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