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

# rdkit.Chem.Pharm2D.Generate module

generation of 2D pharmacophores

Notes

> - The terminology for this gets a bit rocky, so here’s a glossary of what terms used here mean:

>   > 1. N-point pharmacophore a combination of N features along with distances between them.

>   > 2. N-point proto-pharmacophore: a combination of N feature definitions without distances. Each N-point proto-pharmacophore defines a manifold of potential N-point pharmacophores.

>   > 3. N-point scaffold: a collection of the distances defining an N-point pharmacophore without feature identities.

> 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.Generate.Gen2DFingerprint(mol, sigFactory, perms=None, dMat=None, bitInfo=None)

  generates a 2D fingerprint for a molecule using the parameters in _sig_

  Arguments

  > - mol: the molecule for which the signature should be generated

  > - sigFactory : the SigFactory object with signature parameters NOTE: no preprocessing is carried out for _sigFactory_.

  >   > It must be pre-initialized.

  > - perms: (optional) a sequence of permutation indices limiting which pharmacophore combinations are allowed

  > - dMat: (optional) the distance matrix to be used

  > - bitInfo: (optional) used to return the atoms involved in the bits