial plan

* Plan for copolymer s-group availability

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* Restrict copolymer s-group option

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* Address code review feedback

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* Refine copolymer option checks

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* Simplify copolymer option logic

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* Polish copolymer option filtering

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* Tighten copolymer availability check

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* Trim sgroup memo dependencies

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

* Simplify copolymer scheme selection

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* Type annotate sgroup test helper

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* Memoize schemes and count SRUs

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* epam#7492 - autotests transform isolated test execution to clear canvas test execution for undo redo actionsspects (epam#9131)

* Isolated test execution has been transformed to clear canvas test execution for undo redo actions.

* Screenshots updated

* epam#7493 Transformed isolated test execution to clear canvas test execution for right-click.spec.ts (epam#9133)

* epam#9119 add expects and change repeating code (epam#9128)

* add expects and change repeating code

* add changes for failed test

* epam#9108 Incorrect valence for nitrogen (epam#9124)

* Initial plan

* Allow nitrogen valence 5

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

* fixes

---------

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* epam#9126 Some keyboard shortcuts don't work on Macromolecules canvas (epam#9127)

* Initial plan

* Fix macromolecules hotkeys

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

* Adjust macromolecule hotkey tests

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* Clarify sequence-mode hotkey comment

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

* Document bond hotkey options

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* Refactor bond hotkey helper

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

* Tidy hotkey comments

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* Revert macromolecule hotkey tests

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* Fixes

---------

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* refactor: reEmage and resimpleObject toggle points logic (epam#9222)

* 9151:constructor should have readonly (epam#9241)

* refactor:use nullish coeliscine (epam#9242)

* Fix attachment point sorting comparator (epam#9281)

* Fix reduce call in DistanceSnapView with initial value (epam#9268)

* test: document intentional noop helper (epam#9264)

* fix(core): avoid unused ClearTool instantiation in test (epam#9206)

* Fix dialog keyboard handler accessibility issue (epam#9200)

* fix(core): make EmptySnakeLayoutNode non-empty (epam#9265)

* epam#9227 - The return value of "useState" should be destructured and named symmetrically (epam#9228)

* Initial plan

* Fix useState asymmetric naming: rename isStuctureChecking to isStructureChecking

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---------

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* epam#9223- Redundant casts and non-null assertions should be avoided  (epam#9224)

* Initial plan

* Remove redundant TypeScript casts and non-null assertions

Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com>

* Fix type errors: properly handle false values and keep necessary cast

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* epam#9223- remove redundant type assertion for actionmenu

---------

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* epam#9217 - React props should be read-only (epam#9219)

* Initial plan

* Make React props read-only in 5 components

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* Remove package-lock.json from commit

* Remove package-lock.json from commit

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* Restore package-lock.json to original state

---------

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* epam#9211 - Switch cases should end with an unconditional "break" statement (epam#9212)

* Initial plan

* Initial analysis - identify switch case fall-through issues

Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com>

* Fix switch case fall-through in action/index.js and state/index.js

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* Refactor to reduce code duplication in switch cases

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* Add JSDoc and improve variable naming

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* Revert "Initial analysis - identify switch case fall-through issues"

This reverts commit 2286028.

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* epam#9259 -  If statements should not be the only statement in else blocks  (epam#9261)

* Initial plan

* Refactor: Replace nested if in else block with else if in CoreAtom.ts

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---------

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* epam#9293 Autotests: Cyclic imports in autotests (epam#9294)

* Initial plan

* fix(autotests): remove circular imports in tests utilities and monomer dialog

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

* refactor(autotests): eliminate remaining cyclic imports in tests

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

* refactor(autotests): rollback requested files and replace delay helper calls

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

* fixes

* f2

---------

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* epam#9251 - Redundant React fragments should be removed (epam#9252)

* Initial plan

* Remove redundant React fragment in ErrorsCheck component

Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com>

* Remove package-lock.json changes from PR

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* epam#9236 - Ternary operators should not be nested  (epam#9247)

