MolecularDiffusion.cli.analyze

Analyze CLI subcommands for 3D molecule analysis.

Provides subcommands for: - optimize: XTB geometry optimization - metrics: Validity/connectivity metrics - compare: RMSD, energy, and optional bond analysis - xyz2mol: XYZ to SMILES conversion + fingerprints

Attributes

CONTEXT_SETTINGS

Functions

analyze()	Analyze 3D molecular structures.
compare(directory, mol_converter, n_subsets, csv_path, ...)	Compare XYZ files with their optimized counterparts.
metrics(input_dir, output, metrics_type, recheck_topo, ...)	Compute validity and connectivity metrics for XYZ files.
optimize(input_dir, output_dir, charge, level, ...)	Optimize XYZ geometries using xTB.
xtb_electronic(input_dir, output, method, charge, ...)	Compute XTB electronic properties for XYZ files.
xyz2mol(xyz_dir, input_csv, label, timeout, bits, verbose)	Convert XYZ files to SMILES and extract fingerprints/scaffolds.

Module Contents

MolecularDiffusion.cli.analyze.analyze()

Analyze 3D molecular structures.

 Subcommands:

optimize XTB geometry optimization metrics Validity/connectivity metrics compare RMSD, energy, and bond analysis xyz2mol Convert XYZ to SMILES + fingerprints

MolecularDiffusion.cli.analyze.compare(directory, mol_converter, n_subsets, csv_path, charge, level, timeout)

Compare XYZ files with their optimized counterparts.

Computes RMSD, xTB Energy Difference, and Bond Geometry Metrics. Enforces strict connectivity checks.

Requires ‘optimized_xyz’ subdirectory with *_opt.xyz files.

MolecularDiffusion.cli.analyze.metrics(input_dir, output, metrics_type, recheck_topo, check_strain, portion, mol_converter, skip_atoms, n_subsets, timeout)

Compute validity and connectivity metrics for XYZ files.

 Metrics types:

all Run all metrics (core + posebuster + geom_revised) core Basic validity checks (connectivity, atom stability) posebuster PoseBusters checks (bond lengths, angles, clashes) geom_revised Aromatic-aware stability metrics

 .. rubric:: Examples

MolCraftDiff analyze metrics gen_xyz/ MolCraftDiff analyze metrics gen_xyz/ –metrics posebuster MolCraftDiff analyze metrics gen_xyz/ –metrics geom_revised –mol-converter openbabel

MolecularDiffusion.cli.analyze.optimize(input_dir, output_dir, charge, level, timeout, scale_factor, csv_path, filter_column)

Optimize XYZ geometries using xTB.

 .. rubric:: Examples

MolCraftDiff analyze optimize gen_xyz/ MolCraftDiff analyze optimize gen_xyz/ –o optimized/ –level gfn2

MolecularDiffusion.cli.analyze.xtb_electronic(input_dir, output, method, charge, n_unpaired, solvent, properties, corrected, timeout, n_jobs, output_format)

Compute XTB electronic properties for XYZ files.

Uses morfeus to calculate quantum-chemical descriptors at the GFN-xTB level.

 Property groups (molecular-level):

energy Total energy, HOMO, LUMO, gap, Fermi level dipole Dipole moment and vector reactivity IP, EA, electronegativity, hardness, softness global Electrophilicity, nucleophilicity, fugalities solvation Solvation energy, H-bond correction (requires –solvent)

 Property groups (atomic-level):

charges Atomic charges (Mulliken) fukui Fukui indices (f+, f-, f, dual) bond_orders Bond orders between atom pairs

 Output formats:

csv Molecular-level properties only (one row per molecule) json Full data including atomic-level properties ase ASE database with properties in atoms.info/arrays all Generate all three formats

 .. rubric:: Examples

MolCraftDiff analyze xtb-electronic gen_xyz/ MolCraftDiff analyze xtb-electronic gen_xyz/ -p energy -p reactivity MolCraftDiff analyze xtb-electronic gen_xyz/ -s water -p solvation MolCraftDiff analyze xtb-electronic gen_xyz/ -p all -f ase -o results.db

MolecularDiffusion.cli.analyze.xyz2mol(xyz_dir, input_csv, label, timeout, bits, verbose)

Convert XYZ files to SMILES and extract fingerprints/scaffolds.

Outputs are saved to xyz_dir/2d_reprs/:

• smiles_processed.csv

• fingerprints.npy

• scaffolds.txt

• substructures.json

 .. rubric:: Examples

MolCraftDiff analyze xyz2mol gen_xyz/ MolCraftDiff analyze xyz2mol gen_xyz/ –bits 1024 -v

MolecularDiffusion.cli.analyze.CONTEXT_SETTINGS