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//
// Copyright (C) 2003-2021 greg Landrum and other RDKit contributors
//
// @@ 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 <RDBoost/python.h>
#include <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
namespace python = boost::python;
namespace {
template <typename T>
python::object BVToBinaryText(const T &bv) {
std::string res = BitVectToBinaryText(bv);
python::object retval = python::object(
python::handle<>(PyBytes_FromStringAndSize(res.c_str(), res.length())));
return retval;
}
} // namespace
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 NeighborWrapper(python::object queries, python::object bvs,
double (*metric)(const T &, const T &)) {
python::list res;
unsigned int nbvs = python::extract<unsigned int>(bvs.attr("__len__")());
unsigned int nqs = python::extract<unsigned int>(queries.attr("__len__")());
for (unsigned int i = 0; i < nqs; ++i) {
const T *bv1 = python::extract<const T *>(queries[i])();
double closest = -1;
unsigned nbr;
for (unsigned int j = 0; j < nbvs; ++j) {
const T *bv2 = python::extract<const T *>(bvs[j])();
auto sim = metric(*bv1, *bv2);
if (sim > closest) {
closest = sim;
nbr = j;
}
}
res.append(python::make_tuple(nbr, closest));
}
return res;
}
template <typename T>
python::list BulkWrapper(const T *bv1, python::object 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<const T *>(bvs[i])();
auto sim = metric(*bv1, *bv2);
if (returnDistance) {
sim = 1.0 - sim;
}
res.append(sim);
}
return res;
}
template <typename T>
python::list BulkWrapper(const T *bv1, python::object 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])();
auto sim = metric(*bv1, *bv2, a, b);
if (returnDistance) {
sim = 1.0 - sim;
}
res.append(sim);
}
return res;
}
#define METRIC_DEFS(_metricname_) \
template <typename T1, typename T2> \
double _metricname_##_w(const T1 &bv1, const T2 &bv2, bool returnDistance) { \
return SimilarityWrapper(bv1, bv2, \
(double (*)(const T1 &, const T1 &))_metricname_, \
returnDistance); \
} \
template <typename T> \
python::list Bulk##_metricname_(const T *bv1, python::object bvs, \
bool returnDistance) { \
return BulkWrapper(bv1, bvs, \
(double (*)(const T &, const T &))_metricname_, \
returnDistance); \
} \
template <typename T> \
python::list _metricname_##Neighbors(python::object queries, \
python::object bvs) { \
return NeighborWrapper(queries, bvs, \
(double (*)(const T &, const T &))_metricname_); \
}
METRIC_DEFS(TanimotoSimilarity)
METRIC_DEFS(CosineSimilarity)
METRIC_DEFS(KulczynskiSimilarity)
METRIC_DEFS(DiceSimilarity)
METRIC_DEFS(SokalSimilarity)
METRIC_DEFS(McConnaugheySimilarity)
METRIC_DEFS(AsymmetricSimilarity)
METRIC_DEFS(BraunBlanquetSimilarity)
METRIC_DEFS(RusselSimilarity)
METRIC_DEFS(RogotGoldbergSimilarity)
METRIC_DEFS(OnBitSimilarity)
METRIC_DEFS(AllBitSimilarity)
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::object bvs, double a,
double b, bool returnDistance) {
return BulkWrapper(
bv1, bvs, a, b,
(double (*)(const T &, const T &, double, double))TverskySimilarity,
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::object, bool))_bulkname_, \
(python::args("v1"), python::args("v2"), \
python::args("returnDistance") = 0)); \
python::def( \
#_bulkname_, \
(python::list(*)(const EBV *, python::object, 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::object, bool))_bulkname_, \
(python::args("bv1"), python::args("bvList"), \
python::args("returnDistance") = 0)); \
python::def( \
#_bulkname_, \
(python::list(*)(const EBV *, python::object, bool))_bulkname_, \
(python::args("bv1"), python::args("bvList"), \
python::args("returnDistance") = 0), \
_help_); \
python::def(#_funcname_ "Neighbors", \
(python::list(*)(python::object, python::object)) \
_funcname_##Neighbors<ExplicitBitVect>, \
(python::args("bvqueries"), python::args("bvList")), _help_); \
python::def(#_funcname_ "Neighbors_sparse", \
(python::list(*)(python::object, python::object)) \
_funcname_##Neighbors<SparseBitVect>, \
(python::args("bvqueries"), python::args("bvList")), _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)");
BIG_DEF(RogotGoldbergSimilarity, RogotGoldbergSimilarity_w,
BulkRogotGoldbergSimilarity, "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::object, 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::object, 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::args("bv1", "bv2"));
python::def(
"OnBitProjSimilarity",
(DoubleVect(*)(const EBV &, const EBV &))OnBitProjSimilarity,
python::args("bv1", "bv2"),
"Returns a 2-tuple: (B(bv1&bv2) / B(bv1), B(bv1&bv2) / B(bv2))");
python::def("OffBitProjSimilarity",
(DoubleVect(*)(const SBV &, const SBV &))OffBitProjSimilarity,
python::args("bv1", "bv2"));
python::def("OffBitProjSimilarity",
(DoubleVect(*)(const EBV &, const EBV &))OffBitProjSimilarity,
python::args("bv1", "bv2"));
python::def("NumBitsInCommon",
(int (*)(const SBV &, const SBV &))NumBitsInCommon,
python::args("bv1", "bv2"));
python::def("NumBitsInCommon",
(int (*)(const EBV &, const EBV &))NumBitsInCommon,
python::args("bv1", "bv2"),
"Returns the total number of bits in common between the two "
"bit vectors");
python::def("OnBitsInCommon",
(IntVect(*)(const SBV &, const SBV &))OnBitsInCommon,
python::args("bv1", "bv2"));
python::def(
"OnBitsInCommon", (IntVect(*)(const EBV &, const EBV &))OnBitsInCommon,
python::args("bv1", "bv2"),
"Returns the number of on bits in common between the two bit vectors");
python::def("OffBitsInCommon",
(IntVect(*)(const SBV &, const SBV &))OffBitsInCommon,
python::args("bv1", "bv2"));
python::def(
"OffBitsInCommon",
(IntVect(*)(const EBV &, const EBV &))OffBitsInCommon,
python::args("bv1", "bv2"),
"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::args("probe", "ref"));
python::def("AllProbeBitsMatch",
(bool (*)(const EBV &, const EBV &))AllProbeBitsMatch,
python::args("probe", "ref"));
python::def("AllProbeBitsMatch",
(bool (*)(const SBV &, const std::string &))AllProbeBitsMatch,
python::args("probe", "ref"));
python::def(
"AllProbeBitsMatch",
(bool (*)(const EBV &, const std::string &))AllProbeBitsMatch,
python::args("probe", "ref"),
"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::args("bv1"));
python::def(
"BitVectToText", (std::string(*)(const EBV &))BitVectToText,
python::args("bv1"),
"Returns a string of zeros and ones representing the bit vector.");
python::def("BitVectToFPSText",
(std::string(*)(const SBV &))BitVectToFPSText,
python::args("bv1"));
python::def("BitVectToFPSText",
(std::string(*)(const EBV &))BitVectToFPSText,
python::args("bv1"),
"Returns an FPS string representing the bit vector.");
python::def("BitVectToBinaryText",
(python::object(*)(const SBV &))BVToBinaryText,
python::args("bv"));
python::def(
"BitVectToBinaryText", (python::object(*)(const EBV &))BVToBinaryText,
python::args("bv"),
"Returns a binary string (byte array) representing the bit vector.");
}
};
void wrap_BitOps() { BitOps_wrapper::wrap(); }
|
