rdkit.VLib.NodeLib.SmilesOutput

Package rdkit :: Package VLib :: Package NodeLib :: Module SmilesOutput |
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# Source Code for Module rdkit.VLib.NodeLib.SmilesOutput

     1  #  $Id: SmilesOutput.py 997 2009-02-25 06:12:43Z glandrum $
     2  #
     3  #  Copyright (C) 2003 Rational Discovery LLC
     4  #     All Rights Reserved
     5  #
     6  import sys,types
     7  from rdkit import Chem
     8
     9  from rdkit.VLib.Output import OutputNode as BaseOutputNode
    10
    11 -class OutputNode(BaseOutputNode):
    12    """ dumps smiles output
    13
    14    Assumptions:
    15
    16      - destination supports a write() method
    17
    18      - inputs (parents) can be stepped through in lockstep
    19
    20
    21    Usage Example:
    22      >>> smis = ['C1CCC1','C1CC1','C=O','NCC']
    23      >>> mols = [Chem.MolFromSmiles(x) for x in smis]
    24      >>> from rdkit.VLib.Supply import SupplyNode
    25      >>> suppl = SupplyNode(contents=mols)
    26      >>> import StringIO
    27      >>> io = StringIO.StringIO()
    28      >>> node = OutputNode(dest=io,delim=', ')
    29      >>> node.AddParent(suppl)
    30      >>> ms = [x for x in node]
    31      >>> len(ms)
    32      4
    33      >>> txt = io.getvalue()
    34      >>> repr(txt)
    35      "'1, C1CCC1\\\\n2, C1CC1\\\\n3, C=O\\\\n4, CCN\\\\n'"
    36
    37    """
    38 -  def __init__(self,dest=None,delim='\t',idField=None,**kwargs):
    39      BaseOutputNode.__init__(self,dest=dest,strFunc=self.smilesOut)
    40      self._dest = dest
    41      self._idField = idField
    42      self._delim = delim
    43      self._nDumped = 0
    44
    45 -  def reset(self):
    46      BaseOutputNode.reset(self)
    47      self._nDumped=0
    48
    49 -  def smilesOut(self,mol):
    50      self._nDumped += 1
    51      if type(mol) in [types.TupleType,types.ListType]:
    52        args = mol
    53        mol = args[0]
    54        if len(args)>1:
    55          args = args[1:]
    56        else:
    57          args = []
    58      else:
    59        args = []
    60
    61      if self._idField and mol.HasProp(self._idField):
    62        label = mol.GetProp(self._idField)
    63      else:
    64        label = str(self._nDumped)
    65      smi = Chem.MolToSmiles(mol)
    66      outp = [label,smi]+args
    67      return '%s\n'%(self._delim.join(outp))
    68
    69
    70  #------------------------------------
    71  #
    72  #  doctest boilerplate
    73  #
    74 -def _test():
    75    import doctest,sys
    76    return doctest.testmod(sys.modules["__main__"])
    77
    78  if __name__ == '__main__':
    79    import sys
    80    failed,tried = _test()
    81    sys.exit(failed)
    82