* Initial plan

* Refactor nested ternary operators in 4 files

Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com>

* 9236 - undo changes for package-lock

* 9236 - refactor nested arrays for period table

* 9236 - extract modification type attribute logic to reusable utility

---------

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* 9167:fixed all branches in a conditional structure should not have exactly same implementation issue (epam#9230)

* epam#9193:Refactor:(TypeScript) Objects and classes converted or coerced t… (epam#9196)

* 9183:Refactor:(TypeScript) Objects and classes converted or coerced to strings should define

* 9183/fix:delete unnecessary  file

* 9183/refactor:fix according to copilot review comment

* fix:remove unused function

* 9279: create cross-platform script for app build and run (epam#9280)

* epam#9298: (TypeScript) Two branches in a conditional structure should not have exactly the same implementation (epam#9300)

* refactor:implement duplicate branch cleanup in 2 reported lications

* Revert "refactor:implement duplicate branch cleanup in 2 reported lications"

This reverts commit 95dabd1.

* refactor two branches same implementations

* epam#9207- Unused React typed props should be removed (epam#9214)

* 9207/fix:remove unused props

* fix:refactor accroding comments

* fix:rename current to diaog element

* epam#9195 - Refactor: Use optional chaining instead of manual null checks (epam#9201)

* Initial plan

* Refactor: Use optional chaining instead of manual null checks

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* Fix prettier formatting issues

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* Fix code review issues: correct atom lookup and improve if statement logic

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* epam#9195 fix test issues

* epam#9195 fix undo changes for package-lock

* 9195 - replace undefineds with null

* epam#9195 - replace null with undefined

* epam#9195 - replace some undefineds with null

---------

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* epam#9238 - Refactor: (TypeScript) Non-interactive DOM elements should not have interactive ARIA roles (epam#9262)

* Enhance accessibility by adding ARIA roles and attributes to various components

* Refactor ARIA roles to improve accessibility and semantic structure in ColorPicker, Form components, and SpecialSymbolsButton

* Refactor ColorPicker to streamline ID generation for palette

* fix snapshots

* 9174: fix selector duplicated issue (epam#9302)

* epam#9255 - Spacing between inline elements should be explicit (epam#9256)

* Initial plan

* Fix ambiguous JSX whitespace in RnaPresetTabs.tsx

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* Use explicit JSX space expression {' '} as per lint rule

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* Format JSX space expression on single line as per image

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* Use regular space instead of {' '} JSX expression

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* 9162 used collection contents (epam#9208)

* epam#9209 - Refactor: (JavaScript) Loop counters should not be assigned within the loop body (epam#9237)

* Refactor loop structures to use while instead of for for improved readability in utils.js and v3000.js

* Refactor spacebarsplit function for improved readability and maintainability

* refactor: update according to Sonar errors (epam#9272)

* epam#9160-(TypeScript) Unused assignments should be removed (epam#9226)

* 9160/refactor:remove unused assignments

* 9160/refactor:remove unused assignments

* 9160/refactor:try to pass test in github

* remove ubused assignments

* fix:remove unnnessacary changes from structeditor

* fix:revert

* remove  unused assigments

* refactor:use lodash for form and structeditor

* epam#8187 It is possible to create preset with empty name (epam#9075)

* Initial plan

* fix: reject empty monomer group template names

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

* fix: keep preset template updates while validating names

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* test: cover whitespace-only preset names

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* fix: clarify empty preset name error text

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* epam#9276- Literals should not be used for promise rejection #9276iterals should not be used for promise rejection  (epam#9277)

* 9276: fix promise rejection for literal usage

* normalizeError utility added

* added normalizeError utility into all necessary files

* epam#9269: add anput references to labels for iframe in examples (epam#9275)

* refactor: simplify async handling in cut and keydown event methods (epam#9305)

* Support for enhanced stereochemistry markings in macromolecules mode (epam#9095)

* Initial plan

* Add stereoLabel support to CoreAtom and AtomRenderer for macromolecules mode

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

* Fix magic number in positionStereoLabel method

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* fixed size of stereolabel

* fixed displaying abs stereoflags

* fixed moving stereolabel after moving second bonds atom

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* epam#9282 - Empty collections should not be accessed or iterated (epam#9284)

* Fix empty collection access in sequence tests and sgroup action

* Fix: Always initialize `attachmentPoints` as an empty array, disregarding `attrs.attachmentPoints`.

