fix: use rdkit API to remove implicit hydrogens

njzjz commented 6 days ago

Summary by CodeRabbit

New Features
- Enhanced SMILES conversion process with improved implicit hydrogen handling for atoms.
Bug Fixes
- Removed outdated method that previously handled SMILES conversion, streamlining the conversion process.
Tests
- Removed a test related to the now-removed SMILES handling method, reflecting updates in testing strategy.
Chores
- Minor formatting adjustments and removal of unused imports for cleaner code.

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📥 Commits
Files that changed from the base of the PR and between 3619f96a951b30bb978ff1638bc5ad43e5e88e08 and 19284b905d28a7c78f89433ad08359374f74d73e.

📝 Walkthrough

## Walkthrough The changes in this pull request primarily involve the `_path.py` file, where the `_re` method in the `_CollectPaths` class has been removed, and the `convertSMILES` method has been updated to eliminate its previous dependency on `_re`. Additionally, the handling of implicit hydrogens in the `convertSMILES` method has been enhanced. In the test suite `tests/test_reacnetgen.py`, the `test_re` method has been removed, reflecting the changes in the functionality of the `_HTMLResult` class. Minor formatting adjustments have also been made across both files. ## Changes | File | Change Summary | |-------------------------------------|---------------------------------------------------------------------------------------------------------| | reacnetgenerator/_path.py | Removed `_re` method from `_CollectPaths`. Updated `convertSMILES` method to remove call to `_re` and added implicit hydrogen handling. Minor formatting adjustments and removal of unused imports. | | tests/test_reacnetgen.py | Removed `test_re` method from `TestReacNetGen`. Minor formatting adjustments in benchmark function definitions. | ## Sequence Diagram(s) ```mermaid sequenceDiagram participant User participant ConvertSMILES participant RDKit User->>ConvertSMILES: Request SMILES conversion ConvertSMILES->>RDKit: Generate SMILES string RDKit-->>ConvertSMILES: Return SMILES string ConvertSMILES-->>User: Return final SMILES string ```

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codspeed-hq[bot] commented 6 days ago

CodSpeed Performance Report

Merging #2278 will not alter performance

_{Comparing njzjz:remove-implicit-hydrogen (19284b9) with master (f5a25e9)}

Summary

✅ 8 untouched benchmarks

codecov[bot] commented 6 days ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 96.05%. Comparing base (8289d2c) to head (19284b9). Report is 9 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #2278 +/- ## ========================================== + Coverage 94.98% 96.05% +1.06% ========================================== Files 17 17 Lines 1415 1418 +3 ========================================== + Hits 1344 1362 +18 + Misses 71 56 -15 ```

:umbrella: View full report in Codecov by Sentry.
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deepmodeling / reacnetgenerator