Module FeatDirUtils

Find the IDs of the neighboring atom IDs

ARGUMENTS:
atomId - atom of interest
adjMat - adjacency matrix for the compound

Compute the direction vector for an aromatic feature

ARGUMENTS:
   coords - an list of atom coordinates the format is [x1, y1, z1, x2, y2, z3 ....]
   featAtoms - list of atom IDs that make up the feature
   featLoc - location of the aromatic feature specified as a numeric array
   scale - the size of the direction vector

Get the direction vectors for Acceptor of type 2

This is the acceptor with two adjacent heavy atoms. We will special case a few things here.
If the acceptor atom is an oxygen we will assume a sp3 hybridization
the acceptor directions (two of them)
reflect that configurations. Otherwise the direction vector in plane with the neighboring
heavy atoms

ARGUMENTS:
    coords - an list of atom coordinates the format is [x1, y1, z1, x2, y2, z3 ....]
    adjMat - adjacency martix of the compound
    featAtoms - list of atoms that are part of the feature
    scale - length of the direction vector

Get the direction vectors for Donor of type 3

This is a donor with three heavy atoms as neighbors. We will assume
a tetrahedral arrangement of these neighbors. So the direction we are seeking
is the last fourth arm of the sp3 arrangment

ARGUMENTS:
  coords - an list of atom coordinates the format is [x1, y1, z1, x2, y2, z3 ....]
  adjMat - adjacency martix of the compound
  featAtoms - list of atoms that are part of the feature
  scale - length of the direction vector

Get the direction vectors for Donor of type 2

This is a donor with two heavy atoms as neighbors. The atom may are may not have
hydrogen on it. Here are the situations with the neighbors that will be considered here
  1. two heavy atoms and two hydrogens: we will assume a sp3 arrangement here
  2. two heavy atoms and one hydrogen: this can either be sp2 or sp3
  3. two heavy atoms and no hydrogens
  
ARGUMENTS:
  coords - an list of atom coordinates the format is [x1, y1, z1, x2, y2, z3 ....]
  adjMat - adjacency martix of the compound
  atomNames - element names of the atoms in the compound
  featAtoms - list of atoms that are part of the feature
  scale - length of the direction vector

Get the direction vectors for Donor of type 1

This is a donor with one heavy atom. It is not clear where we should we should be putting the
direction vector for this. It should probably be a cone. In this case we will just use the
direction vector from the donor atom to the heavy atom
  
ARGUMENTS:
  coords - an list of atom coordinates the format is [x1, y1, z1, x2, y2, z3 ....]
  adjMat - adjacency martix of the compound
  atomNames - element names of the atoms in the compound
  featAtoms - list of atoms that are part of the feature
  scale - length of the direction vector

Get the direction vectors for Acceptor of type 1

This is a acceptor with one heavy atom neighbor. There are two possibilities we will
consider here
1. The bond to the heavy atom is a single bond e.g. CO
   In this case we don't know the exact direction and we just use the inversion of this bond direction
   and mark this direction as a 'cone'
2. The bond to the heavy atom is a double bond e.g. C=O
   In this case the we have two possible direction except in some special cases e.g. SO2
   where again we will use bond direction
   
ARGUMENTS:
  coords - an list of atom coordinates the format is [x1, y1, z1, x2, y2, z3 ....]
  adjMat - adjacency martix of the compound
  atomNames - element names of the atoms in the compound
  featAtoms - list of atoms that are part of the feature
  scale - length of the direction vector

__warningregistry__

Value:

{('Not importing directory \'/usr/lib/python2.5/site-packages/Numeric\ ': missing __init__.py', <type 'exceptions.ImportWarning'>, 7): 1}