rdkit.Chem.GraphDescriptors

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# Source Code for Module rdkit.Chem.GraphDescriptors

      1  # $Id$
      2  #
      3  # Copyright (C) 2003-2006 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  """ Calculation of topological/topochemical descriptors.
     12
     13
     14
     15  """
     16  from __future__ import print_function
     17  from rdkit import Chem
     18  from rdkit.Chem import Graphs
     19  from rdkit.Chem import rdchem
     20  from rdkit.Chem import rdMolDescriptors
     21  # FIX: remove this dependency here and below
     22  from rdkit.Chem import pyPeriodicTable as PeriodicTable
     23  import numpy
     24  import math
     25  from rdkit.ML.InfoTheory import entropy
     26
     27  periodicTable = rdchem.GetPeriodicTable()
     28
     29  _log2val = math.log(2)
     30 -def _log2(x):
     31    return math.log(x) / _log2val
     32
     33 -def _VertexDegrees(mat,onlyOnes=0):
     34    """  *Internal Use Only*
     35
     36    this is just a row sum of the matrix... simple, neh?
     37
     38    """
     39    if not onlyOnes:
     40      res = sum(mat)
     41    else:
     42      res = sum(numpy.equal(mat,1))
     43    return res
     44
     45 -def _NumAdjacencies(mol,dMat):
     46    """  *Internal Use Only*
     47
     48    """
     49    res = mol.GetNumBonds()
     50    return res
     51
     52 -def _GetCountDict(arr):
     53    """  *Internal Use Only*
     54
     55    """
     56    res = {}
     57    for v in arr:
     58      res[v] = res.get(v,0)+1
     59    return res
     60
     61
     62 -def _pyHallKierAlpha(m):
     63    """ calculate the Hall-Kier alpha value for a molecule
     64
     65     From equations (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)
     66
     67    """
     68    alphaSum = 0.0
     69    rC = PeriodicTable.nameTable['C'][5]
     70    for atom in m.GetAtoms():
     71      atNum=atom.GetAtomicNum()
     72      if not atNum: continue
     73      symb = atom.GetSymbol()
     74      alphaV = PeriodicTable.hallKierAlphas.get(symb,None)
     75      if alphaV is not None:
     76        hyb = atom.GetHybridization()-2
     77        if(hyb<len(alphaV)):
     78          alpha = alphaV[hyb]
     79          if alpha is None:
     80            alpha = alphaV[-1]
     81        else:
     82          alpha = alphaV[-1]
     83      else:
     84        rA = PeriodicTable.nameTable[symb][5]
     85        alpha = rA/rC - 1
     86      print(atom.GetIdx(),atom.GetSymbol(),alpha)
     87      alphaSum += alpha
     88    return alphaSum
     89  #HallKierAlpha.version="1.0.2"
     90
     91 -def Ipc(mol, avg = 0, dMat = None, forceDMat = 0):
     92    """This returns the information content of the coefficients of the characteristic
     93      polynomial of the adjacency matrix of a hydrogen-suppressed graph of a molecule.
     94
     95      'avg = 1' returns the information content divided by the total population.
