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// $Id: wrap_BitOps.cpp 1926 2012-01-08 06:12:47Z glandrum $
//
// Copyright (C) 2003-2012 greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <boost/python.hpp>
#include <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
namespace python = boost::python;
SBV *ff1(const SBV &bv1, int factor=2) {
return FoldFingerprint(bv1,factor);
}
EBV *ff2(const EBV &ev1, int factor=2) {
return FoldFingerprint(ev1,factor);
}
template <typename T>
double SimilarityWrapper(const T &bv1,const std::string &pkl,
double (*metric)(const T &,const T &),bool returnDistance){
T bv2(pkl);
return SimilarityWrapper(bv1,bv2,metric,returnDistance);
}
template <typename T>
double SimilarityWrapper(const T &bv1,const std::string &pkl,double a,double b,
double (*metric)(const T &,const T &,double,double),bool returnDistance){
T bv2(pkl);
return SimilarityWrapper(bv1,bv2,a,b,metric,returnDistance);
}
template <typename T>
python::list BulkWrapper(const T &bv1,python::list bvs,
double (*metric)(const T &,const T &),
bool returnDistance){
python::list res;
unsigned int nbvs=python::extract<unsigned int>(bvs.attr("__len__")());
for(unsigned int i=0;i<nbvs;++i){
const T &bv2=python::extract<T>(bvs[i])();
res.append(SimilarityWrapper(bv1,bv2,metric,returnDistance));
}
return res;
}
template <typename T>
python::list BulkWrapper(const T &bv1,python::list bvs,double a,double b,
double (*metric)(const T &,const T &,double,double),
bool returnDistance){
python::list res;
unsigned int nbvs=python::extract<unsigned int>(bvs.attr("__len__")());
for(unsigned int i=0;i<nbvs;++i){
const T &bv2=python::extract<T>(bvs[i])();
res.append(SimilarityWrapper(bv1,bv2,a,b,metric,returnDistance));
}
return res;
}
template <typename T1, typename T2>
double TanimotoSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))TanimotoSimilarity,
returnDistance);
}
template <typename T>
python::list BulkTanimotoSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))TanimotoSimilarity,
returnDistance);
}
template <typename T1, typename T2>
double TverskySimilarity_w(const T1 &bv1,const T2 &bv2,double a,double b,bool returnDistance){
return SimilarityWrapper(bv1,bv2,a,b,
(double (*)(const T1&,const T1&,double,double))TverskySimilarity,
returnDistance);
}
template <typename T>
python::list BulkTverskySimilarity(const T &bv1,python::list bvs,double a,double b,
bool returnDistance){
return BulkWrapper(bv1,bvs,a,b,
(double (*)(const T&,const T&,double,double))TverskySimilarity,
returnDistance);
}
template <typename T1, typename T2>
double CosineSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))CosineSimilarity,
returnDistance);
}
template <typename T>
python::list BulkCosineSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))CosineSimilarity,
returnDistance);
}
template <typename T1, typename T2>
double KulczynskiSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))KulczynskiSimilarity,
returnDistance);
}
template <typename T>
python::list BulkKulczynskiSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))KulczynskiSimilarity,
returnDistance);
}
template <typename T1, typename T2>
double DiceSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))DiceSimilarity,
returnDistance);
}
template <typename T>
python::list BulkDiceSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))DiceSimilarity,
returnDistance);
}
template <typename T1, typename T2>
double SokalSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))SokalSimilarity,
returnDistance);
}
template <typename T>
python::list BulkSokalSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))SokalSimilarity,
returnDistance);
}
template <typename T1, typename T2>
double McConnaugheySimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))McConnaugheySimilarity,
returnDistance);
}
template <typename T>
python::list BulkMcConnaugheySimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))McConnaugheySimilarity,
returnDistance);
}
template <typename T1, typename T2>
double AsymmetricSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))AsymmetricSimilarity,
returnDistance);
}
template <typename T>
python::list BulkAsymmetricSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))AsymmetricSimilarity,
