Source Code for Module rdkit.Chem.Fragments

 1  # $Id: Fragments.py 997 2009-02-25 06:12:43Z glandrum $ 
 2  # 
 3  # Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  """ functions to match a bunch of fragment descriptors from a file 
 8   
 9  No user-servicable parts inside.  ;-) 
10   
11  """ 
12  import os 
13  from rdkit import RDConfig 
14  from rdkit import Chem 
15   
16   
17  defaultPatternFileName = os.path.join(RDConfig.RDDataDir,'FragmentDescriptors.csv') 
18   
19 -def _CountMatches(mol,patt,unique=1): 
20    res = 0 
21    res = len(mol.GetSubstructMatches(patt)) 
22    return res 
23   
24  fns = [] 
25 -def _LoadPatterns(fileName=None): 
26    if fileName is None: 
27      fileName = defaultPatternFileName 
28    try: 
29      inF = open(fileName,'r') 
30    except IOError: 
31      pass 
32    else: 
33      for line in inF.readlines(): 
34        if len(line) and line[0] != '#': 
35          splitL = line.split('\t') 
36          if len(splitL)>=3: 
37            name = splitL[0] 
38            descr = splitL[1] 
39            sma = splitL[2] 
40            descr=descr.replace('"','') 
41            ok=1 
42            try: 
43              patt = Chem.MolFromSmarts(sma) 
44            except: 
45              ok=0 
46            else: 
47              if not patt or patt.GetNumAtoms()==0: ok=0 
48            if not ok: raise ImportError,'Smarts %s could not be parsed'%(repr(sma)) 
49            fn = lambda x,y=1,z=patt:_CountMatches(x,z,unique=y) 
50            fn.__doc__ = descr 
51            name = name.replace('=','_') 
52            name = name.replace('-','_') 
53            fns.append((name,fn)) 
54           
55  _LoadPatterns()             
56  for name,fn in fns: 
57    exec('%s=fn'%(name)) 
58  fn=None 
59