     96
     97      From D. Bonchev & N. Trinajstic, J. Chem. Phys. vol 67, 4517-4533 (1977)
     98
     99    """
    100    if forceDMat or dMat is None:
    101      if forceDMat:
    102        dMat = Chem.GetDistanceMatrix(mol,0)
    103        mol._adjMat = dMat
    104      else:
    105        try:
    106          dMat = mol._adjMat
    107        except AttributeError:
    108          dMat = Chem.GetDistanceMatrix(mol,0)
    109          mol._adjMat = dMat
    110
    111    adjMat = numpy.equal(dMat,1)
    112    cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat))
    113    if avg:
    114      return entropy.InfoEntropy(cPoly)
    115    else:
    116      return sum(cPoly)*entropy.InfoEntropy(cPoly)
    117  Ipc.version="1.0.0"
    118
    119
    120
    121 -def _pyKappa1(mol):
    122    """ Hall-Kier Kappa1 value
    123
    124     From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    125
    126    """
    127    P1 = mol.GetNumBonds(1)
    128    A = mol.GetNumHeavyAtoms()
    129    alpha = HallKierAlpha(mol)
    130    denom = P1 + alpha
    131    if denom:
    132      kappa = (A + alpha)*(A + alpha - 1)**2 / denom**2
    133    else:
    134      kappa = 0.0
    135    return kappa
    136  #Kappa1.version="1.0.0"
    137
    138
    139 -def _pyKappa2(mol):
    140    """  Hall-Kier Kappa2 value
    141
    142     From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    143
    144    """
    145    P2 = len(Chem.FindAllPathsOfLengthN(mol,2))
    146    A = mol.GetNumHeavyAtoms()
    147    alpha = HallKierAlpha(mol)
    148    denom = (P2 + alpha)**2
    149    if denom:
    150      kappa = (A + alpha - 1)*(A + alpha - 2)**2 / denom
    151    else:
    152      kappa = 0
    153    return kappa
    154  #Kappa2.version="1.0.0"
    155
    156 -def _pyKappa3(mol):
    157    """  Hall-Kier Kappa3 value
    158
    159     From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    160
    161    """
    162    P3 = len(Chem.FindAllPathsOfLengthN(mol,3))
    163    A = mol.GetNumHeavyAtoms()
    164    alpha = HallKierAlpha(mol)
    165    denom = (P3 + alpha)**2
    166    if denom:
    167      if A % 2 == 1:
    168        kappa = (A + alpha - 1)*(A + alpha - 3)**2 / denom
    169      else:
    170        kappa = (A + alpha - 2)*(A + alpha - 3)**2 / denom
    171    else:
    172      kappa = 0
    173    return kappa
    174  #Kappa3.version="1.0.0"
    175
    176  HallKierAlpha = lambda x:rdMolDescriptors.CalcHallKierAlpha(x)
    177  HallKierAlpha.version=rdMolDescriptors._CalcHallKierAlpha_version
    178  Kappa1 = lambda x:rdMolDescriptors.CalcKappa1(x)
    179  Kappa1.version=rdMolDescriptors._CalcKappa1_version
    180  Kappa2 = lambda x:rdMolDescriptors.CalcKappa2(x)
    181  Kappa2.version=rdMolDescriptors._CalcKappa2_version
    182  Kappa3 = lambda x:rdMolDescriptors.CalcKappa3(x)
    183  Kappa3.version=rdMolDescriptors._CalcKappa3_version
    184
    185
    186 -def Chi0(mol):
    187    """ From equations (1),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    188
    189    """
    190    deltas = [x.GetDegree() for x in mol.GetAtoms()]
    191    while 0 in deltas:
    192      deltas.remove(0)
    193    deltas = numpy.array(deltas,'d')
    194    res = sum(numpy.sqrt(1./deltas))
    195    return res
    196  Chi0.version="1.0.0"
    197
    198
    199 -def Chi1(mol):
    200    """ From equations (1),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    201
    202    """
    203    c1s = [x.GetBeginAtom().GetDegree()*x.GetEndAtom().GetDegree() for x in mol.GetBonds()]
    204    while 0 in c1s:
    205      c1s.remove(0)
    206    c1s = numpy.array(c1s,'d')
    207    res = sum(numpy.sqrt(1./c1s))
    208    return res
    209  Chi1.version="1.0.0"
    210
    211 -def _nVal(atom):
    212    return periodicTable.GetNOuterElecs(atom.GetAtomicNum())-atom.GetTotalNumHs()
    213
    214 -def _hkDeltas(mol,skipHs=1):
    215    global periodicTable
    216    res = []
    217    if hasattr(mol,'_hkDeltas') and mol._hkDeltas is not None:
    218      return mol._hkDeltas
    219    for atom in mol.GetAtoms():
    220      n = atom.GetAtomicNum()
    221      if n>1:
