schrodinger.livedesign.rgroup_decomposition module

Collection of functions used for RGroup Decomposition.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.livedesign.rgroup_decomposition.rgroup_decompose(scaffold_mol: rdkit.Chem.rdchem.Mol, match_mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None) → List[dict]

Decomposes a molecule into its core and R-groups given a scaffold

Parameters

• scaffold_mol – scaffold molecule on which to find R-groups

• match_mol – source molecule for R-group decomposition

• stereospecific – whether to consider bond stereochemistry and atom chirality of scaffold

Returns

list of dicts of R-group matches

schrodinger.livedesign.rgroup_decomposition.replace_rgroups_with_dummy_atoms(mol: rdkit.Chem.rdchem.Mol) → rdkit.Chem.rdchem.Mol

schrodinger.livedesign.rgroup_decomposition.get_scaff_without_non_graph_hydrogen_rgroups(decomp)

Removes non-graph hydrogen rgroups from the given scaffold so that the scaffold coordinates can be used to align the match mol.

schrodinger.livedesign.rgroup_decomposition.assert_valid_scaffold(scaffold_mol: rdkit.Chem.rdchem.Mol)

Determines if provided scaffold is valid by checking for adjacent rgroups and attachment points.

schrodinger.livedesign.rgroup_decomposition.get_rgroup_decomp(scaffold_mol: rdkit.Chem.rdchem.Mol, match_mol: rdkit.Chem.rdchem.Mol, options: schrodinger.rdkit.substructure.QueryOptions) → List[dict]