mirror of
https://github.com/rdkit/rdkit.git
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c63ddaffa2
* refactor python wrappers * fix FilterHierarchyMatcher converted already registered warning
372 lines
18 KiB
C++
372 lines
18 KiB
C++
//
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// Copyright (C) 2003-2021 greg Landrum and other RDKit contributors
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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 <RDBoost/python.h>
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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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namespace {
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template <typename T>
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python::object BVToBinaryText(const T &bv) {
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std::string res = BitVectToBinaryText(bv);
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python::object retval = python::object(
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python::handle<>(PyBytes_FromStringAndSize(res.c_str(), res.length())));
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return retval;
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}
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} // namespace
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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 &),
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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,
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double b,
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double (*metric)(const T &, const T &, double, double),
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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 NeighborWrapper(python::object queries, python::object bvs,
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double (*metric)(const T &, const T &)) {
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python::list res;
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unsigned int nbvs = python::len(bvs);
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unsigned int nqs = python::len(queries);
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for (unsigned int i = 0; i < nqs; ++i) {
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const T *bv1 = python::extract<const T *>(queries[i])();
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double closest = -1;
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unsigned nbr;
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for (unsigned int j = 0; j < nbvs; ++j) {
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const T *bv2 = python::extract<const T *>(bvs[j])();
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auto sim = metric(*bv1, *bv2);
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if (sim > closest) {
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closest = sim;
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nbr = j;
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}
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}
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res.append(python::make_tuple(nbr, closest));
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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::object 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::len(bvs);
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for (unsigned int i = 0; i < nbvs; ++i) {
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const T *bv2 = python::extract<const T *>(bvs[i])();
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auto sim = metric(*bv1, *bv2);
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if (returnDistance) {
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sim = 1.0 - sim;
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}
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res.append(sim);
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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::object 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::len(bvs);
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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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auto sim = metric(*bv1, *bv2, a, b);
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if (returnDistance) {
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sim = 1.0 - sim;
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}
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res.append(sim);
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}
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return res;
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}
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#define METRIC_DEFS(_metricname_) \
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template <typename T1, typename T2> \
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double _metricname_##_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 &))_metricname_, \
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returnDistance); \
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} \
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template <typename T> \
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python::list Bulk##_metricname_(const T *bv1, python::object bvs, \
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bool returnDistance) { \
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return BulkWrapper(bv1, bvs, \
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(double (*)(const T &, const T &))_metricname_, \
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returnDistance); \
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} \
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template <typename T> \
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python::list _metricname_##Neighbors(python::object queries, \
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python::object bvs) { \
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return NeighborWrapper(queries, bvs, \
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(double (*)(const T &, const T &))_metricname_); \
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}
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METRIC_DEFS(TanimotoSimilarity)
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METRIC_DEFS(CosineSimilarity)
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METRIC_DEFS(KulczynskiSimilarity)
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METRIC_DEFS(DiceSimilarity)
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METRIC_DEFS(SokalSimilarity)
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METRIC_DEFS(McConnaugheySimilarity)
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METRIC_DEFS(AsymmetricSimilarity)
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METRIC_DEFS(BraunBlanquetSimilarity)
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METRIC_DEFS(RusselSimilarity)
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METRIC_DEFS(RogotGoldbergSimilarity)
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METRIC_DEFS(OnBitSimilarity)
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METRIC_DEFS(AllBitSimilarity)
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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,
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bool returnDistance) {
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return SimilarityWrapper(
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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::object bvs, double a,
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double b, bool returnDistance) {
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return BulkWrapper(
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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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#define DBL_DEF(_funcname_, _bulkname_, _help_) \
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{ \
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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( \
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#_bulkname_, \
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(python::list (*)(const EBV *, python::object, bool))_bulkname_, \
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(python::args("v1"), python::args("v2"), \
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python::args("returnDistance") = 0)); \
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python::def( \
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#_bulkname_, \
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(python::list (*)(const EBV *, python::object, bool))_bulkname_, \
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(python::args("v1"), python::args("v2"), \
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python::args("returnDistance") = 0), \
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_help_); \
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}
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#define BIG_DEF(_funcname_, _name_w_, _bulkname_, _help_) \
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{ \
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python::def(#_funcname_, \
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(double (*)(const SBV &, const SBV &, bool))_name_w_, \
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(python::args("bv1"), python::args("bv2"), \
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python::args("returnDistance") = 0)); \
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python::def(#_funcname_, \
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(double (*)(const EBV &, const EBV &, bool))_name_w_, \
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(python::args("bv1"), python::args("bv2"), \
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python::args("returnDistance") = 0), \
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_help_); \
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python::def(#_funcname_, \
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(double (*)(const SBV &, const std::string &, bool))_name_w_, \
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(python::args("bv1"), python::args("pkl"), \
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python::args("returnDistance") = 0)); \
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python::def(#_funcname_, \
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(double (*)(const EBV &, const std::string &, bool))_name_w_, \
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(python::args("bv1"), python::args("pkl"), \
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python::args("returnDistance") = 0), \
