Source Code for Module rdkit.Chem.Graphs

 1  # $Id: Graphs.py 1528 2010-09-26 17:04:37Z glandrum $ 
 2  # 
 3  # Copyright (C) 2001-2008 greg landrum and rational discovery llc 
 4  # 
 5  #   @@ All Rights Reserved @@ 
 6  #  This file is part of the RDKit. 
 7  #  The contents are covered by the terms of the BSD license 
 8  #  which is included in the file license.txt, found at the root 
 9  #  of the RDKit source tree. 
10  # 
11  """ Python functions for manipulating molecular graphs 
12   
13  In theory much of the functionality in here should be migrating into the 
14  C/C++ codebase. 
15   
16  """ 
17  import numpy 
18  from rdkit import Chem 
19  from rdkit import DataStructs 
20  import types 
21   
22 -def CharacteristicPolynomial(mol,mat=None): 
23    """ calculates the characteristic polynomial for a molecular graph 
24   
25      if mat is not passed in, the molecule's Weighted Adjacency Matrix will 
26      be used. 
27   
28      The approach used is the Le Verrier-Faddeev-Frame method described 
29      in _Chemical Graph Theory, 2nd Edition_ by Nenad Trinajstic (CRC Press, 
30      1992), pg 76. 
31       
32    """ 
33    nAtoms = mol.GetNumAtoms() 
34    if mat is None: 
35      # FIX: complete this: 
36      #A = mol.GetWeightedAdjacencyMatrix() 
37      pass 
38    else: 
39      A = mat 
40    I = 1.*numpy.identity(nAtoms) 
41    An = A 
42    res = numpy.zeros(nAtoms+1,numpy.float) 
43    res[0] = 1.0 
44    for n in xrange(1,nAtoms+1): 
45      res[n] = 1./n*numpy.trace(An) 
46      Bn = An - res[n]*I 
47      An = numpy.dot(A,Bn) 
48   
49    res[1:] *= -1 
50    return res 
51