Source Code for Package rdkit.DataStructs

 1  # $Id: __init__.py 997 2009-02-25 06:12:43Z glandrum $ 
 2  # 
 3  #  Copyright (C) 2004-2006  Rational Discovery LLC 
 4  # 
 5  #   @@ All Rights Reserved  @@ 
 6  # 
 7  from rdkit import rdBase 
 8  import cDataStructs 
 9  __doc__=cDataStructs.__doc__ 
10  from cDataStructs import * 
11   
12   
13  similarityFunctions=[ 
14    ('Tanimoto',TanimotoSimilarity,''), 
15    ("Dice",DiceSimilarity,''), 
16    ("Cosine",CosineSimilarity,''), 
17    ("Sokal",SokalSimilarity,''), 
18    ("Russel",RusselSimilarity,''), 
19    ("Kulczynski",KulczynskiSimilarity,''), 
20    ("McConnaughey",McConnaugheySimilarity,''), 
21    ("Asymmetric",AsymmetricSimilarity,''), 
22    ("BraunBlanquet",BraunBlanquetSimilarity,''), 
23    ] 
24   
25 -def FingerprintSimilarity(fp1,fp2,metric=TanimotoSimilarity): 
26    """ returns the calculated similarity between two fingerprints, 
27      handles any folding that may need to be done to ensure that they 
28      are compatible 
29   
30    """ 
31    sz1 = fp1.GetNumBits() 
32    sz2 = fp2.GetNumBits() 
33    if sz1<sz2: 
34      fp2 = FoldFingerprint(fp2,sz2/sz1) 
35    elif sz2<sz1: 
36      fp1 = FoldFingerprint(fp1,sz1/sz2) 
37    return metric(fp1,fp2) 
38   
39 -def FoldToTargetDensity(fp,density=0.3,minLength=64): 
40    while float(fp.GetNumOnBits())/len(fp)>density and len(fp)/2>minLength: 
41      fp = FoldFingerprint(fp,2) 
42    return fp 
43   
44  ExplicitBitVect.ToBitString = BitVectToText 
45  SparseBitVect.ToBitString = BitVectToText 
46