Source Code for Module Chem.FragmentMatcher

 1  # $Id: FragmentMatcher.py 2 2006-05-06 22:54:39Z glandrum $ 
 2  # 
 3  # Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  """ exposes a class for matching fragments of molecules. 
 8   
 9  The class exposes a simple API: 
10   
11  If you want a matcher that hits C=O, you'd do: 
12  >>> p = FragmentMatcher() 
13  >>> p.Init('C=O') 
14   
15  you can then match with: 
16  >>> mol = Chem.MolFromSmiles('CC(=O)O') 
17  >>> p.HasMatch(mol) 
18  1 
19  >>> p.HasMatch(Chem.MolFromSmiles('CC(C)C')) 
20  0 
21   
22  information about the matches: 
23  >>> len(p.GetMatches(Chem.MolFromSmiles('CC=O'))) 
24  1 
25  >>> len(p.GetMatches(Chem.MolFromSmiles('O=CC=O'))) 
26  2 
27   
28  or, you can add exclusion fragments (defined as smarts) with: 
29  >>> p.AddExclusion('c1ccccc1') 
30   
31  now the matcher will not hit anything that has a benzene ring. 
32  >>> p.HasMatch(Chem.MolFromSmiles('CC=O')) 
33  1 
34  >>> p.HasMatch(Chem.MolFromSmiles('c1ccccc1CC=O')) 
35  0 
36   
37   
38  """ 
39  import Chem 
40   
41   
42 -class FragmentMatcher(object): 
43 -  def __init__(self): 
44      self._onPatt = None 
45      self._offPatts = [] 
46   
47 -  def AddExclusion(self,sma): 
48      self._offPatts.append(Chem.MolFromSmarts(sma)) 
49 -  def Init(self,sma): 
50      self._onPatt = Chem.MolFromSmarts(sma) 
51   
52 -  def GetSMARTS(self): 
53      pass 
54 -  def GetExclusionSMARTS(self): 
55      pass 
56   
57   
58 -  def HasMatch(self,mol): 
59      if self._onPatt is None: 
60        return 0 
61      t = mol.HasSubstructMatch(self._onPatt) 
62      if not t: 
63        return 0 
64      else: 
65        for patt in self._offPatts: 
66          if mol.HasSubstructMatch(patt): 
67            return 0 
68      return 1 
69     
70 -  def GetMatch(self,mol): 
71      if self._onPatt is None: 
72        return None 
73      return mol.GetSubstructMatch(self._onPatt) 
74     
75 -  def GetMatches(self,mol,uniquify=1): 
76      if self._onPatt is None: 
77        return None 
78      return mol.GetSubstructMatches(self._onPatt,uniquify) 
79     
80 -  def GetBond(self,idx): 
81      if self._onPatt is None: 
82        return None 
83      return self._onPatt.GetBondWithIdx(idx) 
84       
85       
86  #------------------------------------ 
87  # 
88  #  doctest boilerplate 
89  # 
90 -def _test(): 
91    import doctest,sys 
92    return doctest.testmod(sys.modules["__main__"]) 
93   
94  if __name__ == '__main__': 
95    import sys 
96    failed,tried = _test() 
97    sys.exit(failed) 
98