feat: pyo3 bindings (MWE)#100
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Replace pure-Python TRC implementation and format parsers with the native libqdx PyO3 extension. Re-export native types (PyTRC, PyTopology, PyResidues, PyChains, enums) directly from libqdx. - Delete pdb.py, mmcif.py, sdf.py (~1,619 lines) - Reduce mol.py from ~1,128 to ~99 lines (re-exports + AminoAcidSeq) - Rewire convert/__init__.py to delegate to libqdx - Update objects.py and exess modules for new type interfaces - Update QM/MM example to use TRC constructor and numpy geometry - Update test assertions for numpy geometry arrays Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Adds comprehensive module docstring to mol.py documenting all re-exported types (TRC, Topology, Residues, Chains, enums, ref types) with descriptions and usage examples. Restores Args/Returns docstrings on convert functions (load_structure, save_structure, from_pdb, etc.). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Re-add comments for the content-guessing heuristic fallback and multi-model PDB wrapping logic, which are non-obvious code paths. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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📖 Docs preview: https://talo.github.io/rush-py/pr-100/ |
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A few more changes will come with the next libqdx version.