[mattwthompson]

Description

Closes #191

Mostly moves tyff.utils.molecule into tyff.molecule. There is no only one map_smiles function and it uses an RDKit code path to avoid different behavior from OpenFF if OEChem is installed and licensed.

Checklist

• Add tests
• Lint
• Update docstrings
• AI disclosure

[codecov-commenter]

Codecov Report

❌ Patch coverage is 91.17647% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 82.11%. Comparing base (6a816ff) to head (c47c8f2).

Files with missing lines	Patch %	Lines
tyff/molecule.py	89.65%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #211      +/-   ##
==========================================
+ Coverage   82.06%   82.11%   +0.04%     
==========================================
  Files          59       58       -1     
  Lines        5313     5311       -2     
==========================================
+ Hits         4360     4361       +1     
+ Misses        953      950       -3     

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[Copilot]

🟢 Approval recommended

No active issues were found and the change is a clean, self-contained refactor consolidating duplicate helpers with all call sites updated.

No open issues 🎉

What changed in this PR

This PR resolves #191 by eliminating a duplicate map_smiles implementation. Previously tyff/molecule.py defined an OpenFF-based map_smiles (Molecule.from_smiles(...).to_smiles(mapped=True)), while tyff/utils/molecule.py defined an RDKit-based one plus mol_to_smiles/unmap_smiles. The RDKit code path is preferred because these mapped SMILES are used as dictionary keys where literal string comparison stands in for chemical equivalence, so it must avoid toolkit-dependent (OEChem vs. RDKit) output differences. The PR moves the RDKit helpers into tyff/molecule.py, deletes tyff/utils/molecule.py, and updates all call sites.

Changes:

• Moved mol_to_smiles, map_smiles, and unmap_smiles (RDKit implementations) into tyff/molecule.py, replacing the OpenFF-based map_smiles, and added from __future__ import annotations for the Chem.Mol type hint.
• Deleted tyff/utils/molecule.py.
• Updated all importers (tyff/targets/thermo.py, tyff/targets/dimers.py, and tyff/_tests/targets/test_thermo.py) to use tyff.molecule.

File	Description
tyff/​molecule.py	Now hosts the consolidated RDKit-based mol_to_smiles/map_smiles/unmap_smiles, replacing the OpenFF map_smiles.
tyff/​utils/​molecule.py	Deleted; its functions were relocated to tyff/molecule.py.
tyff/​targets/​thermo.py	Import and call sites updated from tyff.utils.molecule to tyff.molecule.
tyff/​targets/​dimers.py	Import and mol_to_smiles call sites updated to tyff.molecule.
tyff/​_tests/​targets/​test_thermo.py	Test import of map_smiles updated to tyff.molecule.

I verified there are no remaining references to tyff.utils.molecule, no external uses of the removed tyff.molecule.Molecule symbol, and no stale references in docs or __init__ modules. The change is a clean, self-contained refactor and I found no objective issues to flag.

_{Review effort: Balanced}