Add conformer generation workflow (#30) - #75
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Resolves #30: a conformer generation workflow for screening. - thermo/conformers.py: RDKit is the conformer backend. `generate(smiles, ...)` embeds conformers with ETKDG, optionally MMFF-optimises + energy-window/RMSD prunes them, and returns energy-sorted ASE Atoms. `write_conformers` writes them as .xyz so a directory can be fed straight to `screen`. - Public API: `generate_conformers` / `write_conformers` exported from `ThermoScreening.thermo`. - CLI: `thermo conformers <SMILES>` writes the ensemble, then `thermo screen <dir>` screens it (verified end-to-end with xtb-cli). RDKit is already a declared dependency; the import is guarded with a clear message if absent. Closes #30
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## main #75 +/- ##
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+ Coverage 96.73% 96.80% +0.06%
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Files 24 25 +1
Lines 1564 1629 +65
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- Misses 51 52 +1
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- conformers module docstring: say MMFF (there is no UFF fallback). - run_conformers: catch ValueError/ImportError and print a clean stderr message + exit 1, instead of surfacing a raw traceback.
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Resolves #30 — a conformer generation workflow for molecule screening, per the issue's two notes (decide RDKit as backend; expose a small public API before wiring into screening).
What changed
thermo/conformers.py(new) — RDKit is the conformer backend.generate(smiles, max_conformers=, optimize=, prune_rms_thresh=, energy_window=, random_seed=)embeds conformers with ETKDGv3, optionally MMFF-optimises and sorts by energy, and prunes by RMSD + an optional energy window. Returns energy-sorted ASEAtoms.write_conformers(...)writes them as.xyzso a directory feeds straight intoscreen.generate_conformers/write_conformersexported fromThermoScreening.thermo.thermo conformers "<SMILES>" --max-conformers N [--energy-window K] [--no-optimize]writes the ensemble; thenthermo screen <dir>screens it.Verified end-to-end
thermo conformers "CCCC"→ 2 conformers →thermo screen butane_confs --engine xtb-cli→ 2 results, 0 failed.Tests
tests/thermo/test_conformers.py(embed, max-count, energy-window, no-optimize, bad-SMILES, write→read, public export) + CLI parse/run +main()dispatch. RDKit is a declared dependency so these run in CI; the RDKit import is guarded with a clear message if absent (# pragma: no cover).Closes #30. Full suite: 268 passed / 11 skipped; patch fully covered.