    222        nV = periodicTable.GetNOuterElecs(n)
    223        nHs = atom.GetTotalNumHs()
    224        if n <= 10:
    225          # first row
    226          res.append(float(nV-nHs))
    227        else:
    228          # second row and up
    229          res.append(float(nV-nHs)/float(n-nV-1))
    230      elif n==1:
    231        if not skipHs:
    232          res.append(0.0)
    233      else:
    234        res.append(0.0)
    235    mol._hkDeltas = res
    236    return res
    237
    238 -def _pyChi0v(mol):
    239    """  From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    240
    241    """
    242    deltas = _hkDeltas(mol)
    243    while 0 in deltas:
    244      deltas.remove(0)
    245    mol._hkDeltas=None
    246    res = sum(numpy.sqrt(1./numpy.array(deltas)))
    247    return res
    248
    249 -def _pyChi1v(mol):
    250    """  From equations (5),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    251
    252    """
    253    deltas = numpy.array(_hkDeltas(mol,skipHs=0))
    254    res = 0.0
    255    for bond in mol.GetBonds():
    256      v = deltas[bond.GetBeginAtomIdx()]*deltas[bond.GetEndAtomIdx()]
    257      if v != 0.0:
    258        res += numpy.sqrt(1./v)
    259    return res
    260
    261 -def _pyChiNv_(mol,order=2):
    262    """  From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    263
    264    **NOTE**: because the current path finding code does, by design,
    265    detect rings as paths (e.g. in C1CC1 there is *1* atom path of
    266    length 3), values of ChiNv with N >= 3 may give results that differ
    267    from those provided by the old code in molecules that have rings of
    268    size 3.
    269
    270    """
    271    deltas = numpy.array([(1. / numpy.sqrt(hkd) if hkd!=0.0 else 0.0) for hkd in _hkDeltas(mol, skipHs=0)])
    272    accum = 0.0
    273    for path in Chem.FindAllPathsOfLengthN(mol, order + 1, useBonds=0):
    274      accum += numpy.prod(deltas[numpy.array(path)])
    275    return accum
    276
    277 -def _pyChi2v(mol):
    278    """ From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    279
    280    """
    281    return _pyChiNv_(mol,2)
    282
    283 -def _pyChi3v(mol):
    284    """ From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    285
    286    """
    287    return _pyChiNv_(mol,3)
    288
    289 -def _pyChi4v(mol):
    290    """ From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
    291
    292    **NOTE**: because the current path finding code does, by design,
    293    detect rings as paths (e.g. in C1CC1 there is *1* atom path of
    294    length 3), values of Chi4v may give results that differ from those
    295    provided by the old code in molecules that have 3 rings.
    296
    297    """
    298    return _pyChiNv_(mol,4)
    299
    300 -def _pyChi0n(mol):
    301    """  Similar to Hall Kier Chi0v, but uses nVal instead of valence
    302    This makes a big difference after we get out of the first row.
    303
    304    """
    305    deltas = [_nVal(x) for x in mol.GetAtoms()]
    306    while deltas.count(0):
    307      deltas.remove(0)
    308    deltas = numpy.array(deltas,'d')
    309    res = sum(numpy.sqrt(1./deltas))
    310    return res
    311
    312 -def _pyChi1n(mol):
    313    """  Similar to Hall Kier Chi1v, but uses nVal instead of valence
    314
    315    """
    316    delts = numpy.array([_nVal(x) for x in mol.GetAtoms()],'d')
    317    res = 0.0
    318    for bond in mol.GetBonds():
    319      v = delts[bond.GetBeginAtomIdx()]*delts[bond.GetEndAtomIdx()]
    320      if v != 0.0:
    321        res += numpy.sqrt(1./v)
    322    return res
    323
    324 -def _pyChiNn_(mol,order=2):
    325    """  Similar to Hall Kier ChiNv, but uses nVal instead of valence
    326    This makes a big difference after we get out of the first row.
    327
    328    **NOTE**: because the current path finding code does, by design,
    329    detect rings as paths (e.g. in C1CC1 there is *1* atom path of
    330    length 3), values of ChiNn with N >= 3 may give results that differ
    331    from those provided by the old code in molecules that have rings of
    332    size 3.
