#
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# Created by Greg Landrum, May 2009
from __future__ import print_function
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FunctionalGroups
import os

def 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'),))

  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

  """
  reaction._setImplicitPropertiesFlag(True)
  reaction.Initialize()
  nReactants = reaction.GetNumReactantTemplates()
  nProducts = reaction.GetNumProductTemplates()
  nWarn,nError = reaction.Validate()

  if not nError:
    try:
      queryDict = Chem.ParseMolQueryDefFile(funcGroupFilename)
    except:
      raise IOError('cannot open', funcGroupFilename)
    else:
      reactantLabels = reaction.AddRecursiveQueriesToReaction(queryDict, propName, getLabels=True)

  return nWarn,nError,nReactants,nProducts,reactantLabels

def 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]

  >>> 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']

  
  """
  nWarn,nError,nReacts,nProds,reactantLabels = PreprocessReaction(reaction)
  if nError: raise ValueError('bad reaction')
  if len(bbLists) != nReacts: raise ValueError('%d reactants in reaction, %d bb lists supplied'%(nReacts,len(bbLists)))
  def _uniqueOnly(lst):
    seen=[]
    for entry in lst:
      if entry:
        smi = '.'.join(sorted([Chem.MolToSmiles(x,True) for x in entry]))
        if smi not in seen:
          seen.append(smi)
          yield entry
  
  ps = AllChem.EnumerateLibraryFromReaction(reaction,bbLists)
  if not uniqueProductsOnly:
    return ps
  else:
    return _uniqueOnly(ps)




#------------------------------------
#
#  doctest boilerplate
#
def _test():
  import doctest,sys
  return doctest.testmod(sys.modules["__main__"])


if __name__ == '__main__':
  import sys
  failed,tried = _test()
  sys.exit(failed)

