Source Code for Module rdkit.Chem.PropertyMol

  1  # $Id: PropertyMol.py 1628 2011-01-13 04:31:57Z glandrum $ 
  2  # 
  3  # Copyright (C) 2007-2010 Greg Landrum 
  4  # All Rights Reserved 
  5  # 
  6  from rdkit import Chem 
  7   
  8 -class PropertyMol(Chem.Mol): 
  9    """ allows rdkit molecules to be pickled with their properties saved. 
 10   
 11     >>> import cPickle 
 12     >>> m = Chem.MolFromMolFile('test_data/benzene.mol') 
 13     >>> m.GetProp('_Name') 
 14     'benzene.mol' 
 15   
 16     by default pickling removes properties: 
 17     >>> m2 = cPickle.loads(cPickle.dumps(m)) 
 18     >>> m2.HasProp('_Name') 
 19     0 
 20   
 21     Property mols solve this: 
 22     >>> pm = PropertyMol(m) 
 23     >>> pm.GetProp('_Name') 
 24     'benzene.mol' 
 25     >>> pm.SetProp('MyProp','foo') 
 26     >>> pm.HasProp('MyProp') 
 27     1 
 28   
 29     >>> pm2 = cPickle.loads(cPickle.dumps(pm)) 
 30     >>> Chem.MolToSmiles(pm2) 
 31     'c1ccccc1' 
 32     >>> pm2.GetProp('_Name') 
 33     'benzene.mol' 
 34     >>> pm2.HasProp('MyProp') 
 35     1 
 36     >>> pm2.GetProp('MyProp') 
 37     'foo' 
 38     >>> pm2.HasProp('MissingProp') 
 39     0 
 40   
 41     Property mols are a bit more permissive about the types 
 42     of property values: 
 43     >>> pm.SetProp('IntVal',1) 
 44   
 45     That wouldn't work with a standard mol: 
 46     >>> m.SetProp('IntVal',1) 
 47     Traceback (most recent call last): 
 48       ... 
 49     ArgumentError: Python argument types in 
 50         Mol.SetProp(Mol, str, int) 
 51     did not match C++ signature: 
 52       ... 
 53   
 54     but the Property mols still convert all values to strings before storing: 
 55     >>> pm.GetProp('IntVal') 
 56     '1' 
 57      
 58     This is a test for sf.net issue 2880943: make sure properties end up in SD files: 
 59     >>> import tempfile,os 
 60     >>> fn = tempfile.mktemp('.sdf') 
 61     >>> w = Chem.SDWriter(fn) 
 62     >>> w.write(pm) 
 63     >>> w=None 
 64     >>> txt = file(fn,'r').read() 
 65     >>> '<IntVal>' in txt 
 66     True 
 67     >>> try: 
 68     ...   os.unlink(fn) 
 69     ... except: 
 70     ...   pass 
 71   
 72     The next level of that bug: does writing a *depickled* propertymol 
 73     to an SD file include properties: 
 74     >>> fn = tempfile.mktemp('.sdf') 
 75     >>> w = Chem.SDWriter(fn) 
 76     >>> pm = cPickle.loads(cPickle.dumps(pm)) 
 77     >>> w.write(pm) 
 78     >>> w=None 
 79     >>> txt = file(fn,'r').read() 
 80     >>> '<IntVal>' in txt 
 81     True 
 82     >>> try: 
 83     ...   os.unlink(fn) 
 84     ... except: 
 85     ...   pass 
 86   
 87   
 88      
 89    """ 
 90    __getstate_manages_dict__=True 
 91 -  def __init__(self,mol): 
 92      if not isinstance(mol,Chem.Mol): return 
 93      Chem.Mol.__init__(self,mol.ToBinary()) 
 94      for pn in mol.GetPropNames(includePrivate=True): 
 95        self.SetProp(pn,mol.GetProp(pn)) 
 96 -  def SetProp(self,nm,val): 
 97      Chem.Mol.SetProp(self,nm,str(val)) 
 98 -  def __getstate__(self): 
 99      pDict={} 
100      for pn in self.GetPropNames(includePrivate=True): 
101        pDict[pn] = self.GetProp(pn) 
102      return {'pkl':self.ToBinary(), 
103              'propD':pDict} 
104 -  def __setstate__(self,stateD): 
105      Chem.Mol.__init__(self,stateD['pkl']) 
106      for prop,val in stateD['propD'].iteritems(): 
107        self.SetProp(prop,val) 
108   
109       
110  #------------------------------------ 
111  # 
112  #  doctest boilerplate 
113  # 
114 -def _test(): 
115    import doctest,sys 
116    return doctest.testmod(sys.modules["__main__"],optionflags=doctest.ELLIPSIS) 
117   
118  if __name__ == '__main__': 
119    import sys 
120    failed,tried = _test() 
121    sys.exit(failed) 
122