Source Code for Module rdkit.Chem.Randomize

 1  # $Id: Randomize.py 1528 2010-09-26 17:04:37Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2005-2006 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  import random 
12  from rdkit import Chem 
13   
14 -def RandomizeMolBlock(molB): 
15    splitB = molB.split('\n') 
16    res = [] 
17    res.extend(splitB[0:3]) 
18    idx = 3 
19    inL = splitB[idx] 
20    res.append(inL) 
21    nAts = int(inL[0:3]) 
22    nBonds = int(inL[3:6]) 
23   
24    idx+=1 
25    atLines = splitB[idx:idx+nAts] 
26   
27    order = range(nAts) 
28    random.shuffle(order) 
29   
30    for i in order: 
31      res.append(atLines[i]) 
32   
33    #print 'ORDER:',order 
34    idx += nAts 
35    for i in range(nBonds): 
36      inL = splitB[idx] 
37      idx1 = int(inL[0:3])-1 
38      idx2 = int(inL[3:6])-1 
39      idx1 = order.index(idx1) 
40      idx2 = order.index(idx2) 
41      inL = '% 3d% 3d'%(idx1+1,idx2+1)+inL[6:] 
42      res.append(inL) 
43      idx += 1 
44    res.append('M  END') 
45    return '\n'.join(res) 
46   
47 -def RandomizeMol(mol): 
48    mb = Chem.MolToMolBlock(mol) 
49    #print '-----------------' 
50    #print mb 
51    mb = RandomizeMolBlock(mb) 
52    #print mb 
53    return Chem.MolFromMolBlock(mb) 
54   
55 -def CheckCanonicalization(mol,nReps=10): 
56    refSmi = Chem.MolToSmiles(mol,False) 
57    for i in range(nReps): 
58      m2 = RandomizeMol(mol) 
59      smi = Chem.MolToSmiles(m2,False) 
60      if smi!=refSmi: 
61        raise ValueError,'\nRef: %s\n   : %s'%(refSmi,smi) 
62   
63   
64                
65  if __name__=='__main__': 
66    from rdkit.Chem import Randomize 
67    CheckCanonicalization(Chem.MolFromSmiles('CON')) 
68    CheckCanonicalization(Chem.MolFromSmiles('c1ccccn1')) 
69    CheckCanonicalization(Chem.MolFromSmiles('C/C=C/F')) 
70