    333
    334    """
    335    nval = [_nVal(x) for x in mol.GetAtoms()]
    336    deltas = numpy.array([(1. / numpy.sqrt(x) if x else 0.0) for x in nval])
    337    accum = 0.0
    338    for path in Chem.FindAllPathsOfLengthN(mol,order+1,useBonds=0):
    339      accum += numpy.prod(deltas[numpy.array(path)])
    340    return accum
    341
    342 -def _pyChi2n(mol):
    343    """  Similar to Hall Kier Chi2v, but uses nVal instead of valence
    344    This makes a big difference after we get out of the first row.
    345
    346    """
    347    return _pyChiNn_(mol,2)
    348
    349 -def _pyChi3n(mol):
    350    """  Similar to Hall Kier Chi3v, but uses nVal instead of valence
    351    This makes a big difference after we get out of the first row.
    352
    353    """
    354    return _pyChiNn_(mol,3)
    355
    356 -def _pyChi4n(mol):
    357    """  Similar to Hall Kier Chi4v, but uses nVal instead of valence
    358    This makes a big difference after we get out of the first row.
    359
    360
    361    **NOTE**: because the current path finding code does, by design,
    362    detect rings as paths (e.g. in C1CC1 there is *1* atom path of
    363    length 3), values of Chi4n may give results that differ from those
    364    provided by the old code in molecules that have 3 rings.
    365
    366    """
    367    return _pyChiNn_(mol,4)
    368
    369  Chi0v = lambda x:rdMolDescriptors.CalcChi0v(x)
    370  Chi0v.version=rdMolDescriptors._CalcChi0v_version
    371  Chi1v = lambda x:rdMolDescriptors.CalcChi1v(x)
    372  Chi1v.version=rdMolDescriptors._CalcChi1v_version
    373  Chi2v = lambda x:rdMolDescriptors.CalcChi2v(x)
    374  Chi2v.version=rdMolDescriptors._CalcChi2v_version
    375  Chi3v = lambda x:rdMolDescriptors.CalcChi3v(x)
    376  Chi3v.version=rdMolDescriptors._CalcChi3v_version
    377  Chi4v = lambda x:rdMolDescriptors.CalcChi4v(x)
    378  Chi4v.version=rdMolDescriptors._CalcChi4v_version
    379  ChiNv_ = lambda x,y:rdMolDescriptors.CalcChiNv(x,y)
    380  ChiNv_.version=rdMolDescriptors._CalcChiNv_version
    381
    382  Chi0n = lambda x:rdMolDescriptors.CalcChi0n(x)
    383  Chi0n.version=rdMolDescriptors._CalcChi0n_version
    384  Chi1n = lambda x:rdMolDescriptors.CalcChi1n(x)
    385  Chi1n.version=rdMolDescriptors._CalcChi1n_version
    386  Chi2n = lambda x:rdMolDescriptors.CalcChi2n(x)
    387  Chi2n.version=rdMolDescriptors._CalcChi2n_version
    388  Chi3n = lambda x:rdMolDescriptors.CalcChi3n(x)
    389  Chi3n.version=rdMolDescriptors._CalcChi3n_version
    390  Chi4n = lambda x:rdMolDescriptors.CalcChi4n(x)
    391  Chi4n.version=rdMolDescriptors._CalcChi4n_version
    392  ChiNn_ = lambda x,y:rdMolDescriptors.CalcChiNn(x,y)
    393  ChiNn_.version=rdMolDescriptors._CalcChiNn_version
    394
    395 -def BalabanJ(mol,dMat=None,forceDMat=0):
    396    """ Calculate Balaban's J value for a molecule
    397
    398    **Arguments**
    399
    400      - mol: a molecule
    401
    402      - dMat: (optional) a distance/adjacency matrix for the molecule, if this
    403        is not provide, one will be calculated
    404
    405      - forceDMat: (optional) if this is set, the distance/adjacency matrix
    406        will be recalculated regardless of whether or not _dMat_ is provided
    407        or the molecule already has one
    408
    409    **Returns**
    410
    411      - a float containing the J value
    412
    413    We follow the notation of Balaban's paper:
    414      Chem. Phys. Lett. vol 89, 399-404, (1982)
    415
    416    """
    417    # if no dMat is passed in, calculate one ourselves
    418    if forceDMat or dMat is None:
    419      if forceDMat:
    420        # FIX: should we be using atom weights here or not?
