mirror of
https://github.com/rdkit/rdkit.git
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368 lines
16 KiB
C++
368 lines
16 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2012 greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <boost/python.hpp>
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#include <DataStructs/BitVects.h>
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#include <DataStructs/BitOps.h>
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namespace python = boost::python;
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SBV *ff1(const SBV &bv1, int factor=2) {
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return FoldFingerprint(bv1,factor);
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}
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EBV *ff2(const EBV &ev1, int factor=2) {
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return FoldFingerprint(ev1,factor);
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}
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template <typename T>
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double SimilarityWrapper(const T &bv1,const std::string &pkl,
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double (*metric)(const T &,const T &),bool returnDistance){
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T bv2(pkl);
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return SimilarityWrapper(bv1,bv2,metric,returnDistance);
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}
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template <typename T>
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double SimilarityWrapper(const T &bv1,const std::string &pkl,double a,double b,
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double (*metric)(const T &,const T &,double,double),bool returnDistance){
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T bv2(pkl);
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return SimilarityWrapper(bv1,bv2,a,b,metric,returnDistance);
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}
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template <typename T>
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python::list BulkWrapper(const T &bv1,python::list bvs,
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double (*metric)(const T &,const T &),
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bool returnDistance){
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python::list res;
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unsigned int nbvs=python::extract<unsigned int>(bvs.attr("__len__")());
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for(unsigned int i=0;i<nbvs;++i){
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const T &bv2=python::extract<T>(bvs[i])();
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res.append(SimilarityWrapper(bv1,bv2,metric,returnDistance));
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}
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return res;
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}
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template <typename T>
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python::list BulkWrapper(const T &bv1,python::list bvs,double a,double b,
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double (*metric)(const T &,const T &,double,double),
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bool returnDistance){
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python::list res;
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unsigned int nbvs=python::extract<unsigned int>(bvs.attr("__len__")());
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for(unsigned int i=0;i<nbvs;++i){
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const T &bv2=python::extract<T>(bvs[i])();
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res.append(SimilarityWrapper(bv1,bv2,a,b,metric,returnDistance));
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}
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return res;
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}
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template <typename T1, typename T2>
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double TanimotoSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))TanimotoSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkTanimotoSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))TanimotoSimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double TverskySimilarity_w(const T1 &bv1,const T2 &bv2,double a,double b,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,a,b,
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(double (*)(const T1&,const T1&,double,double))TverskySimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkTverskySimilarity(const T &bv1,python::list bvs,double a,double b,
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bool returnDistance){
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return BulkWrapper(bv1,bvs,a,b,
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(double (*)(const T&,const T&,double,double))TverskySimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double CosineSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))CosineSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkCosineSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))CosineSimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double KulczynskiSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))KulczynskiSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkKulczynskiSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))KulczynskiSimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double DiceSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))DiceSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkDiceSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))DiceSimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double SokalSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))SokalSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkSokalSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))SokalSimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double McConnaugheySimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))McConnaugheySimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkMcConnaugheySimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))McConnaugheySimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double AsymmetricSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))AsymmetricSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkAsymmetricSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))AsymmetricSimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double BraunBlanquetSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))BraunBlanquetSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkBraunBlanquetSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))BraunBlanquetSimilarity,
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returnDistance);
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}
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template <typename T1, typename T2>
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double RusselSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
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return SimilarityWrapper(bv1,bv2,
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(double (*)(const T1&,const T1&))RusselSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkRusselSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))RusselSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkOnBitSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))OnBitSimilarity,
