schrodinger.rdkit.substructure module¶

Substructure searching and alignment

class schrodinger.rdkit.substructure.QueryOptions(stereospecific: bool = True, fuzzy_aromatic_matching: bool = True, tautomer_insensitive: bool = False)¶

Bases: tuple

Variables

stereospecific – whether to consider stereochemistry and chirality
fuzzy_aromatic_matching – whether to make aromatic queries less strict
tautomer_insensitive – whether to consider tautomer insensitivity

stereospecific: bool¶: Alias for field number 0

fuzzy_aromatic_matching: bool¶: Alias for field number 1

tautomer_insensitive: bool¶: Alias for field number 2

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

schrodinger.rdkit.substructure.replace_generic_h_queries(query)¶: Replaces QH, AH, MH, and XH queries with something which works in the RDKit. Reminder: - QH = “any atom except carbon” - AH = “any atom, including H” - MH = “any metal, or H” - XH = “halogen or H”

schrodinger.rdkit.substructure.expand_query(base_query: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None) → Generator[rdkit.Chem.rdchem.Mol, None, None]¶: Expands a given query, accounting for tautomer matching, link nodes, and variable bonds. If the substructure options dictate it, each generated query is also adjusted.

schrodinger.rdkit.substructure.substructure_matches(mol: rdkit.Chem.rdchem.Mol, query_mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None)¶: Generates all substructure matches against a given query mol

schrodinger.rdkit.substructure.verify_template_has_coordinates(mol: rdkit.Chem.rdchem.Mol)¶

Raises: ValueError – if the mol has no coordinates present

schrodinger.rdkit.substructure.apply_substructure_coordinates(mol: rdkit.Chem.rdchem.Mol, template_mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None)¶

Applies coordinates from the provided template to the input mol; used for compound alignment requests in image generation.

Parameters

mol – mol to apply new coordinates
template_mol – reference from which to draw coordinates
options – query options for substructure matching

Raises

ValueError – if the mol has no coordinates present

NOTE: If the substructure match to the template fails, the alignment is skipped altogether, leaving the input mol coordinates as they were

schrodinger.rdkit.substructure.apply_substructure_coordinates_from_mapping(mol: rdkit.Chem.rdchem.Mol, template_mol: rdkit.Chem.rdchem.Mol, atom_mapping: Iterable[Tuple[int, int]])¶

Applies coordinates from the provided template to the input mol utilizing an explicit atom mapping

Parameters

mol – mol to apply new coordinates
template_mol – reference from which to draw coordinates
atom_mapping – (template_idx, mol_idx) pairs to use

Raises

ValueError – if the mol has no coordinates present