rdkit.Chem.AtomPairs.Torsions

Package rdkit :: Package Chem :: Package AtomPairs :: Module Torsions |
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# Source Code for Module rdkit.Chem.AtomPairs.Torsions

      1  # $Id$
      2  #
      3  #  Copyright (C) 2004-2006 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  """ Contains an implementation of Topological-torsion fingerprints, as
     12  described in:
     13
     14  R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan;
     15  "Topological Torsion: A New Molecular Descriptor for SAR Applications.
     16  Comparison with Other Descriptors" JCICS 27, 82-85 (1987).
     17
     18  """
     19  from rdkit import Chem
     20  from rdkit.Chem import rdMolDescriptors
     21  from rdkit.Chem.AtomPairs import Utils
     22
     23 -def pyScorePath(mol,path,size,atomCodes=None):
     24    """ Returns a score for an individual path.
     25
     26    >>> m = Chem.MolFromSmiles('CCCCC')
     27    >>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0),1)
     28    >>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1),2)
     29    >>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2),2)
     30    >>> c4 = Utils.GetAtomCode(m.GetAtomWithIdx(3),1)
     31    >>> t = c1 | (c2 << rdMolDescriptors.AtomPairsParameters.codeSize) | (c3 << (rdMolDescriptors.AtomPairsParameters.codeSize*2)) | (c4 << (rdMolDescriptors.AtomPairsParameters.codeSize*3))
     32    >>> pyScorePath(m,(0,1,2,3),4)==t
     33    1
     34
     35    The scores are path direction independent:
     36    >>> pyScorePath(m,(3,2,1,0),4)==t
     37    1
     38
     39
     40    >>> m = Chem.MolFromSmiles('C=CC(=O)O')
     41    >>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0),1)
     42    >>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1),2)
     43    >>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2),2)
     44    >>> c4 = Utils.GetAtomCode(m.GetAtomWithIdx(4),1)
     45    >>> t = c1 | (c2 << rdMolDescriptors.AtomPairsParameters.codeSize) | (c3 << (rdMolDescriptors.AtomPairsParameters.codeSize*2)) | (c4 << (rdMolDescriptors.AtomPairsParameters.codeSize*3))
     46    >>> pyScorePath(m,(0,1,2,4),4)==t
     47    1
     48
     49    """
     50    codes = [None]*size
     51    for i in range(size):
     52      if i==0 or i==(size-1):
     53        sub = 1
     54      else:
     55        sub = 2
     56      if not atomCodes:
     57        codes[i] = Utils.GetAtomCode(mol.GetAtomWithIdx(path[i]),sub)
     58      else:
     59        base = atomCodes[path[i]]
     60        codes[i]=base-sub
     61
     62    # "canonicalize" the code vector:
     63    beg=0
     64    end = len(codes)-1
     65    while(beg < end):
     66      if codes[beg] > codes[end]:
     67        codes.reverse()
     68        break
     69      elif codes[beg]==codes[end]:
     70        beg += 1
     71        end -= 1
     72      else:
     73        break
     74    accum = 0
     75    for i in range(size):
     76      accum |= codes[i] << (rdMolDescriptors.AtomPairsParameters.codeSize*i)
     77    return accum
     78
     79 -def ExplainPathScore(score,size=4):
     80    """
     81
     82    >>> m = Chem.MolFromSmiles('C=CC')
     83    >>> score=pyScorePath(m,(0,1,2),3)
     84    >>> ExplainPathScore(score,3)
     85    (('C', 1, 0), ('C', 2, 1), ('C', 1, 1))
     86
     87    Again, it's order independent:
     88    >>> score=pyScorePath(m,(2,1,0),3)
     89    >>> ExplainPathScore(score,3)
     90    (('C', 1, 0), ('C', 2, 1), ('C', 1, 1))
     91
     92
     93    >>> m = Chem.MolFromSmiles('C=CO')
     94    >>> score=pyScorePath(m,(0,1,2),3)
     95    >>> ExplainPathScore(score,3)
     96    (('C', 1, 1), ('C', 2, 1), ('O', 1, 0))
     97
     98    >>> m = Chem.MolFromSmiles('OC=CO')
     99    >>> score=pyScorePath(m,(0,1,2,3),4)
    100    >>> ExplainPathScore(score,4)
    101    (('O', 1, 0), ('C', 2, 1), ('C', 2, 1), ('O', 1, 0))
    102
    103    >>> m = Chem.MolFromSmiles('CC=CO')
    104    >>> score=pyScorePath(m,(0,1,2,3),4)
    105    >>> ExplainPathScore(score,4)
    106    (('C', 1, 0), ('C', 2, 1), ('C', 2, 1), ('O', 1, 0))
    107
    108
    109    >>> m = Chem.MolFromSmiles('C=CC(=O)O')
    110    >>> score=pyScorePath(m,(0,1,2,3),4)
    111    >>> ExplainPathScore(score,4)
    112    (('C', 1, 1), ('C', 2, 1), ('C', 3, 1), ('O', 1, 1))
    113    >>> score=pyScorePath(m,(0,1,2,4),4)
    114    >>> ExplainPathScore(score,4)
    115    (('C', 1, 1), ('C', 2, 1), ('C', 3, 1), ('O', 1, 0))
    116
    117
    118    >>> m = Chem.MolFromSmiles('OOOO')
    119    >>> score=pyScorePath(m,(0,1,2),3)
    120    >>> ExplainPathScore(score,3)
    121    (('O', 1, 0), ('O', 2, 0), ('O', 2, 0))
    122    >>> score=pyScorePath(m,(0,1,2,3),4)
    123    >>> ExplainPathScore(score,4)
    124    (('O', 1, 0), ('O', 2, 0), ('O', 2, 0), ('O', 1, 0))
    125
    126    """
    127    codeMask=(1<<rdMolDescriptors.AtomPairsParameters.codeSize)-1
    128    res=[None]*size
    129    #print '>>>>>>>>>>>',score,size,codeMask
    130    for i in range(size):
    131      if i==0 or i==(size-1):
    132        sub = 1
    133      else:
    134        sub = 2
    135      code = score&codeMask
    136      #print i,code,score
    137      score = score>>rdMolDescriptors.AtomPairsParameters.codeSize
    138      symb,nBranch,nPi = Utils.ExplainAtomCode(code)
    139      expl = symb,nBranch+sub,nPi
    140      res[i] = expl
    141    return tuple(res)
    142
    143  from rdkit.Chem.rdMolDescriptors import GetTopologicalTorsionFingerprint,GetHashedTopologicalTorsionFingerprint
    144  GetTopologicalTorsionFingerprintAsIntVect=rdMolDescriptors.GetTopologicalTorsionFingerprint
    145 -def GetTopologicalTorsionFingerprintAsIds(mol,targetSize=4):
    146    iv = GetTopologicalTorsionFingerprint(mol,targetSize)
    147    res=[]
    148    for k,v in iv.GetNonzeroElements().iteritems():
    149      res.extend([k]*v)
    150    res.sort()
    151    return res
    152
    153
    154
    155
    156  #------------------------------------
    157  #
    158  #  doctest boilerplate
    159  #
    160 -def _test():
    161    import doctest,sys
    162    return doctest.testmod(sys.modules["__main__"])
    163
    164
    165  if __name__ == '__main__':
    166    import sys
    167    failed,tried = _test()
    168    sys.exit(failed)
    169