MolecularDiffusion.runmodes.analyze.compare_to_optimized¶

Helpers for comparing an initial geometry with an optimized counterpart.

This is an internal helper library, not a command. The directory-walking front end that used to live here is now the xyz+optimized layout of --metrics conformer (see conformer_metrics.py).

Two consumers depend on it:

conformer_metrics.py – compute_all_metrics for the legacy layout;
runmodes/generate/tasks_conformer.py – get_xtb_energy for the optional energy column. Removing that function breaks conformer generation, not just analysis.

Functions¶

`compute_all_metrics`(→ dict)	Compute all available metrics for a single pair.
`compute_coord_rmsd`(→ float)	Compute RMSD between two coordinate sets.
`get_xtb_energy`(→ Optional[float])	Compute xTB single-point energy for an XYZ file (returns Hartree).
`xyz2mol_converter`(→ Optional[rdkit.Chem.Mol])	Convert XYZ to RDKit Mol using xyz2mol logic.
`xyz2mol_openbabel`(→ Optional[rdkit.Chem.Mol])	Convert XYZ to RDKit Mol using OpenBabel (via pybel).

Module Contents¶

MolecularDiffusion.runmodes.analyze.compare_to_optimized.compute_all_metrics(init_file: pathlib.Path, opt_file: pathlib.Path, args: argparse.Namespace) → dict¶: Compute all available metrics for a single pair.

MolecularDiffusion.runmodes.analyze.compare_to_optimized.compute_coord_rmsd(coords1: numpy.ndarray, coords2: numpy.ndarray) → float¶: Compute RMSD between two coordinate sets.

MolecularDiffusion.runmodes.analyze.compare_to_optimized.get_xtb_energy(xyz_path: str, charge: int = 0, level: str = 'gfn2', timeout: int = 120) → float | None¶: Compute xTB single-point energy for an XYZ file (returns Hartree).

MolecularDiffusion.runmodes.analyze.compare_to_optimized.xyz2mol_converter(xyz_file: str, timeout: int = 10) → rdkit.Chem.Mol | None¶: Convert XYZ to RDKit Mol using xyz2mol logic.

MolecularDiffusion.runmodes.analyze.compare_to_optimized.xyz2mol_openbabel(xyz_file: str) → rdkit.Chem.Mol | None¶: Convert XYZ to RDKit Mol using OpenBabel (via pybel).