[Copilot]

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

Removed all instance methods and dependencies from SmilesFormatter class, retaining only the static utility method isContainsCoordinates() which is the sole usage point in serverFormatter.ts.

Additionally, removed all unused SMILES serialization code that was only used by the deleted SmilesFormatter methods, including the entire SmiSerializer class and related helper modules.

Changes Made:

Commit 1: Refactored SmilesFormatter class (45 lines removed)

• Removed instance methods: getStructureFromStructAsync, getStructureFromStringAsync
• Removed constructor and all private fields
• Removed implements StructFormatter interface declaration
• Removed all import statements (no longer needed)

Commit 2: Removed unused SMILES serialization code (2,174 lines removed)

• Removed SmiSerializer class
• Removed Smiles class with all prototype methods: writeAtom(), updateSideBonds(), saveMolecule(), writeCycleNumber(), markCisTrans(), calcBondDirection(), writeRadicals(), isBondInRing()
• Removed helper modules: cis_trans.js (219 lines), dfs.js (187 lines), stereocenters.js (729 lines)
• Removed test files: dfs.test.js, smiles.test.js
• Removed type definitions and exports
• Deleted entire smi directory from domain/serializers

Before (64 lines):

export class SmilesFormatter implements StructFormatter {
  readonly #smiSerializer: SmiSerializer;
  // ... more fields
  
  constructor(...) { /* ... */ }
  async getStructureFromStructAsync(struct: Struct): Promise<string> { /* ... */ }
  getStructureFromStringAsync(stringifiedStruct: string): Promise<Struct> { /* ... */ }
  static isContainsCoordinates(smiles: string) { /* ... */ }
}

After (21 lines):

export class SmilesFormatter {
  static isContainsCoordinates(smiles: string) {
    return /\([\d.,;-]+\)/.test(smiles);
  }
}

Impact:

• Total: 2,219 lines of code removed
• Reduced circular dependencies from 264 to 260
• All 271 unit tests pass
• Build successful with no breaking changes

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

• Fixes Refactor: Remove all methods from SmilesFormatter class except one - isContainsCoordinates #8590

Original prompt

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This section details on the original issue you should resolve

<issue_title>Refactor: Remove all methods from SmilesFormatter class except one - isContainsCoordinates</issue_title>
<issue_description>Please remove all methods from SmilesFormatter class except one - isContainsCoordinates since they are not not used any more.

Class location: packages\ketcher-core\src\application\formatters\serverFormatter.ts
</issue_description>

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

• Fixes Refactor: Remove all methods from SmilesFormatter class except one - isContainsCoordinates #8590

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[AlexeyGirin]

@copilot remove also all functions that were used in removed methods of SmilesFormatter class if they are not user anywhere.
For example: Smiles.prototype.writeAtom = function, Smiles.prototype.updateSideBonds and etc

[Copilot]

@copilot remove also all functions that were used in removed methods of SmilesFormatter class if they are not user anywhere.
For example: Smiles.prototype.writeAtom = function, `Smiles.prototype....

Removed all unused SMILES serialization code (2,174 lines) in commit 72df6bd:

• Deleted SmiSerializer class
• Deleted Smiles class with all prototype methods: writeAtom(), updateSideBonds(), saveMolecule(), writeCycleNumber(), markCisTrans(), calcBondDirection(), writeRadicals(), isBondInRing()
• Deleted helper modules: cis_trans.js, dfs.js, stereocenters.js
• Deleted entire smi directory with tests and type definitions

Build and tests pass successfully.