schrodinger.application.scaffold_enumeration.markush module

schrodinger.application.scaffold_enumeration.markush.place_rgroups(mol, atom_indices_and_rgroups)

Generator that yields realizations of mol with (some) atoms replaced by R-groups.

Parameters:

• mol (rdkit.Chem.Mol) – Molecule.
• atom_indices_and_rgroups (list(int, rdkit.Chem.Mol)) – List of atom indices paired with corresponding R-groups.

schrodinger.application.scaffold_enumeration.markush.canonicalize_R_labels(mol)

Translates different conventions of R-group labelling into the RDKit “native” (AtomRLabel).

Parameters:mol (rdkit.Chem.Mol) – Molecule.

schrodinger.application.scaffold_enumeration.markush.get_rlabels_set(mol)

Returns set of R-labels carried by the atoms in the mol.

Parameters:mol (rdkit.Chem.Mol) – Molecule. Returns:Set or R-labels. Return type:set(int)

schrodinger.application.scaffold_enumeration.markush.get_rlabels_map(mol)

Returns map from R-labels to atom indices.

Parameters:mol (rdkit.Chem.Mol) – Molecule. Returns:Map from R-labels to atom indices. Return type:dict of int:list(int)