Package rdkit :: Package Chem :: Package SimpleEnum :: Module Enumerator

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# Module Enumerator

source code

Functions | [hide private]

PreprocessReaction(reaction, funcGroupFilename=os.path.join(RDConfig.RDDataDir,'Functional_Group_Hierarchy.txt'), propName='molFileValue')
>>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','boronic1.rxn') >>> rxn = AllChem.ReactionFromRxnFile(testFile) >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn) >>> nWarn 0 >>> nError 0 >>> nReacts 2 >>> nProds 1 >>> reactantLabels (((0, 'halogen.bromine.aromatic'),), ((1, 'boronicacid'),))

source code

EnumerateReaction(reaction, bbLists, uniqueProductsOnly=False, funcGroupFilename=os.path.join(RDConfig.RDDataDir,'Functional_Group_Hierarchy.txt'), propName='molFileValue')
>>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','boronic1.rxn') >>> rxn = AllChem.ReactionFromRxnFile(testFile) >>> reacts1=['Brc1ccccc1','Brc1ncccc1','Brc1cnccc1'] >>> reacts1=[Chem.MolFromSmiles(x) for x in reacts1] >>> reacts2=['CCB(O)O','CCCB(O)O'] >>> reacts2=[Chem.MolFromSmiles(x) for x in reacts2]

source code

_test() | source code

Imports: RDConfig, Chem, AllChem, FunctionalGroups, os

Function Details | [hide private]

### PreprocessReaction(reaction, funcGroupFilename=os.path.join(RDConfig.RDDataDir,'Functional_Group_Hierarchy.txt'), propName='molFileValue')

source code

    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','boronic1.rxn')
    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    >>> nWarn
    0
    >>> nError
    0
    >>> nReacts
    2
    >>> nProds
    1
    >>> reactantLabels
    (((0, 'halogen.bromine.aromatic'),), ((1, 'boronicacid'),))

    If there are functional group labels in the input reaction (via atoms with molFileValue properties),
    the corresponding atoms will have queries added to them so that they only match such things. We can
    see this here:
    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    >>> r1 = rxn.GetReactantTemplate(0)
    >>> m1 = Chem.MolFromSmiles('CCBr')
    >>> m2 = Chem.MolFromSmiles('c1ccccc1Br')

    These both match because the reaction file itself just has R1-Br:
    >>> m1.HasSubstructMatch(r1)
    True
    >>> m2.HasSubstructMatch(r1)
    True

    After preprocessing, we only match the aromatic Br:
    >>> d = PreprocessReaction(rxn)
    >>> m1.HasSubstructMatch(r1)
    False
    >>> m2.HasSubstructMatch(r1)
    True

    We also support or queries in the values field (separated by commas):
    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','azide_reaction.rxn')
    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    >>> reactantLabels = PreprocessReaction(rxn)[-1]
    >>> reactantLabels
    (((1, 'azide'),), ((1, 'carboxylicacid,acidchloride'),))
    >>> m1 = Chem.MolFromSmiles('CC(=O)O')
    >>> m2 = Chem.MolFromSmiles('CC(=O)Cl')
    >>> m3 = Chem.MolFromSmiles('CC(=O)N')
    >>> r2 = rxn.GetReactantTemplate(1)
    >>> m1.HasSubstructMatch(r2)
    True
    >>> m2.HasSubstructMatch(r2)
    True
    >>> m3.HasSubstructMatch(r2)
    False

    unrecognized final group types are returned as None:
    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','bad_value1.rxn')
    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    Traceback (most recent call last):
      File "/usr/prog/python/2.6.6_gnu/lib/python2.6/doctest.py", line 1253, in __run
        compileflags, 1) in test.globs
      File "<doctest __main__.PreprocessReaction[36]>", line 1, in <module>
        nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
      File "Enumerator.py", line 105, in PreprocessReaction
        reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName='molFileValue', getLabels=True)
    RuntimeError: KeyErrorException

    One unrecognized group type in a comma-separated list makes the whole thing fail:
    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','bad_value2.rxn')
    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    Traceback (most recent call last):
      File "/usr/prog/python/2.6.6_gnu/lib/python2.6/doctest.py", line 1253, in __run
        compileflags, 1) in test.globs
      File "<doctest __main__.PreprocessReaction[36]>", line 1, in <module>
        nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
      File "Enumerator.py", line 105, in PreprocessReaction
        reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName='molFileValue', getLabels=True)
    RuntimeError: KeyErrorException
    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','bad_value3.rxn')
    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    >>> nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
    Traceback (most recent call last):
      File "/usr/prog/python/2.6.6_gnu/lib/python2.6/doctest.py", line 1253, in __run
        compileflags, 1) in test.globs
      File "<doctest __main__.PreprocessReaction[36]>", line 1, in <module>
        nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(rxn)
      File "Enumerator.py", line 105, in PreprocessReaction
        reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName='molFileValue', getLabels=True)
    RuntimeError: KeyErrorException

### EnumerateReaction(reaction, bbLists, uniqueProductsOnly=False, funcGroupFilename=os.path.join(RDConfig.RDDataDir,'Functional_Group_Hierarchy.txt'), propName='molFileValue')

source code

    >>> testFile = os.path.join(RDConfig.RDCodeDir,'Chem','SimpleEnum','test_data','boronic1.rxn')
    >>> rxn = AllChem.ReactionFromRxnFile(testFile)
    >>> reacts1=['Brc1ccccc1','Brc1ncccc1','Brc1cnccc1']
    >>> reacts1=[Chem.MolFromSmiles(x) for x in reacts1]
    >>> reacts2=['CCB(O)O','CCCB(O)O']
    >>> reacts2=[Chem.MolFromSmiles(x) for x in reacts2]

    >>> prods = EnumerateReaction(rxn,(reacts1,reacts2))
    >>> prods = list(prods)

    This is a bit nasty because of the symmetry of the boronic acid:
    >>> len(prods)
    12

    >>> smis = list(set([Chem.MolToSmiles(x[0]) for x in prods]))
    >>> smis.sort()
    >>> len(smis)
    6
    >>> print(smis)
    ['CCCc1ccccc1', 'CCCc1ccccn1', 'CCCc1cccnc1', 'CCc1ccccc1', 'CCc1ccccn1', 'CCc1cccnc1']

    The nastiness can be avoided at the cost of some memory by asking for only unique products:
    >>> prods = EnumerateReaction(rxn,(reacts1,reacts2),uniqueProductsOnly=True)
    >>> prods = list(prods)
    >>> len(prods)
    6
    >>> print(sorted([Chem.MolToSmiles(x[0]) for x in prods]))
    ['CCCc1ccccc1', 'CCCc1ccccn1', 'CCCc1cccnc1', 'CCc1ccccc1', 'CCc1ccccn1', 'CCc1cccnc1']