Source Code for Module rdkit.Chem.EState.Fingerprinter

 1  ## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c 
 2   
 3  # $Id: Fingerprinter.py 997 2009-02-25 06:12:43Z glandrum $ 
 4  # 
 5  #  Copyright (C) 2002-2006  greg Landrum and Rational Discovery LLC 
 6  # 
 7  #   @@ All Rights Reserved  @@ 
 8  # 
 9  """  EState fingerprinting 
10   
11  """ 
12  import numpy 
13  from rdkit.Chem.EState import EStateIndices 
14  from rdkit.Chem.EState import AtomTypes 
15   
16 -def FingerprintMol(mol): 
17    """ generates the EState fingerprints for the molecule 
18   
19    Concept from the paper: Hall and Kier JCICS _35_ 1039-1045 (1995) 
20   
21    two numeric arrays are returned: 
22      The first (of ints) contains the number of times each possible atom type is hit 
23      The second (of floats) contains the sum of the EState indices for atoms of 
24        each type. 
25   
26    """ 
27    if AtomTypes.esPatterns is None: 
28      AtomTypes.BuildPatts() 
29    esIndices = EStateIndices(mol) 
30   
31    nPatts = len(AtomTypes.esPatterns) 
32    counts = numpy.zeros(nPatts,numpy.int) 
33    sums = numpy.zeros(nPatts,numpy.float) 
34   
35    for i,(name,pattern) in enumerate(AtomTypes.esPatterns): 
36      matches = mol.GetSubstructMatches(pattern,uniquify=1) 
37      counts[i] = len(matches) 
38      for match in matches: 
39        sums[i] += esIndices[match[0]] 
40    return counts,sums 
41   
42   
43  if __name__ == '__main__': 
44    from rdkit import Chem 
45    smis = ['CC','CCC','c1[nH]cnc1CC(N)C(O)=O','NCCc1ccc(O)c(O)c1'] 
46    for smi in smis: 
47      m = Chem.MolFromSmiles(smi) 
48      print smi,Chem.MolToSmiles(m) 
49      types = AtomTypes.TypeAtoms(m) 
50      for i in range(m.GetNumAtoms()): 
51        print '%d %4s: %s'%(i+1,m.GetAtomWithIdx(i).GetSymbol(),str(types[i])) 
52      es = EStateIndices(m) 
53      counts,sums = FingerprintMol(m) 
54      for i in range(len(AtomTypes.esPatterns)): 
55        if counts[i]: 
56          name,patt = AtomTypes.esPatterns[i] 
57          print '%6s, % 2d, % 5.4f'%(name,counts[i],sums[i]) 
58      for i in range(len(es)): 
59        print '% 2d, % 5.4f'%(i+1,es[i]) 
60      print '--------' 
61