returnDistance);
}
template <typename T1, typename T2>
double BraunBlanquetSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))BraunBlanquetSimilarity,
returnDistance);
}
template <typename T>
python::list BulkBraunBlanquetSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))BraunBlanquetSimilarity,
returnDistance);
}
template <typename T1, typename T2>
double RusselSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
return SimilarityWrapper(bv1,bv2,
(double (*)(const T1&,const T1&))RusselSimilarity,
returnDistance);
}
template <typename T>
python::list BulkRusselSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))RusselSimilarity,
returnDistance);
}
template <typename T>
python::list BulkOnBitSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))OnBitSimilarity,
returnDistance);
}
template <typename T>
python::list BulkAllBitSimilarity(const T &bv1,python::list bvs,bool returnDistance){
return BulkWrapper(bv1,bvs,
(double (*)(const T&,const T&))AllBitSimilarity,
returnDistance);
}
#define DBL_DEF(_funcname_,_bulkname_,_help_) { \
python::def( # _funcname_,(double (*)(const SBV &,const SBV &))_funcname_,\
(python::args("v1"),python::args("v2"))); \
python::def( # _funcname_,(double (*)(const EBV &,const EBV &))_funcname_,\
(python::args("v1"),python::args("v2")),_help_);\
python::def( # _bulkname_,(python::list (*)(const EBV &,python::list,bool))_bulkname_,\
(python::args("v1"),python::args("v2"),python::args("returnDistance")=0));\
python::def( # _bulkname_,(python::list (*)(const EBV &,python::list,bool))_bulkname_,\
(python::args("v1"),python::args("v2"),python::args("returnDistance")=0),_help_);}
#define BIG_DEF(_funcname_,_name_w_,_bulkname_,_help_) { \
python::def( # _funcname_,(double (*)(const SBV &,const SBV &,bool))_name_w_,\
(python::args("bv1"),python::args("bv2"),python::args("returnDistance")=0)); \
python::def( # _funcname_,(double (*)(const EBV &,const EBV &,bool))_name_w_,\
(python::args("bv1"),python::args("bv2"),python::args("returnDistance")=0),_help_);\
python::def( # _funcname_,(double (*)(const SBV &,const std::string &,bool))_name_w_,\
(python::args("bv1"),python::args("pkl"),python::args("returnDistance")=0));\
python::def( # _funcname_,(double (*)(const EBV &,const std::string &,bool))_name_w_,\
(python::args("bv1"),python::args("pkl"),python::args("returnDistance")=0),_help_);\
python::def( # _bulkname_,(python::list (*)(const SBV &,python::list,bool))_bulkname_,\
(python::args("bv1"),python::args("bvList"),python::args("returnDistance")=0));\
python::def( # _bulkname_,(python::list (*)(const EBV &,python::list,bool))_bulkname_,\
(python::args("bv1"),python::args("bvList"),python::args("returnDistance")=0),_help_);}
struct BitOps_wrapper {
static void wrap(){
BIG_DEF(TanimotoSimilarity,TanimotoSimilarity_w,BulkTanimotoSimilarity,
"B(bv1&bv2) / (B(bv1) + B(bv2) - B(bv1&bv2))");
BIG_DEF(CosineSimilarity,CosineSimilarity_w,BulkCosineSimilarity,
"B(bv1&bv2) / sqrt(B(bv1) * B(bv2))");
BIG_DEF(KulczynskiSimilarity,KulczynskiSimilarity_w,BulkKulczynskiSimilarity,
"B(bv1&bv2)*(B(bv1) + B(bv2)) / (2 * B(bv1) * B(bv2))");
BIG_DEF(DiceSimilarity,DiceSimilarity_w,BulkDiceSimilarity,
"2*B(bv1&bv2) / (B(bv1) + B(bv2))");
BIG_DEF(SokalSimilarity,SokalSimilarity_w,BulkSokalSimilarity,
"B(bv1&bv2) / (2*B(bv1) + 2*B(bv2) - 3*B(bv1&bv2))");
BIG_DEF(McConnaugheySimilarity,McConnaugheySimilarity_w,BulkMcConnaugheySimilarity,
"(B(bv1&bv2) * (B(bv1)+B(bv2)) - B(bv1)*B(bv2)) / (B(bv1) * B(bv2))");
BIG_DEF(AsymmetricSimilarity,AsymmetricSimilarity_w,BulkAsymmetricSimilarity,
"B(bv1&bv2) / min(B(bv1),B(bv2))");
BIG_DEF(BraunBlanquetSimilarity,BraunBlanquetSimilarity_w,BulkBraunBlanquetSimilarity,
"B(bv1&bv2) / max(B(bv1),B(bv2))");
BIG_DEF(RusselSimilarity,RusselSimilarity_w,BulkRusselSimilarity,
"B(bv1&bv2) / B(bv1)");
{
std::string help="B(bv1&bv2) / (a*B(bv1)+b*B(bv2)+(1-a-b)*B(bv1&bv2)";
python::def( "TverskySimilarity",
(double (*)(const SBV &,const SBV &,double,double,bool))TverskySimilarity_w,
(python::args("bv1"),python::args("bv2"),python::args("a"),
python::args("b"),python::args("returnDistance")=0));
python::def( "TverskySimilarity",
(double (*)(const EBV &,const EBV &,double,double,bool))TverskySimilarity_w,
