schrodinger.application.scaffold_enumeration.markush module

schrodinger.application.scaffold_enumeration.markush.place_rgroups(mol, atom_indices_and_rgroups, appended_rgroups=None)[source]

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.

  • appended_rgroups – List of appended rgroups so far.

Rtype appended_rgroups

list(rdkit.Chem.Mol)

schrodinger.application.scaffold_enumeration.markush.canonicalize_R_labels(mol)[source]

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)[source]

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)[source]

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)