Source Code for Module VLib.NodeLib.demo

 1  #  $Id: demo.py 2 2006-05-06 22:54:39Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2003 Rational Discovery LLC 
 4  #     All Rights Reserved 
 5  # 
 6  import RDConfig 
 7  import Chem,os.path 
 8   
 9  from VLib.NodeLib import * 
10  from VLib import Supply,Filter 
11   
12  # this would be a real input, from an sd file: 
13  #fName = os.path.join(RDConfig.RDCodeDir,'VLib','NodeLib','test_data','NCI_aids.10.dupes.sdf') 
14  #supplier = SDSupply.SDSupplyNode(fName) 
15  # instead though, we want a simpler input: 
16  smis = ['CCOC','CCO.Cl','CC(=O)[O-].[Na+]','CC[Cu]CC','OCC','C[N+](C)(C)C.[Cl-]', 
17          '[Na+].[Cl-]'] 
18  mols = [Chem.MolFromSmiles(x) for x in smis] 
19  # name the molecules (only needed because we built them from smiles): 
20  for i in range(len(mols)): 
21    mols[i].SetProp('Name','Mol-%d'%(i+1)) 
22  supplier = Supply.SupplyNode(contents=mols) 
23  # should be 7 here 
24  print 'initial:',len([x for x in supplier]) 
25   
26  # filter out anything with a transition metal or lanthanide: 
27  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]' 
28  smaFilter= SmartsMolFilter.SmartsFilter(patterns=[metals],counts=[1]) 
29  smaFilter.SetNegate(1) 
30  smaFilter.AddParent(supplier) 
31  # should be 6 here 
32  print 'post-smaFilter:',len([x for x in smaFilter]) 
33   
34  salts = ['[Cl;H1&X1,-]','[Na+]','[O;H2,H1&-,X0&-2]'] 
35  remover = SmartsRemover.SmartsRemover(patterns=salts) 
36  remover.AddParent(smaFilter) 
37  atsFilter = Filter.FilterNode(func=lambda x:x.GetNumAtoms()>1) 
38  atsFilter.AddParent(remover) 
39  # should be 5 here 
40  print 'post-remover:',len([x for x in atsFilter]) 
41   
42  dupeFilter = SmilesDupeFilter.DupeFilter() 
43  dupeFilter.AddParent(atsFilter) 
44  # should be 4 here 
45  print 'post-dupes:',len([x for x in dupeFilter]) 
46   
47   
48  import StringIO 
49  # a StringIO object acts like a file: 
50  io = StringIO.StringIO() 
51  output = SmilesOutput.OutputNode(dest=io,delim=', ',idField='Name') 
52  output.AddParent(dupeFilter) 
53  print 'post-output:',len([x for x in output]) 
54  print 'OUTPUT:' 
55  print io.getvalue() 
56