schrodinger.application.scaffold_enumeration.markush module¶
- schrodinger.application.scaffold_enumeration.markush.place_rgroups(mol, atom_indices_and_rgroups, appended_rgroups=None)¶
Generator that yields realizations of
molwith (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)¶
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)