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84 lines
1.8 KiB
Python
Executable File
84 lines
1.8 KiB
Python
Executable File
# $Id$
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#
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# Copyright (C) 2003 Rational Discovery LLC
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# All Rights Reserved
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#
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import sys,types
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import Chem
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from VLib.Output import OutputNode as BaseOutputNode
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class OutputNode(BaseOutputNode):
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""" dumps smiles output
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Assumptions:
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- destination supports a write() method
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- inputs (parents) can be stepped through in lockstep
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Usage Example:
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>>> smis = ['C1CCC1','C1CC1','C=O','NCC']
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>>> mols = [Chem.MolFromSmiles(x) for x in smis]
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>>> from VLib.Supply import SupplyNode
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>>> suppl = SupplyNode(contents=mols)
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>>> import StringIO
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>>> io = StringIO.StringIO()
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>>> node = OutputNode(dest=io,delim=', ')
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>>> node.AddParent(suppl)
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>>> ms = [x for x in node]
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>>> len(ms)
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4
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>>> txt = io.getvalue()
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>>> repr(txt)
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"'1, C1CCC1\\\\n2, C1CC1\\\\n3, C=O\\\\n4, CCN\\\\n'"
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"""
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def __init__(self,dest=None,delim='\t',idField=None,**kwargs):
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BaseOutputNode.__init__(self,dest=dest,strFunc=self.smilesOut)
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self._dest = dest
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self._idField = idField
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self._delim = delim
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self._nDumped = 0
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def reset(self):
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BaseOutputNode.reset(self)
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self._nDumped=0
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def smilesOut(self,mol):
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self._nDumped += 1
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if type(mol) in [types.TupleType,types.ListType]:
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args = mol
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mol = args[0]
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if len(args)>1:
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args = args[1:]
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else:
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args = []
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else:
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args = []
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if self._idField and mol.HasProp(self._idField):
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label = mol.GetProp(self._idField)
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else:
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label = str(self._nDumped)
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smi = Chem.MolToSmiles(mol)
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outp = [label,smi]+args
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return '%s\n'%(self._delim.join(outp))
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#------------------------------------
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#
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# doctest boilerplate
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#
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def _test():
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import doctest,sys
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return doctest.testmod(sys.modules["__main__"])
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if __name__ == '__main__':
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import sys
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failed,tried = _test()
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sys.exit(failed)
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