schrodinger.application.scaffold_enumeration.markush module¶
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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.
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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.
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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)
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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)