Package rdkit :: Package Chem :: Module Graphs
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Source Code for Module rdkit.Chem.Graphs

 1  # $Id$ 
 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  from rdkit.six.moves import xrange 
21  import types 
22   
23   
24 -def CharacteristicPolynomial(mol, mat=None):
25 """ calculates the characteristic polynomial for a molecular graph 26 27 if mat is not passed in, the molecule's Weighted Adjacency Matrix will 28 be used. 29 30 The approach used is the Le Verrier-Faddeev-Frame method described 31 in _Chemical Graph Theory, 2nd Edition_ by Nenad Trinajstic (CRC Press, 32 1992), pg 76. 33 34 """ 35 nAtoms = mol.GetNumAtoms() 36 if mat is None: 37 # FIX: complete this: 38 #A = mol.GetWeightedAdjacencyMatrix() 39 pass 40 else: 41 A = mat 42 I = 1. * numpy.identity(nAtoms) 43 An = A 44 res = numpy.zeros(nAtoms + 1, numpy.float) 45 res[0] = 1.0 46 for n in xrange(1, nAtoms + 1): 47 res[n] = 1. / n * numpy.trace(An) 48 Bn = An - res[n] * I 49 An = numpy.dot(A, Bn) 50 51 res[1:] *= -1 52 return res
53