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: NamedTuple

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

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

Ensure that SRU groups:

have 2 or 4 XBONDS
do not have atoms that overlap
for ladder polymers, if XBCORR bonds are set, they should be set to the
same bonds as the XBONDS (order of XBCORR bonds determines how the repeating groups are stitched together)

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.cg_substructure_matches(cg_mol: rdkit.Chem.rdchem.Mol, cg_query: rdkit.Chem.rdchem.Mol)¶

Generates a single coarsegrain substructure matches against a given query coarsegrain mol. Matching will also consider chain IDs and attachment point/bond types, meaning R3-R1 bonds will not match backbone bonds.

Assumes CG structure was read in through HELM string.

Parameters

cg_mol – coarsegrain mol with monomer labels set as atomLabel property
cg_query – coarsegrain query mol with monomer labels set as atomLabel property

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