rdkit.Chem.Pharm2D.Matcher module — The RDKit 2025.09.6 documentation

# 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`