#3418 smiles_loader.cpp has 3,057 lines of code, which is greater than 2,000 authorized. Split it into smaller files

[Copilot]

Remove-me-section

smiles_loader.cpp was oversized; parsing and stereochemistry helpers were extracted into dedicated source files while keeping loader behavior intact. Follow-up applied clang-format to the new sources per review feedback.

• Refactor: Kept public loader entry points in smiles_loader.cpp, moved parsing-heavy routines to smiles_loader_parsers.cpp, and stereochemistry helpers to smiles_loader_stereo.cpp.
• Build: Existing CMake globbing continues to pick up the new source files without further changes.
• Formatting: Applied clang-format to the newly split SMILES loader files.

SmilesLoader loader(scanner);
loader.loadMolecule(mol); // unchanged usage; implementation now split across smaller units

Generic request

• PR name follows the pattern #1234 – issue name
• branch name does not contain '#'
• base branch (master or release/xx) is correct
• PR is linked with the issue
• task status changed to "Code review"
• code follows product standards
• regression tests updated

For release/xx branch

• backmerge to master (or newer release/xx) branch is created

Optional

• unit-tests written
• documentation updated

Backmerge request

• PR name follows the pattern Backmerge: #1234 – issue name
• PR is linked with the issue
• base branch (master or release/xx) is correct
• code contains only backmerge changes

Bump request

• PR name follows the pattern Bump version to ...
• add brackets [ ] for 'skip ci' and put it into the body
• milestone is linked to PR
• all tickets are closed inside the relevant milestone

Original prompt

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This section details on the original issue you should resolve

<issue_title>smiles_loader.cpp has 3,057 lines of code, which is greater than 2,000 authorized. Split it into smaller files</issue_title>
<issue_description>Problem:
core/indigo-core/molecule/src/smiles_loader.cpp has 3,057 lines of code, which is greater than 2,000 authorized. Split it into smaller files.

Why is this an issue?
A source file that grows too much tends to aggregate too many responsibilities and inevitably becomes harder to understand and therefore to maintain. Above a specific threshold, it is strongly advised to refactor it into smaller pieces of code which focus on well defined tasks. Those smaller files will not only be easier to understand but also probably easier to test.

Problem locations:
core/indigo-core/molecule/src/smiles_loader.cpp</issue_description>

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

• Fixes smiles_loader.cpp has 3,057 lines of code, which is greater than 2,000 authorized. Split it into smaller files #3418

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[AlexeyGirin]

@copilot you did changes in right direction but we need them to be clang formatted.
Please correct

[Copilot]

@copilot you did changes in right direction but we need them to be clang formatted.
Please correct

Applied clang-format to the new SMILES loader files (commit 2026370).