    421        dMat = Chem.GetDistanceMatrix(mol,useBO=1,useAtomWts=0,force=1)
    422        mol._balabanMat = dMat
    423        adjMat = Chem.GetAdjacencyMatrix(mol,useBO=0,emptyVal=0,force=0,prefix="NoBO")
    424        mol._adjMat = adjMat
    425      else:
    426        try:
    427          # first check if the molecule already has one
    428          dMat = mol._balabanMat
    429        except AttributeError:
    430          # nope, gotta calculate one
    431          dMat = Chem.GetDistanceMatrix(mol,useBO=1,useAtomWts=0,force=0,prefix="Balaban")
    432          # now store it
    433          mol._balabanMat = dMat
    434        try:
    435          adjMat = mol._adjMat
    436        except AttributeError:
    437          adjMat = Chem.GetAdjacencyMatrix(mol,useBO=0,emptyVal=0,force=0,prefix="NoBO")
    438          mol._adjMat = adjMat
    439    else:
    440      adjMat = Chem.GetAdjacencyMatrix(mol,useBO=0,emptyVal=0,force=0,prefix="NoBO")
    441
    442    s = _VertexDegrees(dMat)
    443    q = _NumAdjacencies(mol,dMat)
    444    n = mol.GetNumAtoms()
    445    mu = q - n + 1
    446
    447    sum = 0.
    448    nS = len(s)
    449    for i in range(nS):
    450      si = s[i]
    451      for j in range(i,nS):
    452        if adjMat[i,j] == 1:
    453          sum += 1./numpy.sqrt(si*s[j])
    454
    455    if mu+1 != 0:
    456      J = float(q) / float(mu + 1) * sum
    457    else:
    458      J = 0
    459
    460    return J
    461  BalabanJ.version="1.0.0"
    462
    463
    464  #------------------------------------------------------------------------
    465  #
    466  # Start block of BertzCT stuff.
