Source Code for Module rdkit.Chem.Fragments

 1  # $Id: Fragments.py 1528 2010-09-26 17:04:37Z glandrum $ 
 2  # 
 3  # Copyright (C) 2002-2010 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved @@ 
 6  #  This file is part of the RDKit. 
 7  #  The contents are covered by the terms of the BSD license 
 8  #  which is included in the file license.txt, found at the root 
 9  #  of the RDKit source tree. 
10  # 
11  """ functions to match a bunch of fragment descriptors from a file 
12   
13  No user-servicable parts inside.  ;-) 
14   
15  """ 
16  import os 
17  from rdkit import RDConfig 
18  from rdkit import Chem 
19   
20   
21  defaultPatternFileName = os.path.join(RDConfig.RDDataDir,'FragmentDescriptors.csv') 
22   
23 -def _CountMatches(mol,patt,unique=True): 
24    return len(mol.GetSubstructMatches(patt,uniquify=unique)) 
25   
26  fns = [] 
27 -def _LoadPatterns(fileName=None): 
28    if fileName is None: 
29      fileName = defaultPatternFileName 
30    try: 
31      inF = open(fileName,'r') 
32    except IOError: 
33      pass 
34    else: 
35      for line in inF.readlines(): 
36        if len(line) and line[0] != '#': 
37          splitL = line.split('\t') 
38          if len(splitL)>=3: 
39            name = splitL[0] 
40            descr = splitL[1] 
41            sma = splitL[2] 
42            descr=descr.replace('"','') 
43            ok=1 
44            try: 
45              patt = Chem.MolFromSmarts(sma) 
46            except: 
47              ok=0 
48            else: 
49              if not patt or patt.GetNumAtoms()==0: ok=0 
50            if not ok: raise ImportError,'Smarts %s could not be parsed'%(repr(sma)) 
51            fn = lambda mol,countUnique=True,pattern=patt:_CountMatches(mol,pattern,unique=countUnique) 
52            fn.__doc__ = descr 
53            name = name.replace('=','_') 
54            name = name.replace('-','_') 
55            fns.append((name,fn)) 
56           
57  _LoadPatterns()             
58  for name,fn in fns: 
59    exec('%s=fn'%(name)) 
60  fn=None 
61