rdkit.Chem.SimpleEnum.Enumerator

Package rdkit :: Package Chem :: Package SimpleEnum :: Module Enumerator |
[hide private]
[frames] | no frames]

# Source Code for Module rdkit.Chem.SimpleEnum.Enumerator

      1  #
      2  #  Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
      3  #  All rights reserved.
      4  #
      5  # Redistribution and use in source and binary forms, with or without
      6  # modification, are permitted provided that the following conditions are
      7  # met:
      8  #
      9  #     * Redistributions of source code must retain the above copyright
     10  #       notice, this list of conditions and the following disclaimer.
     11  #     * Redistributions in binary form must reproduce the above
     12  #       copyright notice, this list of conditions and the following
     13  #       disclaimer in the documentation and/or other materials provided
     14  #       with the distribution.
     15  #     * Neither the name of Novartis Institutes for BioMedical Research Inc.
     16  #       nor the names of its contributors may be used to endorse or promote
     17  #       products derived from this software without specific prior written permission.
     18  #
     19  # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
     20  # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
     21  # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
     22  # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
     23  # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
     24  # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
     25  # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
     26  # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
     27  # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
     28  # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
     29  # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
     30  #
     31  # Created by Greg Landrum, May 2009
     32  from __future__ import print_function
     33  from rdkit import RDConfig
     34  from rdkit import Chem
     35  from rdkit.Chem import AllChem
     36  from rdkit.Chem import FunctionalGroups
     37  from rdkit.Chem import rdChemReactions
     38
     39
     40  import os
     41
     42 -def PreprocessReaction(reaction,funcGroupFilename=os.path.join(RDConfig.RDDataDir,'Functional_Group_Hierarchy.txt'),propName='molFileValue'):
     43    """
     44    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','boronic1.rxn')
     45    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
     46    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
     47    >>> nWarn
     48    0
     49    >>> nError
     50    0
     51    >>> nReacts
     52    2
     53    >>> nProds
     54    1
     55    >>> reactantLabels
     56    (((0, 'halogen.bromine.aromatic'),), ((1, 'boronicacid'),))
     57
     58    If there are functional group labels in the input reaction (via atoms with molFileValue properties),
     59    the corresponding atoms will have queries added to them so that they only match such things. We can
     60    see this here:
     61    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
     62    >>> r1 = rxn.GetReactantTemplate(0)
     63    >>> m1 = Chem.MolFromSmiles('CCBr')
     64    >>> m2 = Chem.MolFromSmiles('c1ccccc1Br')
     65
     66    These both match because the reaction file itself just has R1-Br:
     67    >>> m1.HasSubstructMatch(r1)
     68    True
     69    >>> m2.HasSubstructMatch(r1)
     70    True
     71
     72    After preprocessing, we only match the aromatic Br:
     73    >>> d = PreprocessReaction(rxn)
     74    >>> m1.HasSubstructMatch(r1)
     75    False
     76    >>> m2.HasSubstructMatch(r1)
     77    True
     78
     79    We also support or queries in the values field (separated by commas):
     80    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','azide_reaction.rxn')
     81    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
     82    >>> reactantLabels = PreprocessReaction(rxn)[-1]
     83    >>> reactantLabels
     84    (((1, 'azide'),), ((1, 'carboxylicacid,acidchloride'),))
     85    >>> m1 = Chem.MolFromSmiles('CC(=O)O')
     86    >>> m2 = Chem.MolFromSmiles('CC(=O)Cl')
     87    >>> m3 = Chem.MolFromSmiles('CC(=O)N')
     88    >>> r2 = rxn.GetReactantTemplate(1)
     89    >>> m1.HasSubstructMatch(r2)
     90    True
     91    >>> m2.HasSubstructMatch(r2)
     92    True
     93    >>> m3.HasSubstructMatch(r2)
     94    False
     95
     96    unrecognized final group types are returned as None:
     97    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','bad_value1.rxn')
     98    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
     99    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    100    Traceback (most recent call last):
    101      File "/usr/prog/python/2.6.6_gnu/lib/python2.6/doctest.py", line 1253, in __run
    102        compileflags, 1) in test.globs
    103      File "<doctest __main__.PreprocessReaction[36]>", line 1, in <module>
    104        nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    105      File "Enumerator.py", line 105, in PreprocessReaction
    106        reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName='molFileValue', getLabels=True)
