MolecularDiffusion.utils.smilify¶

Attributes¶

`TIMEOUT`
`bond_dict`
`lg`

Exceptions¶

TimeoutException

Common base class for all non-exit exceptions.

Classes¶

Molecule

Functions¶

`check_connected`(am[, tol])
`check_symmetric`(am[, tol])
`cov_radius`(→ float)	Return covalent radius (Å) for a chemical symbol (via ASE).
`get_cutoffs`(z[, radii, mult])
`guess_bond_matrix`(→ torch.LongTensor)	Return an (n, n) bond‐order matrix, using Open Babel if available.
`read_xyz_ob`(→ Tuple[List[str], torch.Tensor])
`simple_idx_match_check`(mol, ase_atoms)
`simple_idx_match_check`(mol, ase_atoms)
`smilfy_xtb`(filename)	Assume neutral molecule
`smilify_cell2mol`(filename[, z, coordinates, timeout, ...])	Convert XYZ to mol using cell2mol with optional timeout.
`smilify_openbabel`(filename)

Module Contents¶

exception MolecularDiffusion.utils.smilify.TimeoutException¶

Bases: Exception

Common base class for all non-exit exceptions.

Initialize self. See help(type(self)) for accurate signature.

class MolecularDiffusion.utils.smilify.Molecule(symbols: List[str], positions: torch.Tensor, *, scale: float = 1.2, total_charge: int = 0)¶

bond_matrix¶

num_atoms¶

positions¶

rdkit_mol¶

symbols¶

total_charge = 0¶

MolecularDiffusion.utils.smilify.check_connected(am, tol=1e-08)¶

MolecularDiffusion.utils.smilify.check_symmetric(am, tol=1e-08)¶

MolecularDiffusion.utils.smilify.cov_radius(symbol: str) → float¶: Return covalent radius (Å) for a chemical symbol (via ASE).

MolecularDiffusion.utils.smilify.get_cutoffs(z, radii=ase.data.covalent_radii, mult=1)¶

MolecularDiffusion.utils.smilify.guess_bond_matrix(symbols: List[str], positions: torch.Tensor, *, scale: float = 1.2, total_charge: int | None = None) → torch.LongTensor¶: Return an (n, n) bond‐order matrix, using Open Babel if available. If total_charge is given, we tell OBMol about it so it can distribute formal charges when perceiving bond orders.

MolecularDiffusion.utils.smilify.read_xyz_ob(path: os.PathLike | str) → Tuple[List[str], torch.Tensor]¶

MolecularDiffusion.utils.smilify.simple_idx_match_check(rdkit_mol, ase_symbols)¶: Check that RDKit atom order matches the ASE symbol list exactly.

MolecularDiffusion.utils.smilify.simple_idx_match_check(mol, ase_atoms)¶

MolecularDiffusion.utils.smilify.smilfy_xtb(filename)¶

Assume neutral molecule If fails, change charge to +1 (there could be a better method to detect charge as either +1 or-1)

Then if fails again, loosen the critaria to not sanitize the molecule.

MolecularDiffusion.utils.smilify.smilify_cell2mol(filename, z=None, coordinates=None, timeout=30, total_charge=0)¶: Convert XYZ to mol using cell2mol with optional timeout.

MolecularDiffusion.utils.smilify.smilify_openbabel(filename)¶

MolecularDiffusion.utils.smilify.TIMEOUT = 300¶

MolecularDiffusion.utils.smilify.bond_dict¶

MolecularDiffusion.utils.smilify.lg¶