Source Code for Module rdkit.VLib.NodeLib.demo

 1  #  $Id: demo.py 997 2009-02-25 06:12:43Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2003 Rational Discovery LLC 
 4  #     All Rights Reserved 
 5  # 
 6  from rdkit import RDConfig 
 7  from rdkit import Chem 
 8  import os.path 
 9   
10  from rdkit.VLib.NodeLib import * 
11  from rdkit.VLib import Supply,Filter 
12   
13  # this would be a real input, from an sd file: 
14  #fName = os.path.join(RDConfig.RDCodeDir,'VLib','NodeLib','test_data','NCI_aids.10.dupes.sdf') 
15  #supplier = SDSupply.SDSupplyNode(fName) 
16  # instead though, we want a simpler input: 
17  smis = ['CCOC','CCO.Cl','CC(=O)[O-].[Na+]','CC[Cu]CC','OCC','C[N+](C)(C)C.[Cl-]', 
18          '[Na+].[Cl-]'] 
19  mols = [Chem.MolFromSmiles(x) for x in smis] 
20  # name the molecules (only needed because we built them from smiles): 
21  for i in range(len(mols)): 
22    mols[i].SetProp('Name','Mol-%d'%(i+1)) 
23  supplier = Supply.SupplyNode(contents=mols) 
24  # should be 7 here 
25  print 'initial:',len([x for x in supplier]) 
26   
27  # filter out anything with a transition metal or lanthanide: 
28  metals = '[#21,#22,#23,#24,#25,#26,#27,#28,#29,#39,#40,#41,#42,#43,#44,#45,#46,#47,#57,#58,#59,#60,#61,#62,#63,#64,#65,#66,#67,#68,#69,#70,#71,#72,#73,#74,#75,#76,#77,#78,#79]' 
29  smaFilter= SmartsMolFilter.SmartsFilter(patterns=[metals],counts=[1]) 
30  smaFilter.SetNegate(1) 
31  smaFilter.AddParent(supplier) 
32  # should be 6 here 
33  print 'post-smaFilter:',len([x for x in smaFilter]) 
34   
35  salts = ['[Cl;H1&X1,-]','[Na+]','[O;H2,H1&-,X0&-2]'] 
36  remover = SmartsRemover.SmartsRemover(patterns=salts) 
37  remover.AddParent(smaFilter) 
38  atsFilter = Filter.FilterNode(func=lambda x:x.GetNumAtoms()>1) 
39  atsFilter.AddParent(remover) 
40  # should be 5 here 
41  print 'post-remover:',len([x for x in atsFilter]) 
42   
43  dupeFilter = SmilesDupeFilter.DupeFilter() 
44  dupeFilter.AddParent(atsFilter) 
45  # should be 4 here 
46  print 'post-dupes:',len([x for x in dupeFilter]) 
47   
48   
49  import StringIO 
50  # a StringIO object acts like a file: 
51  io = StringIO.StringIO() 
52  output = SmilesOutput.OutputNode(dest=io,delim=', ',idField='Name') 
53  output.AddParent(dupeFilter) 
54  print 'post-output:',len([x for x in output]) 
55  print 'OUTPUT:' 
56  print io.getvalue() 
57