    467  #
    468
    469
    470 -def _AssignSymmetryClasses(mol, vdList, bdMat, forceBDMat, numAtoms, cutoff):
    471    """
    472       Used by BertzCT
    473
    474       vdList: the number of neighbors each atom has
    475       bdMat: "balaban" distance matrix
    476
    477    """
    478    if forceBDMat:
    479      bdMat = Chem.GetDistanceMatrix(mol,useBO=1,useAtomWts=0,force=1,
    480                                     prefix="Balaban")
    481      mol._balabanMat = bdMat
    482
    483    atomIdx = 0
    484    keysSeen = []
    485    symList = [0]*numAtoms
    486    for i in range(numAtoms):
    487      tmpList = bdMat[i].tolist()
    488      tmpList.sort()
    489      theKey = tuple(['%.4f'%x for x in tmpList[:cutoff]])
    490      try:
    491        idx = keysSeen.index(theKey)
    492      except ValueError:
    493        idx = len(keysSeen)
    494        keysSeen.append(theKey)
    495      symList[i] = idx+1
    496    return tuple(symList)
    497
    498 -def _LookUpBondOrder(atom1Id, atom2Id, bondDic):
    499    """
    500       Used by BertzCT
    501    """
    502    if atom1Id < atom2Id:
    503      theKey = (atom1Id,atom2Id)
    504    else:
    505      theKey = (atom2Id,atom1Id)
    506    tmp = bondDic[theKey]
    507    if tmp == Chem.BondType.AROMATIC:
    508      tmp = 1.5
    509    else:
    510      tmp = float(tmp)
    511    #tmp = int(tmp)
    512    return tmp
    513
    514
    515 -def _CalculateEntropies(connectionDict, atomTypeDict, numAtoms):
    516    """
    517       Used by BertzCT
    518    """
    519    connectionList = list(connectionDict.values())
    520    totConnections = sum(connectionList)
    521    connectionIE = totConnections*(entropy.InfoEntropy(numpy.array(connectionList)) +
    522                                   math.log(totConnections)/_log2val)
    523    atomTypeList = list(atomTypeDict.values())
    524    atomTypeIE = numAtoms*entropy.InfoEntropy(numpy.array(atomTypeList))
    525    return atomTypeIE + connectionIE
    526
    527 -def _CreateBondDictEtc(mol, numAtoms):
    528    """ _Internal Use Only_
    529       Used by BertzCT
    530
    531    """
    532    bondDict = {}
    533    nList = [None]*numAtoms
    534    vdList = [0]*numAtoms
    535    for aBond in mol.GetBonds():
    536      atom1=aBond.GetBeginAtomIdx()
    537      atom2=aBond.GetEndAtomIdx()
    538      if atom1>atom2: atom2,atom1=atom1,atom2
    539      if not aBond.GetIsAromatic():
    540        bondDict[(atom1,atom2)] = aBond.GetBondType()
    541      else:
    542        # mark Kekulized systems as aromatic
    543        bondDict[(atom1,atom2)] = Chem.BondType.AROMATIC
    544      if nList[atom1] is None:
    545        nList[atom1] = [atom2]
    546      elif atom2 not in nList[atom1]:
    547        nList[atom1].append(atom2)
    548      if nList[atom2] is None:
    549        nList[atom2] = [atom1]
    550      elif atom1 not in nList[atom2]:
    551        nList[atom2].append(atom1)
    552
    553    for i,element in enumerate(nList):
    554      try:
    555        element.sort()
    556        vdList[i] = len(element)
    557      except Exception:
    558        vdList[i] = 0
    559    return bondDict, nList, vdList
    560
    561 -def BertzCT(mol, cutoff = 100, dMat = None, forceDMat = 1):
    562    """ A topological index meant to quantify "complexity" of molecules.
    563
    564       Consists of a sum of two terms, one representing the complexity
    565       of the bonding, the other representing the complexity of the
    566       distribution of heteroatoms.
    567
    568       From S. H. Bertz, J. Am. Chem. Soc., vol 103, 3599-3601 (1981)
    569
    570       "cutoff" is an integer value used to limit the computational
    571       expense.  A cutoff value tells the program to consider vertices
    572       topologically identical if their distance vectors (sets of
    573       distances to all other vertices) are equal out to the "cutoff"th
    574       nearest-neighbor.
    575
    576       **NOTE**  The original implementation had the following comment:
    577           > this implementation treats aromatic rings as the
    578           > corresponding Kekule structure with alternating bonds,
    579           > for purposes of counting "connections".
    580         Upon further thought, this is the WRONG thing to do.  It
    581          results in the possibility of a molecule giving two different
    582          CT values depending on the kekulization.  For example, in the
    583          old implementation, these two SMILES:
    584             CC2=CN=C1C3=C(C(C)=C(C=N3)C)C=CC1=C2C
    585             CC3=CN=C2C1=NC=C(C)C(C)=C1C=CC2=C3C
    586          which correspond to differentk kekule forms, yield different
    587          values.
