gmol.base.wrapper.rdkit

Functions

find_all_bonds_with_atom_idx(mol, atom_indices)	Find all chemical bonds in the molecule given atom indices.
generate_conformer(mol[, max_attempts, ...])
get_all_bonds(mol)
mol2smi(mol[, kekuleSmiles])
read_mols(file_path[, sanitize, remove_h])	Read a molecular file into a list of RDKit Mol objects.
smi2mol(smiles[, kekuilze, sanitize])
write_mols(save_path, mols[, sdf_kekulize])	Write a list of RDKit Mol objects to a file.

smi2mol(smiles: str, kekuilze: bool = False, sanitize: bool = True) → Mol

mol2smi(mol: Mol, kekuleSmiles: bool = True) → str

get_all_bonds(mol: Mol) → list[tuple[int, int]]

find_all_bonds_with_atom_idx(mol: Mol, atom_indices: list[int]) → list[tuple[int, int]]

Find all chemical bonds in the molecule given atom indices.

generate_conformer(mol: Mol, max_attempts: int = 5, optimize_iters: int = 500, ignore_failures: bool = True) → Mol

read_mols(file_path: Path | str, sanitize: bool = True, remove_h: bool = False) → list[Mol]

Read a molecular file into a list of RDKit Mol objects.

Supported formats: .mol2, .sdf, .pdb.

Parameters:

• file_path – Path to the molecular file.

• sanitize – If True, sanitize each molecule after reading.

• remove_h – If True, remove explicit hydrogens from each molecule.

Returns:

List of RDKit Mol objects; entries that failed to parse are omitted.

write_mols(save_path: Path | str, mols: Mol | None | Iterable[Mol | None], sdf_kekulize: bool = False) → None

Write a list of RDKit Mol objects to a file.

Supported extensions are .sdf and .pdb.

Parameters:

• save_path – Path to the output file.

• mols – Molecule or list of molecules to write; None entries are skipped.

• sdf_kekulize – If True, kekulize molecules when writing to an SDF file.