Source Code for Module rdkit.Chem.Graphs

 1  # $Id: Graphs.py 997 2009-02-25 06:12:43Z glandrum $ 
 2  # 
 3  # Copyright (C) 2001-2008 greg landrum and rational discovery llc 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  """ Python functions for manipulating molecular graphs 
 8   
 9  In theory much of the functionality in here should be migrating into the 
10  C/C++ codebase. 
11   
12  """ 
13  import numpy 
14  from rdkit import Chem 
15  from rdkit import DataStructs 
16  import types 
17   
18 -def CharacteristicPolynomial(mol,mat=None): 
19    """ calculates the characteristic polynomial for a molecular graph 
20   
21      if mat is not passed in, the molecule's Weighted Adjacency Matrix will 
22      be used. 
23   
24      The approach used is the Le Verrier-Faddeev-Frame method described 
25      in _Chemical Graph Theory, 2nd Edition_ by Nenad Trinajstic (CRC Press, 
26      1992), pg 76. 
27       
28    """ 
29    nAtoms = mol.GetNumAtoms() 
30    if mat is None: 
31      # FIX: complete this: 
32      #A = mol.GetWeightedAdjacencyMatrix() 
33      pass 
34    else: 
35      A = mat 
36    I = 1.*numpy.identity(nAtoms) 
37    An = A 
38    res = numpy.zeros(nAtoms+1,numpy.float) 
39    res[0] = 1.0 
40    for n in xrange(1,nAtoms+1): 
41      res[n] = 1./n*numpy.trace(An) 
42      Bn = An - res[n]*I 
43      An = numpy.dot(A,Bn) 
44   
45    res[1:] *= -1 
46    return res 
47