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