#3416 query_molecule.cpp has 2,740 lines of code, which is greater than 2,000 authorized. Split it into smaller files

[Copilot]

Remove-me-section

• Notify reviewers about the pull request
• Keep only necessary sections below for the review

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

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query_molecule.cpp exceeded the size threshold and concentrated multiple responsibilities. This refactor splits it into focused translation units while preserving behavior.

• Changes

  • Moved node/atom/bond implementations, cloning, merging, and constraint logic into query_molecule_nodes.cpp.
  • Moved query atom/bond parsing helpers, SMARTS list handling, and bond-type derivation into query_molecule_parsing.cpp.
  • Trimmed query_molecule.cpp to orchestrate higher-level query molecule logic and includes.
  • Applied repository clang-format and enforced include order guards on the new translation units.

• Example

// Previously in query_molecule.cpp, now in query_molecule_parsing.cpp
bool QueryMolecule::_isAtomOrListAndProps(Atom* p_query_atom,
                                          std::vector<std::unique_ptr<Atom>>& list,
                                          bool& neg,
                                          std::map<int, std::unique_ptr<Atom>>& properties);

Original prompt

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This section details on the original issue you should resolve

<issue_title>query_molecule.cpp has 2,740 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/query_molecule.cpp has 2,740 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/query_molecule.cpp</issue_description>

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

• Fixes query_molecule.cpp has 2,740 lines of code, which is greater than 2,000 authorized. Split it into smaller files #3416

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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

Formatted the new query_molecule sources with the repo clang-format and kept the main header first (commit 9cb6b39).