    588         The new implementation uses consistent (aromatic) bond orders
    589          for aromatic bonds.
    590
    591         THIS MEANS THAT THIS IMPLEMENTATION IS NOT BACKWARDS COMPATIBLE.
    592
    593         Any molecule containing aromatic rings will yield different
    594         values with this implementation.  The new behavior is the correct
    595         one, so we're going to live with the breakage.
    596
    597       **NOTE** this barfs if the molecule contains a second (or
    598         nth) fragment that is one atom.
    599
    600    """
    601    atomTypeDict = {}
    602    connectionDict = {}
    603    numAtoms = mol.GetNumAtoms()
    604    if forceDMat or dMat is None:
    605      if forceDMat:
    606        # nope, gotta calculate one
    607        dMat = Chem.GetDistanceMatrix(mol,useBO=0,useAtomWts=0,force=1)
    608        mol._adjMat = dMat
    609      else:
    610        try:
    611          dMat = mol._adjMat
    612        except AttributeError:
    613          dMat = Chem.GetDistanceMatrix(mol,useBO=0,useAtomWts=0,force=1)
    614          mol._adjMat = dMat
    615
    616    if numAtoms < 2:
    617      return 0
    618
    619    bondDict, neighborList, vdList = _CreateBondDictEtc(mol, numAtoms)
    620    symmetryClasses = _AssignSymmetryClasses(mol, vdList, dMat, forceDMat, numAtoms, cutoff)
    621    #print('Symmm Classes:',symmetryClasses)
    622    for atomIdx in range(numAtoms):
    623      hingeAtomNumber = mol.GetAtomWithIdx(atomIdx).GetAtomicNum()
    624      atomTypeDict[hingeAtomNumber] = atomTypeDict.get(hingeAtomNumber,0)+1
    625
    626      hingeAtomClass = symmetryClasses[atomIdx]
    627      numNeighbors = vdList[atomIdx]
    628      for i in range(numNeighbors):
    629        neighbor_iIdx = neighborList[atomIdx][i]
    630        NiClass = symmetryClasses[neighbor_iIdx]
    631        bond_i_order = _LookUpBondOrder(atomIdx, neighbor_iIdx, bondDict)
    632        #print('\t',atomIdx,i,hingeAtomClass,NiClass,bond_i_order)
    633        if (bond_i_order > 1) and (neighbor_iIdx > atomIdx):
    634          numConnections = bond_i_order*(bond_i_order - 1)/2
    635          connectionKey = (min(hingeAtomClass, NiClass), max(hingeAtomClass, NiClass))
    636          connectionDict[connectionKey] = connectionDict.get(connectionKey,0)+numConnections
    637
    638        for j in range(i+1, numNeighbors):
    639          neighbor_jIdx = neighborList[atomIdx][j]
    640          NjClass = symmetryClasses[neighbor_jIdx]
    641          bond_j_order = _LookUpBondOrder(atomIdx, neighbor_jIdx, bondDict)
    642          numConnections = bond_i_order*bond_j_order
    643          connectionKey = (min(NiClass, NjClass), hingeAtomClass, max(NiClass, NjClass))
    644          connectionDict[connectionKey] = connectionDict.get(connectionKey,0)+numConnections
    645
    646    if not connectionDict:
    647      connectionDict = {'a':1}
    648
    649    return _CalculateEntropies(connectionDict, atomTypeDict, numAtoms)
    650  BertzCT.version="2.0.0"
    651  # Recent Revisions:
    652  #  1.0.0 -> 2.0.0:
    653  #    - force distance matrix updates properly (Fixed as part of Issue 125)
    654  #    - handle single-atom fragments (Issue 136)
    655
    656
    657  #
    658  # End block of BertzCT stuff.
    659  #
    660  #------------------------------------------------------------------------
    661