Package rdkit :: Package Chem :: Package Pharm2D :: Module Generate

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# Module Generate

source code

    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 betwen 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

Functions | [hide private]

_ShortestPathsMatch(match, featureSet, sig, dMat, sigFactory) Internal use only | source code

Gen2DFingerprint(mol, sigFactory, perms=None, dMat=None) generates a 2D fingerprint for a molecule using the parameters in _sig_ | source code

Variables | [hide private]

| logger = `logger()`
| _verbose = `0`

Imports: Utils, SigFactory

Function Details | [hide private]

### Gen2DFingerprint(mol, sigFactory, perms=None, dMat=None)

source code

    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