Molecule Manipulation and Information Tools¶

Get Molecule with Canonical Numbering¶

group_decomposition.utils.get_canonical_molecule(smile: str)[source]¶: Ensures that molecule numbering is consistent with creating molecule from canonical SMILES for consistency.

Get Atomic Numbers in a Molecule¶

group_decomposition.utils.get_molecules_atomicnum(molecule)[source]¶: Given molecule object, get list of atomic numbers.

Find Molecules Atoms in Rings¶

group_decomposition.utils.get_molecules_atomsinrings(molecule)[source]¶: Given molecule object, get Boolean list of if atoms are in a ring.

Link Molecular Fragments¶

group_decomposition.utils.link_molecules(mol_1: Mol, mol_2: Mol, dl_1: int, dl_2: int)[source]¶

Given two mols, each with dummy atoms that have dummyAtomLabels, link the molecules between the dummy atoms specified by labels dl_1 and dl_2

Modified from https://www.oloren.ai/blog/add_rgroup.html Written by David Huang, Oloren AI, modified by Kevin Lefrancois-Gagnon

Parameters:

mol_1 – Chem.Mol object
mol_2 – Chem.Mol object
dl_1 – the isotope of the dummy atom in mol_1 which will be replaced by mol_2
dl_2 – the isotope of the dummy atom in mol_2 which will be replaced by mol_1

Returns:

Chem.Mol object with mol_1 and mol_2 linked where dl_1 and dl_2 were

Trim Placeholder Atoms¶

group_decomposition.utils.trim_placeholders(rwmol)[source]¶: Given Chem.RWmol, remove atoms with atomic number 0.