(python::args("bv1"),python::args("bv2"),python::args("a"),
python::args("b"),python::args("returnDistance")=0),help.c_str());
python::def( "TverskySimilarity",
(double (*)(const SBV &,const std::string &,double,double,bool))TverskySimilarity_w,
(python::args("bv1"),python::args("pkl"),python::args("a"),
python::args("b"),python::args("returnDistance")=0));
python::def( "TverskySimilarity",
(double (*)(const EBV &,const std::string &,double,double,bool))TverskySimilarity_w,
(python::args("bv1"),python::args("pkl"),python::args("a"),
python::args("b"),python::args("returnDistance")=0),help.c_str());
python::def( "BulkTverskySimilarity",
(python::list (*)(const SBV &,python::list,double,double,bool))BulkTverskySimilarity,
(python::args("bv1"),python::args("bvList"),python::args("a"),
python::args("b"),python::args("returnDistance")=0));
python::def( "BulkTverskySimilarity",
(python::list (*)(const EBV &,python::list,double,double,bool))BulkTverskySimilarity,
(python::args("bv1"),python::args("bvList"),python::args("a"),
python::args("b"),python::args("returnDistance")=0),help.c_str());
}
DBL_DEF(OnBitSimilarity,BulkOnBitSimilarity,
"B(bv1&bv2) / B(bv1|bv2)");
DBL_DEF(AllBitSimilarity,BulkAllBitSimilarity,
"(B(bv1) - B(bv1^bv2)) / B(bv1)");
python::def("OnBitProjSimilarity",
(DoubleVect (*)(const SBV&,const SBV&))OnBitProjSimilarity);
python::def("OnBitProjSimilarity",
(DoubleVect (*)(const EBV&,const EBV&))OnBitProjSimilarity,
"Returns a 2-tuple: (B(bv1&bv2) / B(bv1), B(bv1&bv2) / B(bv2))");
python::def("OffBitProjSimilarity",
(DoubleVect (*)(const SBV&,const SBV&))OffBitProjSimilarity);
python::def("OffBitProjSimilarity",
(DoubleVect (*)(const EBV&,const EBV&))OffBitProjSimilarity);
python::def("NumBitsInCommon",
(int (*)(const SBV&,const SBV&))NumBitsInCommon);
python::def("NumBitsInCommon",
(int (*)(const EBV&,const EBV&))NumBitsInCommon,
"Returns the total number of bits in common between the two bit vectors"
);
python::def("OnBitsInCommon",
(IntVect (*)(const SBV&,const SBV&))OnBitsInCommon);
python::def("OnBitsInCommon",
(IntVect (*)(const EBV&,const EBV&))OnBitsInCommon,
"Returns the number of on bits in common between the two bit vectors"
);
python::def("OffBitsInCommon",
(IntVect (*)(const SBV&,const SBV&))OffBitsInCommon);
python::def("OffBitsInCommon",
(IntVect (*)(const EBV&,const EBV&))OffBitsInCommon,
"Returns the number of off bits in common between the two bit vectors"
);
python::def("FoldFingerprint",
(SBV *(*)(const SBV &,unsigned int))FoldFingerprint,
(python::arg("bv"),python::arg("foldFactor")=2),
python::return_value_policy<python::manage_new_object>());
python::def("FoldFingerprint",
(EBV *(*)(const EBV &,unsigned int))FoldFingerprint,
(python::arg("bv"),python::arg("foldFactor")=2),
python::return_value_policy<python::manage_new_object>(),
"Folds the fingerprint by the provided amount. The default, foldFactor=2, returns a fingerprint that is half the size of the original.");
python::def("AllProbeBitsMatch",
(bool (*)(const SBV &,const SBV &))AllProbeBitsMatch);
python::def("AllProbeBitsMatch",
(bool (*)(const EBV &,const EBV &))AllProbeBitsMatch);
python::def("AllProbeBitsMatch",
(bool (*)(const SBV &,const std::string &))AllProbeBitsMatch);
python::def("AllProbeBitsMatch",(bool (*)(const EBV &,const std::string &))AllProbeBitsMatch,
"Returns True if all bits in the first argument match all bits in the \n\
vector defined by the pickle in the second argument.\n");
python::def("BitVectToText",
(std::string (*)(const SBV&))BitVectToText);
python::def("BitVectToText",
(std::string (*)(const EBV&))BitVectToText,
"Returns a string of zeros and ones representing the bit vector."
);
python::def("BitVectToFPSText",
(std::string (*)(const SBV&))BitVectToFPSText);
python::def("BitVectToFPSText",
(std::string (*)(const EBV&))BitVectToFPSText,
"Returns an FPS string representing the bit vector."
);
python::def("BitVectToBinaryText",
(std::string (*)(const SBV&))BitVectToBinaryText);
python::def("BitVectToBinaryText",
(std::string (*)(const EBV&))BitVectToBinaryText,
"Returns a binary string (byte array) representing the bit vector."
);
}
};
void wrap_BitOps() {
BitOps_wrapper::wrap();
}
|