* epam#9218 - Unused methods of React components should be removed (epam#9221)

* refactor analyse dialog to remove unused class methods

* refactor: move analyseItems constant outside of Analyse component to prevent re-declaration

* epam#9202 - Make EditorHistory constructor private and add getInstance accessor (epam#9213)

* Fix EditorHistory constructor return by using static accessor

* fix: Disable `no-use-before-define` ESLint rule for the `_instance` property.

* style: format EditorHistory.update arguments for improved readability.

* refactor: improve type safety of EditorHistory singleton by adding an instance type guard.

* Update auto_assign.yml to simplify assignee groups (epam#9270)

Removed developers and QA groups from auto assign configuration.

* epam#8896- fix assertion error when adding ket file to canvas (epam#9315)

* epam#9260 - Refactor: Constructors should not contain asynchronous operations  (epam#9296)

* Initial plan

* refactor: move async monomers library init out of CoreEditor constructor

Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com>

* epam#9260 - undo the changes on package-lock

---------

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* Introducing rotation of monomers in Macromolecules mode (epam#9094)

* Initial plan

* Add rotation and flip functionality for monomers in Macromolecules mode

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

* Add interactive rotation handle functionality with 15° snapping

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* Address code review feedback: extract constants, improve comments

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* fixes

* f2

* f3

* f5

* f6

---------

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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
Co-authored-by: aproskurnov <proskurn@gmail.com>
Co-authored-by: AnnaKosol <annakosolapova24@gmail.com>
Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com>
Co-authored-by: Pavel Lukin <124054458+zefiris87@users.noreply.github.com>
Co-authored-by: Yaroslav Kovalsky <71060724+YatsekTest@users.noreply.github.com>
Co-authored-by: SergeiBakirov <sergei_bakirov@epam.com>
Co-authored-by: Yurii Danylenko <Givchik228@gmail.com>
Co-authored-by: Gulia <83670176+guliaisaeva@users.noreply.github.com>
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Co-authored-by: Yurii Danylenko <yurii_danylenko@epam.com>
Co-authored-by: umutzd-alt <umutozdemir997@outlook.com>
@rrodionov91
epam#9328 - Migrate to Indigo v1.42.0-rc.1 in-browser module (epam#9329)
efbded8 
* epam#9328 - Migrate to Indigo v1.42.0-rc.1 in-browser module

* - updated tests
@ljubica-milovic
epam#9327 - Update the help document (3.13.) (epam#9332)
207291a 
* Add files via upload

* Delete documentation/images/3_lasso_menu.png

* Delete documentation/images/Selection-tools-micro-3.13..png

* Add files via upload

* Add files via upload

* Update help.md

* Update help.md
@AlexeyGirin
Autotests: replace manual clear-canvas lifecycle with shared canvas f…
01d8008 
…ixtures (epam#9326)

* Initial plan

* test: migrate clear-canvas lifecycle hooks to canvas fixtures

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

* chore: finalize fixture migration validation

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

* Fixes

* f2

* f3

* f4

* f5

* f6

* www

* f7

* f8

* f9

* f10

* f11

* f12

---------

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 <alexey_girin@epam.com>
@azamatalt @AlexeyGirin
epam#9205 - Prefer tag over ARIA role (epam#9216)
1be51e3 
* fix(macromolecules): use semantic button for favorite toggle

* refactor: replace div elements with native buttons for favorite toggles and update component snapshots.

* f1

* f2

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Co-authored-by: Alexey Girin <alexey_girin@epam.com>
umutzd-alt
Remove unnecessary component prop from TabPanel in TemplateDialog (ep…
6f18bbf 
…am#9346)
@tonyd33
tonyd33 force-pushed the tony/update-3.14 branch 2 times, most recently from e50ace6 to 2ea7b80 Compare March 15, 2026 03:44
@tonyd33
tonyd33 force-pushed the tony/update-3.14 branch 2 times, most recently from 0d51cc8 to 4e4a53c Compare March 15, 2026 04:46
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