rdkit.Chem.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