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returnDistance);
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}
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template <typename T>
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python::list BulkAllBitSimilarity(const T &bv1,python::list bvs,bool returnDistance){
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return BulkWrapper(bv1,bvs,
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(double (*)(const T&,const T&))AllBitSimilarity,
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returnDistance);
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}
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#define DBL_DEF(_funcname_,_bulkname_,_help_) { \
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python::def( # _funcname_,(double (*)(const SBV &,const SBV &))_funcname_,\
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(python::args("v1"),python::args("v2"))); \
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python::def( # _funcname_,(double (*)(const EBV &,const EBV &))_funcname_,\
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(python::args("v1"),python::args("v2")),_help_);\
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python::def( # _bulkname_,(python::list (*)(const EBV &,python::list,bool))_bulkname_,\
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(python::args("v1"),python::args("v2"),python::args("returnDistance")=0));\
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python::def( # _bulkname_,(python::list (*)(const EBV &,python::list,bool))_bulkname_,\
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(python::args("v1"),python::args("v2"),python::args("returnDistance")=0),_help_);}
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#define BIG_DEF(_funcname_,_name_w_,_bulkname_,_help_) { \
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python::def( # _funcname_,(double (*)(const SBV &,const SBV &,bool))_name_w_,\
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(python::args("bv1"),python::args("bv2"),python::args("returnDistance")=0)); \
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python::def( # _funcname_,(double (*)(const EBV &,const EBV &,bool))_name_w_,\
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(python::args("bv1"),python::args("bv2"),python::args("returnDistance")=0),_help_);\
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python::def( # _funcname_,(double (*)(const SBV &,const std::string &,bool))_name_w_,\
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(python::args("bv1"),python::args("pkl"),python::args("returnDistance")=0));\
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python::def( # _funcname_,(double (*)(const EBV &,const std::string &,bool))_name_w_,\
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(python::args("bv1"),python::args("pkl"),python::args("returnDistance")=0),_help_);\
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python::def( # _bulkname_,(python::list (*)(const SBV &,python::list,bool))_bulkname_,\
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(python::args("bv1"),python::args("bvList"),python::args("returnDistance")=0));\
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python::def( # _bulkname_,(python::list (*)(const EBV &,python::list,bool))_bulkname_,\
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(python::args("bv1"),python::args("bvList"),python::args("returnDistance")=0),_help_);}
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struct BitOps_wrapper {
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static void wrap(){
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BIG_DEF(TanimotoSimilarity,TanimotoSimilarity_w,BulkTanimotoSimilarity,
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"B(bv1&bv2) / (B(bv1) + B(bv2) - B(bv1&bv2))");
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BIG_DEF(CosineSimilarity,CosineSimilarity_w,BulkCosineSimilarity,
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"B(bv1&bv2) / sqrt(B(bv1) * B(bv2))");
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BIG_DEF(KulczynskiSimilarity,KulczynskiSimilarity_w,BulkKulczynskiSimilarity,
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"B(bv1&bv2)*(B(bv1) + B(bv2)) / (2 * B(bv1) * B(bv2))");
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BIG_DEF(DiceSimilarity,DiceSimilarity_w,BulkDiceSimilarity,
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"2*B(bv1&bv2) / (B(bv1) + B(bv2))");
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BIG_DEF(SokalSimilarity,SokalSimilarity_w,BulkSokalSimilarity,
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"B(bv1&bv2) / (2*B(bv1) + 2*B(bv2) - 3*B(bv1&bv2))");
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BIG_DEF(McConnaugheySimilarity,McConnaugheySimilarity_w,BulkMcConnaugheySimilarity,
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"(B(bv1&bv2) * (B(bv1)+B(bv2)) - B(bv1)*B(bv2)) / (B(bv1) * B(bv2))");
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BIG_DEF(AsymmetricSimilarity,AsymmetricSimilarity_w,BulkAsymmetricSimilarity,
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"B(bv1&bv2) / min(B(bv1),B(bv2))");
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BIG_DEF(BraunBlanquetSimilarity,BraunBlanquetSimilarity_w,BulkBraunBlanquetSimilarity,
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"B(bv1&bv2) / max(B(bv1),B(bv2))");
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BIG_DEF(RusselSimilarity,RusselSimilarity_w,BulkRusselSimilarity,
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"B(bv1&bv2) / B(bv1)");
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{
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std::string help="B(bv1&bv2) / (a*B(bv1)+b*B(bv2)+(1-a-b)*B(bv1&bv2)";
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python::def( "TverskySimilarity",
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(double (*)(const SBV &,const SBV &,double,double,bool))TverskySimilarity_w,
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(python::args("bv1"),python::args("bv2"),python::args("a"),
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python::args("b"),python::args("returnDistance")=0));
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python::def( "TverskySimilarity",
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(double (*)(const EBV &,const EBV &,double,double,bool))TverskySimilarity_w,
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(python::args("bv1"),python::args("bv2"),python::args("a"),
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python::args("b"),python::args("returnDistance")=0),help.c_str());
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python::def( "TverskySimilarity",
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(double (*)(const SBV &,const std::string &,double,double,bool))TverskySimilarity_w,
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(python::args("bv1"),python::args("pkl"),python::args("a"),
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python::args("b"),python::args("returnDistance")=0));
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python::def( "TverskySimilarity",
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(double (*)(const EBV &,const std::string &,double,double,bool))TverskySimilarity_w,
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(python::args("bv1"),python::args("pkl"),python::args("a"),
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python::args("b"),python::args("returnDistance")=0),help.c_str());
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python::def( "BulkTverskySimilarity",
