fix: use rdkit API to remove implicit hydrogens #2278
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Signed-off-by: Jinzhe Zeng <[email protected]>
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Sequence Diagram(s)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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Signed-off-by: Jinzhe Zeng <[email protected]>
CodSpeed Performance ReportMerging #2278 will not alter performanceComparing Summary
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
reacnetgenerator/_path.py (1)
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1-239: Approve removal of_remethod and suggest documentation updateThe removal of the
_remethod is consistent with the changes in theconvertSMILESmethod and aligns with the PR objective to use the RDKit API directly for handling hydrogens. This simplification improves code maintainability and reduces potential sources of errors.Consider updating the class documentation to reflect the removal of the
_remethod and the changes in the SMILES conversion process, if applicable.
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📒 Files selected for processing (2)
- reacnetgenerator/_path.py (1 hunks)
- tests/test_reacnetgen.py (0 hunks)
💤 Files with no reviewable changes (1)
- tests/test_reacnetgen.py
🔇 Additional comments (2)
reacnetgenerator/_path.py (2)
234-237: Approve changes to handle implicit hydrogens explicitlyThe modifications to the
convertSMILESmethod align with the PR objective to remove implicit hydrogens using the RDKit API. By settingNoImplicitto True for each atom and updating the property cache, the code ensures that all hydrogens are explicitly represented in the molecule. This change improves the accuracy of the SMILES representation and prevents potential issues with implicit hydrogen handling in downstream processes.
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1-239: Summary of changes and their impactThe modifications in this PR successfully implement the objective of using the RDKit API to remove implicit hydrogens. The changes primarily affect the SMILES conversion process in the
_CollectPathsclass:
- The
_remethod has been removed, simplifying the code.- The
convertSMILESmethod now directly uses RDKit's functionality to handle hydrogens explicitly.These changes should improve the accuracy of SMILES representations and ensure consistency in hydrogen handling throughout the molecule processing pipeline. The code is now more streamlined and better aligned with RDKit's capabilities.
Signed-off-by: Jinzhe Zeng <[email protected]>
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #2278 +/- ##
==========================================
+ Coverage 94.98% 96.05% +1.06%
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Files 17 17
Lines 1415 1418 +3
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+ Hits 1344 1362 +18
+ Misses 71 56 -15 ☔ View full report in Codecov by Sentry. |
Summary by CodeRabbit
New Features
Bug Fixes
Tests
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