rdkit.Chem.Pharm2D.Matcher module

functionality for finding pharmacophore matches in molecules

See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way pharmacophores are broken into triangles and labelled.

See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit numbering

rdkit.Chem.Pharm2D.Matcher.GetAtomsMatchingBit(sigFactory, bitIdx, mol, dMat=None, justOne=0, matchingAtoms=None)

Returns a list of lists of atom indices for a bit

Arguments

  • sigFactory: a SigFactory

  • bitIdx: the bit to be queried

  • mol: the molecule to be examined

  • dMat: (optional) the distance matrix of the molecule

  • justOne: (optional) if this is nonzero, only the first match will be returned.

  • matchingAtoms: (optional) if this is nonzero, it should contain a sequence of sequences with the indices of atoms in the molecule which match each of the patterns used by the signature.

Returns

a list of tuples with the matching atoms

exception rdkit.Chem.Pharm2D.Matcher.MatchError

Bases: Exception