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