File: Graphs.py

package info (click to toggle)
rdkit 202009.4-1
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 129,624 kB
  • sloc: cpp: 288,030; python: 75,571; java: 6,999; ansic: 5,481; sql: 1,968; yacc: 1,842; lex: 1,254; makefile: 572; javascript: 461; xml: 229; fortran: 183; sh: 134; cs: 93
file content (51 lines) | stat: -rw-r--r-- 1,365 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
# $Id$
#
# Copyright (C) 2001-2008 greg landrum and rational discovery llc
#
#   @@ All Rights Reserved @@
#  This file is part of the RDKit.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the RDKit source tree.
#
""" Python functions for manipulating molecular graphs

In theory much of the functionality in here should be migrating into the
C/C++ codebase.

"""
import numpy
from rdkit import Chem
from rdkit import DataStructs
import types


def CharacteristicPolynomial(mol, mat=None):
    """ calculates the characteristic polynomial for a molecular graph

      if mat is not passed in, the molecule's Weighted Adjacency Matrix will
      be used.

      The approach used is the Le Verrier-Faddeev-Frame method described
      in _Chemical Graph Theory, 2nd Edition_ by Nenad Trinajstic (CRC Press,
      1992), pg 76.

    """
    nAtoms = mol.GetNumAtoms()
    if mat is None:
        # FIX: complete this:
        #A = mol.GetWeightedAdjacencyMatrix()
        pass
    else:
        A = mat
    I = 1. * numpy.identity(nAtoms)
    An = A
    res = numpy.zeros(nAtoms + 1, numpy.float)
    res[0] = 1.0
    for n in range(1, nAtoms + 1):
        res[n] = 1. / n * numpy.trace(An)
        Bn = An - res[n] * I
        An = numpy.dot(A, Bn)

    res[1:] *= -1
    return res