    107    RuntimeError: KeyErrorException
    108
    109    One unrecognized group type in a comma-separated list makes the whole thing fail:
    110    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','bad_value2.rxn')
    111    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    112    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    113    Traceback (most recent call last):
    114      File "/usr/prog/python/2.6.6_gnu/lib/python2.6/doctest.py", line 1253, in __run
    115        compileflags, 1) in test.globs
    116      File "<doctest __main__.PreprocessReaction[36]>", line 1, in <module>
    117        nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    118      File "Enumerator.py", line 105, in PreprocessReaction
    119        reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName='molFileValue', getLabels=True)
    120    RuntimeError: KeyErrorException
    121    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','bad_value3.rxn')
    122    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    123    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    124    Traceback (most recent call last):
    125      File "/usr/prog/python/2.6.6_gnu/lib/python2.6/doctest.py", line 1253, in __run
    126        compileflags, 1) in test.globs
    127      File "<doctest __main__.PreprocessReaction[36]>", line 1, in <module>
    128        nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    129      File "Enumerator.py", line 105, in PreprocessReaction
    130        reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName='molFileValue', getLabels=True)
    131    RuntimeError: KeyErrorException
    132    >>> rxn = rdChemReactions.ChemicalReaction()
    133    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    134    >>> reactantLabels == []
    135    True
    136    """
    137    reaction._setImplicitPropertiesFlag(True)
    138    reaction.Initialize()
    139    nReactants = reaction.GetNumReactantTemplates()
    140    nProducts = reaction.GetNumProductTemplates()
    141    nWarn,nError = reaction.Validate()
    142
    143    if not nError:
    144      try:
    145        queryDict = Chem.ParseMolQueryDefFile(funcGroupFilename)
    146      except Exception:
    147        raise IOError('cannot open', funcGroupFilename)
    148      else:
    149        reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName, getLabels=True)
    150    else:
    151      reactantLabels = []
    152
    153    return nWarn,nError,nReactants,nProducts,reactantLabels
    154
    155 -def EnumerateReaction(reaction,bbLists,uniqueProductsOnly=False,funcGroupFilename=os.path.join(RDConfig.RDDataDir,'Functional_Group_Hierarchy.txt'),propName='molFileValue'):
    156    """
    157    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','boronic1.rxn')
    158    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    159    >>> reacts1=['Brc1ccccc1','Brc1ncccc1','Brc1cnccc1']
    160    >>> reacts1=[Chem.MolFromSmiles(x) for x in reacts1]
    161    >>> reacts2=['CCB(O)O','CCCB(O)O']
    162    >>> reacts2=[Chem.MolFromSmiles(x) for x in reacts2]
    163
    164    >>> prods = EnumerateReaction(rxn,(reacts1,reacts2))
    165    >>> prods = list(prods)
    166
    167    This is a bit nasty because of the symmetry of the boronic acid:
    168    >>> len(prods)
    169    12
    170
    171    >>> smis = list(set([Chem.MolToSmiles(x[0]) for x in prods]))
    172    >>> smis.sort()
    173    >>> len(smis)
    174    6
    175    >>> print(smis)
    176    ['CCCc1ccccc1', 'CCCc1ccccn1', 'CCCc1cccnc1', 'CCc1ccccc1', 'CCc1ccccn1', 'CCc1cccnc1']
    177
    178    The nastiness can be avoided at the cost of some memory by asking for only unique products:
    179    >>> prods = EnumerateReaction(rxn,(reacts1,reacts2),uniqueProductsOnly=True)
    180    >>> prods = list(prods)
    181    >>> len(prods)
    182    6
    183    >>> print(sorted([Chem.MolToSmiles(x[0]) for x in prods]))
    184    ['CCCc1ccccc1', 'CCCc1ccccn1', 'CCCc1cccnc1', 'CCc1ccccc1', 'CCc1ccccn1', 'CCc1cccnc1']
    185
    186
    187    """
    188    nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(reaction)
    189    if nError: raise ValueError('bad reaction')
    190    if len(bbLists) != nReacts: raise ValueError('%d reactants in reaction, %d bb lists supplied'%(nReacts,len(bbLists)))
    191    def _uniqueOnly(lst):
    192      seen=[]
    193      for entry in lst:
    194        if entry:
    195          smi = '.'.join(sorted([Chem.MolToSmiles(x,True) for x in entry]))
    196          if smi not in seen:
    197            seen.append(smi)
    198            yield entry
    199
    200    ps = AllChem.EnumerateLibraryFromReaction(reaction,bbLists)
    201    if not uniqueProductsOnly:
    202      return ps
    203    else:
    204      return _uniqueOnly(ps)
    205
    206
    207
    208
    209  #------------------------------------
    210  #
    211  #  doctest boilerplate
    212  #
    213 -def _test():
    214    import doctest,sys
    215    return doctest.testmod(sys.modules["__main__"])
    216
    217
    218  if __name__ == '__main__':
    219    import sys
    220    failed,tried = _test()
    221    sys.exit(failed)
    222