Source Code for Module rdkit.Chem.Randomize

 1  # $Id: Randomize.py 997 2009-02-25 06:12:43Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2005-2006 Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  import random 
 8  from rdkit import Chem 
 9   
10 -def RandomizeMolBlock(molB): 
11    splitB = molB.split('\n') 
12    res = [] 
13    res.extend(splitB[0:3]) 
14    idx = 3 
15    inL = splitB[idx] 
16    res.append(inL) 
17    nAts = int(inL[0:3]) 
18    nBonds = int(inL[3:6]) 
19   
20    idx+=1 
21    atLines = splitB[idx:idx+nAts] 
22   
23    order = range(nAts) 
24    random.shuffle(order) 
25   
26    for i in order: 
27      res.append(atLines[i]) 
28   
29    #print 'ORDER:',order 
30    idx += nAts 
31    for i in range(nBonds): 
32      inL = splitB[idx] 
33      idx1 = int(inL[0:3])-1 
34      idx2 = int(inL[3:6])-1 
35      idx1 = order.index(idx1) 
36      idx2 = order.index(idx2) 
37      inL = '% 3d% 3d'%(idx1+1,idx2+1)+inL[6:] 
38      res.append(inL) 
39      idx += 1 
40    res.append('M  END') 
41    return '\n'.join(res) 
42   
43 -def RandomizeMol(mol): 
44    mb = Chem.MolToMolBlock(mol) 
45    #print '-----------------' 
46    #print mb 
47    mb = RandomizeMolBlock(mb) 
48    #print mb 
49    return Chem.MolFromMolBlock(mb) 
50   
51 -def CheckCanonicalization(mol,nReps=10): 
52    refSmi = Chem.MolToSmiles(mol,False) 
53    for i in range(nReps): 
54      m2 = RandomizeMol(mol) 
55      smi = Chem.MolToSmiles(m2,False) 
56      if smi!=refSmi: 
57        raise ValueError,'\nRef: %s\n   : %s'%(refSmi,smi) 
58   
59   
60                
61  if __name__=='__main__': 
62    from rdkit.Chem import Randomize 
63    CheckCanonicalization(Chem.MolFromSmiles('CON')) 
64    CheckCanonicalization(Chem.MolFromSmiles('c1ccccn1')) 
65    CheckCanonicalization(Chem.MolFromSmiles('C/C=C/F')) 
66