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_help_); \
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python::def( \
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#_bulkname_, \
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(python::list (*)(const SBV *, python::object, bool))_bulkname_, \
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(python::args("bv1"), python::args("bvList"), \
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python::args("returnDistance") = 0)); \
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python::def( \
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#_bulkname_, \
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(python::list (*)(const EBV *, python::object, bool))_bulkname_, \
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(python::args("bv1"), python::args("bvList"), \
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python::args("returnDistance") = 0), \
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_help_); \
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python::def(#_funcname_ "Neighbors", \
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(python::list (*)(python::object, python::object)) \
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_funcname_##Neighbors<ExplicitBitVect>, \
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(python::args("bvqueries"), python::args("bvList")), _help_); \
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python::def(#_funcname_ "Neighbors_sparse", \
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(python::list (*)(python::object, python::object)) \
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_funcname_##Neighbors<SparseBitVect>, \
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(python::args("bvqueries"), python::args("bvList")), _help_); \
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}
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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,
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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(
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McConnaugheySimilarity, McConnaugheySimilarity_w,
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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,
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BulkAsymmetricSimilarity, "B(bv1&bv2) / min(B(bv1),B(bv2))");
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BIG_DEF(BraunBlanquetSimilarity, BraunBlanquetSimilarity_w,
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BulkBraunBlanquetSimilarity, "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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BIG_DEF(RogotGoldbergSimilarity, RogotGoldbergSimilarity_w,
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BulkRogotGoldbergSimilarity, "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,
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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,
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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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help.c_str());
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python::def("TverskySimilarity",
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(double (*)(const SBV &, const std::string &, double, double,
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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,
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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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help.c_str());
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python::def(
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"BulkTverskySimilarity",
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(python::list (*)(const SBV *, python::object, double, double,
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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(
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"BulkTverskySimilarity",
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(python::list (*)(const EBV *, python::object, double, double,
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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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help.c_str());
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}
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DBL_DEF(OnBitSimilarity, BulkOnBitSimilarity, "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::args("bv1", "bv2"));
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python::def(
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"OnBitProjSimilarity",
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(DoubleVect (*)(const EBV &, const EBV &))OnBitProjSimilarity,
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python::args("bv1", "bv2"),
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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::args("bv1", "bv2"));
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python::def("OffBitProjSimilarity",
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(DoubleVect (*)(const EBV &, const EBV &))OffBitProjSimilarity,
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python::args("bv1", "bv2"));
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python::def("NumBitsInCommon",
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(int (*)(const SBV &, const SBV &))NumBitsInCommon,
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python::args("bv1", "bv2"));
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python::def("NumBitsInCommon",
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(int (*)(const EBV &, const EBV &))NumBitsInCommon,
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python::args("bv1", "bv2"),
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"Returns the total number of bits in common between the two "
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"bit vectors");
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python::def("OnBitsInCommon",
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(IntVect (*)(const SBV &, const SBV &))OnBitsInCommon,
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python::args("bv1", "bv2"));
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python::def(
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"OnBitsInCommon", (IntVect (*)(const EBV &, const EBV &))OnBitsInCommon,
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python::args("bv1", "bv2"),
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"Returns the number of on bits in common between the two bit vectors");
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python::def("OffBitsInCommon",
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(IntVect (*)(const SBV &, const SBV &))OffBitsInCommon,
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python::args("bv1", "bv2"));
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python::def(
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"OffBitsInCommon",
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(IntVect (*)(const EBV &, const EBV &))OffBitsInCommon,
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python::args("bv1", "bv2"),
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"Returns the number of off bits in common between the two bit vectors");
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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, "
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"foldFactor=2, returns a fingerprint that is half the size of "
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"the original.");
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python::def("AllProbeBitsMatch",
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(bool (*)(const SBV &, const SBV &))AllProbeBitsMatch,
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python::args("probe", "ref"));
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python::def("AllProbeBitsMatch",
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(bool (*)(const EBV &, const EBV &))AllProbeBitsMatch,
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python::args("probe", "ref"));
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python::def("AllProbeBitsMatch",
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(bool (*)(const SBV &, const std::string &))AllProbeBitsMatch,
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python::args("probe", "ref"));
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python::def(
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"AllProbeBitsMatch",
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(bool (*)(const EBV &, const std::string &))AllProbeBitsMatch,
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python::args("probe", "ref"),
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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", (std::string (*)(const SBV &))BitVectToText,
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python::args("bv1"));
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python::def(
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"BitVectToText", (std::string (*)(const EBV &))BitVectToText,
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python::args("bv1"),
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"Returns a string of zeros and ones representing the bit vector.");
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python::def("BitVectToFPSText",
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(std::string (*)(const SBV &))BitVectToFPSText,
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python::args("bv1"));
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python::def("BitVectToFPSText",
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(std::string (*)(const EBV &))BitVectToFPSText,
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python::args("bv1"),
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"Returns an FPS string representing the bit vector.");
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python::def("BitVectToBinaryText",
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(python::object (*)(const SBV &))BVToBinaryText,
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python::args("bv"));
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python::def(
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"BitVectToBinaryText", (python::object (*)(const EBV &))BVToBinaryText,
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python::args("bv"),
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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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void wrap_BitOps() { BitOps_wrapper::wrap(); }
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