Package rdkit :: Package Chem :: Package EState :: Module Fingerprinter
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Source Code for Module rdkit.Chem.EState.Fingerprinter

 1  ## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c 
 2   
 3  # $Id$ 
 4  # 
 5  #  Copyright (C) 2002-2006  greg Landrum and Rational Discovery LLC 
 6  # 
 7  #   @@ All Rights Reserved @@ 
 8  #  This file is part of the RDKit. 
 9  #  The contents are covered by the terms of the BSD license 
10  #  which is included in the file license.txt, found at the root 
11  #  of the RDKit source tree. 
12  # 
13  """  EState fingerprinting 
14   
15  """ 
16  from __future__ import print_function 
17  import numpy 
18  from rdkit.Chem.EState import EStateIndices 
19  from rdkit.Chem.EState import AtomTypes 
20   
21 -def FingerprintMol(mol):
22 """ generates the EState fingerprints for the molecule 23 24 Concept from the paper: Hall and Kier JCICS _35_ 1039-1045 (1995) 25 26 two numeric arrays are returned: 27 The first (of ints) contains the number of times each possible atom type is hit 28 The second (of floats) contains the sum of the EState indices for atoms of 29 each type. 30 31 """ 32 if AtomTypes.esPatterns is None: 33 AtomTypes.BuildPatts() 34 esIndices = EStateIndices(mol) 35 36 nPatts = len(AtomTypes.esPatterns) 37 counts = numpy.zeros(nPatts,numpy.int) 38 sums = numpy.zeros(nPatts,numpy.float) 39 40 for i,(name,pattern) in enumerate(AtomTypes.esPatterns): 41 matches = mol.GetSubstructMatches(pattern,uniquify=1) 42 counts[i] = len(matches) 43 for match in matches: 44 sums[i] += esIndices[match[0]] 45 return counts,sums
46 47 48 if __name__ == '__main__': 49 from rdkit import Chem 50 smis = ['CC','CCC','c1[nH]cnc1CC(N)C(O)=O','NCCc1ccc(O)c(O)c1'] 51 for smi in smis: 52 m = Chem.MolFromSmiles(smi) 53 print(smi,Chem.MolToSmiles(m)) 54 types = AtomTypes.TypeAtoms(m) 55 for i in range(m.GetNumAtoms()): 56 print('%d %4s: %s'%(i+1,m.GetAtomWithIdx(i).GetSymbol(),str(types[i]))) 57 es = EStateIndices(m) 58 counts,sums = FingerprintMol(m) 59 for i in range(len(AtomTypes.esPatterns)): 60 if counts[i]: 61 name,patt = AtomTypes.esPatterns[i] 62 print('%6s, % 2d, % 5.4f'%(name,counts[i],sums[i])) 63 for i in range(len(es)): 64 print('% 2d, % 5.4f'%(i+1,es[i])) 65 print('--------') 66