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(python::list (*)(const SBV &,python::list,double,double,bool))BulkTverskySimilarity,
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(python::args("bv1"),python::args("bvList"),python::args("a"),
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python::args("b"),python::args("returnDistance")=0));
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python::def( "BulkTverskySimilarity",
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(python::list (*)(const EBV &,python::list,double,double,bool))BulkTverskySimilarity,
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(python::args("bv1"),python::args("bvList"),python::args("a"),
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python::args("b"),python::args("returnDistance")=0),help.c_str());
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}
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DBL_DEF(OnBitSimilarity,BulkOnBitSimilarity,
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"B(bv1&bv2) / B(bv1|bv2)");
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DBL_DEF(AllBitSimilarity,BulkAllBitSimilarity,
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"(B(bv1) - B(bv1^bv2)) / B(bv1)");
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python::def("OnBitProjSimilarity",
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(DoubleVect (*)(const SBV&,const SBV&))OnBitProjSimilarity);
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python::def("OnBitProjSimilarity",
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(DoubleVect (*)(const EBV&,const EBV&))OnBitProjSimilarity,
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"Returns a 2-tuple: (B(bv1&bv2) / B(bv1), B(bv1&bv2) / B(bv2))");
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python::def("OffBitProjSimilarity",
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(DoubleVect (*)(const SBV&,const SBV&))OffBitProjSimilarity);
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python::def("OffBitProjSimilarity",
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(DoubleVect (*)(const EBV&,const EBV&))OffBitProjSimilarity);
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python::def("NumBitsInCommon",
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(int (*)(const SBV&,const SBV&))NumBitsInCommon);
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python::def("NumBitsInCommon",
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(int (*)(const EBV&,const EBV&))NumBitsInCommon,
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"Returns the total number of bits in common between the two bit vectors"
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);
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python::def("OnBitsInCommon",
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(IntVect (*)(const SBV&,const SBV&))OnBitsInCommon);
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python::def("OnBitsInCommon",
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(IntVect (*)(const EBV&,const EBV&))OnBitsInCommon,
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"Returns the number of on bits in common between the two bit vectors"
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);
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python::def("OffBitsInCommon",
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(IntVect (*)(const SBV&,const SBV&))OffBitsInCommon);
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python::def("OffBitsInCommon",
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(IntVect (*)(const EBV&,const EBV&))OffBitsInCommon,
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"Returns the number of off bits in common between the two bit vectors"
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);
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python::def("FoldFingerprint",
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(SBV *(*)(const SBV &,unsigned int))FoldFingerprint,
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(python::arg("bv"),python::arg("foldFactor")=2),
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python::return_value_policy<python::manage_new_object>());
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python::def("FoldFingerprint",
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(EBV *(*)(const EBV &,unsigned int))FoldFingerprint,
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(python::arg("bv"),python::arg("foldFactor")=2),
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python::return_value_policy<python::manage_new_object>(),
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"Folds the fingerprint by the provided amount. The default, foldFactor=2, returns a fingerprint that is half the size of the original.");
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python::def("AllProbeBitsMatch",
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(bool (*)(const SBV &,const SBV &))AllProbeBitsMatch);
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python::def("AllProbeBitsMatch",
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(bool (*)(const EBV &,const EBV &))AllProbeBitsMatch);
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python::def("AllProbeBitsMatch",
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(bool (*)(const SBV &,const std::string &))AllProbeBitsMatch);
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python::def("AllProbeBitsMatch",(bool (*)(const EBV &,const std::string &))AllProbeBitsMatch,
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"Returns True if all bits in the first argument match all bits in the \n\
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vector defined by the pickle in the second argument.\n");
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python::def("BitVectToText",
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(std::string (*)(const SBV&))BitVectToText);
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python::def("BitVectToText",
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(std::string (*)(const EBV&))BitVectToText,
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"Returns a string of zeros and ones representing the bit vector."
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);
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python::def("BitVectToFPSText",
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(std::string (*)(const SBV&))BitVectToFPSText);
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python::def("BitVectToFPSText",
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(std::string (*)(const EBV&))BitVectToFPSText,
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"Returns an FPS string representing the bit vector."
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);
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python::def("BitVectToBinaryText",
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(std::string (*)(const SBV&))BitVectToBinaryText);
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python::def("BitVectToBinaryText",
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(std::string (*)(const EBV&))BitVectToBinaryText,
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"Returns a binary string (byte array) representing the bit vector."
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);
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}
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};
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void wrap_BitOps() {
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BitOps_wrapper::wrap();
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}
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