Module Generate

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

Internal use only

  

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

**Arguments**

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

  - sig: the signature object which will be filled.

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

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

**Notes**  

  - no preprocessing is carried out for _sig_. It *must* be pre-initialized.
    Any bits which are already set will not be changed by this operation.