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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
22 """ generates the EState fingerprints for the molecule
23
24 Concept from the paper: Hall and Kier JCICS _35_ 1039-1045 (1995)
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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