MolecularDiffusion.runmodes.analyze.compare_to_optimized¶

Compute unified comparison metrics (RMSD, xTB Energy, Bond Geometry) between initial XYZ files and their optimized counterparts in the optimized_xyz subdirectory.

Features: - Validates connectivity (skip disjoint graphs) - Computes RMSD and Energy difference (via xTB) - Computes Bond Length, Angle, and Torsion differences (via OpenBabel/cell2mol)

Attributes¶

parser

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).
`run_compare_analysis`(args)
`xyz2mol_cell2mol`(→ Optional[rdkit.Chem.Mol])	Convert XYZ to RDKit Mol using cell2mol 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.run_compare_analysis(args: argparse.Namespace)¶

MolecularDiffusion.runmodes.analyze.compare_to_optimized.xyz2mol_cell2mol(xyz_file: str, timeout: int = 10) → rdkit.Chem.Mol | None¶: Convert XYZ to RDKit Mol using cell2mol 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).

MolecularDiffusion.runmodes.analyze.compare_to_optimized.parser¶