rdkit.Chem.AtomPairs.Sheridan

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

      1  #
      2  #  Copyright (C) 2015 Greg Landrum
      3  #
      4  #   @@ All Rights Reserved @@
      5  #  This file is part of the RDKit.
      6  #  The contents are covered by the terms of the BSD license
      7  #  which is included in the file license.txt, found at the root
      8  #  of the RDKit source tree.
      9  #
     10  """ Contains an implementation of Physicochemical property fingerprints, as
     11  described in:
     12  Kearsley, S. K. et al.
     13  "Chemical Similarity Using Physiochemical Property Descriptors."
     14  J. Chem.Inf. Model. 36, 118-127 (1996)
     15  """
     16  from rdkit.DataStructs import IntSparseIntVect
     17  from rdkit import Chem
     18  from rdkit.Chem import rdMolDescriptors
     19  from rdkit import DataStructs
     20
     21  from rdkit.Chem.rdMolDescriptors import GetAtomPairFingerprint,GetTopologicalTorsionFingerprint
     22
     23
     24  numPathBits=rdMolDescriptors.AtomPairsParameters.numPathBits
     25  _maxPathLen=(1<<numPathBits)-1
     26  numFpBits=numPathBits+2*rdMolDescriptors.AtomPairsParameters.codeSize
     27  fpLen=1<<numFpBits
     28
     29  import os.path,re
     30  from rdkit import RDConfig
     31 -def _readPattyDefs(fname=os.path.join(RDConfig.RDDataDir,'SmartsLib','patty_rules.txt')):
     32      with open(fname,'r') as inf:
     33          lines = [x.strip().split('# ')[0].strip() for x in inf]
     34      splitl = [re.split('[ ]*',x) for x in lines if x != '']
     35      matchers = []
     36      for tpl in splitl:
     37          if len(tpl)>1:
     38              mol = Chem.MolFromSmarts(tpl[0])
     39              if mol is None:
     40                  continue
     41              nm = tpl[1]
     42              matchers.append((mol,nm))
     43      return matchers
     44
     45  _pattyDefs=None
     46 -def AssignPattyTypes(mol,defns=None):
     47      """
     48
     49      >>> from rdkit import Chem
     50      >>> AssignPattyTypes(Chem.MolFromSmiles('OCC(=O)O'))
     51      ['POL', 'HYD', 'OTH', 'ANI', 'ANI']
     52
     53      """
     54      global _pattyDefs
     55      if defns is None:
     56          if _pattyDefs is None:
     57              _pattyDefs = _readPattyDefs()
     58          defns = _pattyDefs
     59      res = ['']*mol.GetNumAtoms()
     60      for matcher,nm in defns:
     61          matches = mol.GetSubstructMatches(matcher,uniquify=False)
     62          for match in matches:
     63              res[match[0]] = nm
     64      return res
     65
     66  typMap=dict(CAT=1,ANI=2,POL=3,DON=4,ACC=5,HYD=6,OTH=7)
     67 -def GetBPFingerprint(mol,fpfn=GetAtomPairFingerprint):
     68      """
     69      >>> from rdkit import Chem
     70      >>> fp = GetBPFingerprint(Chem.MolFromSmiles('OCC(=O)O'))
     71      >>> fp.GetTotalVal()
     72      10
     73      >>> nze=fp.GetNonzeroElements()
     74      >>> sorted([(k,v) for k,v in nze.items()])
     75      [(32834, 1), (49219, 2), (98370, 2), (98401, 1), (114753, 2), (114786, 1), (114881, 1)]
     76
     77      """
     78      typs = [typMap[x] for x in AssignPattyTypes(mol)]
     79      fp = fpfn(mol,atomInvariants=typs)
     80      return fp
     81
     82 -def GetBTFingerprint(mol,fpfn=GetTopologicalTorsionFingerprint):
     83      """
     84      >>> from rdkit import Chem
     85      >>> mol = Chem.MolFromSmiles('OCC(N)O')
     86      >>> AssignPattyTypes(mol)
     87      ['POL', 'HYD', 'HYD', 'CAT', 'POL']
     88      >>> fp = GetBTFingerprint(mol)
     89      >>> fp.GetTotalVal()
     90      2
     91      >>> nze=fp.GetNonzeroElements()
     92      >>> sorted([(k,v) for k,v in nze.items()])
     93      [(538446850L, 1), (538446852L, 1)]
     94
     95      """
     96      return GetBPFingerprint(mol,fpfn=fpfn)
     97
     98
     99
    100
    101  #------------------------------------
    102  #
    103  #  doctest boilerplate
    104  #
    105 -def _test():
    106    import doctest,sys
    107    return doctest.testmod(sys.modules["__main__"])
    108
    109
    110  if __name__ == '__main__':
    111    import sys
    112    failed,tried = _test()
    113    sys.exit(failed)
    114