Added functional group nomenclature method #149
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PR Overview
This PR adds a new method for extracting functional group names from molecules and updates test cases and workflow configurations.
- Introduces get_functional_groups to extract and prioritize functional groups based on SMARTS definitions.
- Updates tests to validate functional group extraction and adjusts tolerances in sample generation tests.
- Upgrades Python versions in CI workflows to include newer releases.
Reviewed Changes
| File | Description |
|---|---|
| exmol/exmol.py | Added get_functional_groups method for functional group extraction. |
| tests/test_exmol.py | Added tests for functional groups and adjusted sample generation tolerances. |
| .github/workflows/tests.yml | Updated Python versions from 3.10 to 3.13 (excluding 3.10). |
| .github/workflows/docs.yml | Updated Python version from 3.11 to 3.12 in documentation build workflow. |
Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.
Comments suppressed due to low confidence (3)
exmol/exmol.py:262
- Ensure that '_SMARTS' is initialized at the module level (e.g., _SMARTS = None) before using it to prevent potential NameError issues.
global _SMARTS
exmol/exmol.py:278
- This sorting assumes each item in _SMARTS is a tuple with a rank as the second element; ensure the data in 'smarts.txt' always adheres to this structure to avoid runtime errors.
sorted_smarts = sorted(_SMARTS.items(), key=lambda x: x[1][1])
tests/test_exmol.py:65
- [nitpick] Increasing the tolerance from 1 to 2 may mask potential issues in sample generation; please verify that this change is intentional and that edge cases are adequately covered.
assert abs(len(result[0]) - 12) <= 2
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