Package rdkit :: Package Chem :: Module Randomize
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Source Code for Module rdkit.Chem.Randomize

 1  # $Id$ 
 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.six.moves import range 
13  from rdkit import Chem 
14   
15   
16 -def RandomizeMolBlock(molB):
17 splitB = molB.split('\n') 18 res = [] 19 res.extend(splitB[0:3]) 20 idx = 3 21 inL = splitB[idx] 22 res.append(inL) 23 nAts = int(inL[0:3]) 24 nBonds = int(inL[3:6]) 25 26 idx += 1 27 atLines = splitB[idx:idx + nAts] 28 29 order = list(range(nAts)) 30 random.shuffle(order, random=random.random) 31 32 for i in order: 33 res.append(atLines[i]) 34 35 #print 'ORDER:',order 36 idx += nAts 37 for i in range(nBonds): 38 inL = splitB[idx] 39 idx1 = int(inL[0:3]) - 1 40 idx2 = int(inL[3:6]) - 1 41 idx1 = order.index(idx1) 42 idx2 = order.index(idx2) 43 inL = '% 3d% 3d' % (idx1 + 1, idx2 + 1) + inL[6:] 44 res.append(inL) 45 idx += 1 46 res.append('M END') 47 return '\n'.join(res)
48 49
50 -def RandomizeMol(mol):
51 mb = Chem.MolToMolBlock(mol) 52 #print '-----------------' 53 #print mb 54 mb = RandomizeMolBlock(mb) 55 #print mb 56 return Chem.MolFromMolBlock(mb)
57 58
59 -def CheckCanonicalization(mol, nReps=10):
60 refSmi = Chem.MolToSmiles(mol, False) 61 for i in range(nReps): 62 m2 = RandomizeMol(mol) 63 smi = Chem.MolToSmiles(m2, False) 64 if smi != refSmi: 65 raise ValueError('\nRef: %s\n : %s' % (refSmi, smi))
66 67 68 if __name__ == '__main__': 69 from rdkit.Chem import Randomize 70 CheckCanonicalization(Chem.MolFromSmiles('CON')) 71 CheckCanonicalization(Chem.MolFromSmiles('c1ccccn1')) 72 CheckCanonicalization(Chem.MolFromSmiles('C/C=C/F')) 73