mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
edd922c99c
* stop returning local memory in exceptions * remove a couple unnecessary copies in loops * fix a bug in the way the default MMFF aromatic parameters are constructed * remove a bunch of loop-variable warnings * remove a bunch of clang warnings * disable clang warnings in python wrappers * remove some warnings when building the python wrappers
214 lines
8.0 KiB
C++
214 lines
8.0 KiB
C++
// $Id$
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//
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// Copyright (C) 2007-2008 Greg Landrum
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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 <RDGeneral/BoostStartInclude.h>
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#include <cstdint>
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#include <RDGeneral/BoostEndInclude.h>
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#include <RDGeneral/types.h>
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#include <RDGeneral/Invariant.h>
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#include <RDBoost/PySequenceHolder.h>
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#include <DataStructs/SparseIntVect.h>
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using namespace RDKit;
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namespace {
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template <typename IndexType>
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python::object SIVToBinaryText(const SparseIntVect<IndexType> &siv) {
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std::string res = siv.toString();
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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 IndexType>
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struct siv_pickle_suite : python::pickle_suite {
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static python::tuple getinitargs(const SparseIntVect<IndexType> &self) {
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return python::make_tuple(SIVToBinaryText(self));
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};
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};
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namespace {
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template <typename IndexType>
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void pyUpdateFromSequence(SparseIntVect<IndexType> &vect, python::object &seq) {
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PySequenceHolder<IndexType> seqL(seq);
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for (unsigned int i = 0; i < seqL.size(); ++i) {
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IndexType idx = seqL[i];
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vect.setVal(idx, vect[idx] + 1);
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}
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}
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template <typename IndexType>
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python::dict pyGetNonzeroElements(SparseIntVect<IndexType> &vect) {
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python::dict res;
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auto iter = vect.getNonzeroElements().begin();
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while (iter != vect.getNonzeroElements().end()) {
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res[iter->first] = iter->second;
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++iter;
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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 BulkDice(const T &siv1, python::list sivs, bool returnDistance) {
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python::list res;
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unsigned int nsivs = python::extract<unsigned int>(sivs.attr("__len__")());
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for (unsigned int i = 0; i < nsivs; ++i) {
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double simVal;
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const T &siv2 = python::extract<T>(sivs[i])();
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simVal = DiceSimilarity(siv1, siv2, returnDistance);
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res.append(simVal);
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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 BulkTanimoto(const T &siv1, python::list sivs,
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bool returnDistance) {
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python::list res;
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unsigned int nsivs = python::extract<unsigned int>(sivs.attr("__len__")());
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for (unsigned int i = 0; i < nsivs; ++i) {
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double simVal;
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const T &siv2 = python::extract<T>(sivs[i])();
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simVal = TanimotoSimilarity(siv1, siv2, returnDistance);
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res.append(simVal);
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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 BulkTversky(const T &siv1, python::list sivs, double a, double b,
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bool returnDistance) {
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python::list res;
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unsigned int nsivs = python::extract<unsigned int>(sivs.attr("__len__")());
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for (unsigned int i = 0; i < nsivs; ++i) {
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double simVal;
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const T &siv2 = python::extract<T>(sivs[i])();
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simVal = TverskySimilarity(siv1, siv2, a, b, returnDistance);
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res.append(simVal);
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}
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return res;
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}
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} // namespace
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std::string sparseIntVectDoc =
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"A container class for storing integer\n\
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values within a particular range.\n\
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\n\
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The length of the vector is set at construction time.\n\
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\n\
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As you would expect, _SparseIntVects_ support a set of binary operations\n\
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so you can do things like:\n\
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Arithmetic:\n\
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siv1 += siv2\n\
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siv3 = siv1 + siv2\n\
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siv1 -= siv3\n\
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siv3 = siv1 - siv2\n\
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\"Fuzzy\" binary operations:\n\
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siv3 = siv1 & siv2 the result contains the smallest value in each entry\n\
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siv3 = siv1 | siv2 the result contains the largest value in each entry\n\
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\n\
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Elements can be set and read using indexing (i.e. siv[i] = 4 or val=siv[i])\n\
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\n";
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struct sparseIntVec_wrapper {
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template <typename IndexType>
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static void wrapOne(const char *className) {
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python::class_<SparseIntVect<IndexType>,
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boost::shared_ptr<SparseIntVect<IndexType>>>(
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className, sparseIntVectDoc.c_str(),
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python::init<IndexType>("Constructor"))
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.def(python::init<std::string>())
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// Note: we cannot support __len__ because, at least at the moment
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// (BPL v1.34.1), it must return an int.
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.def("__setitem__", &SparseIntVect<IndexType>::setVal,
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"Set the value at a specified location")
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.def("__getitem__", &SparseIntVect<IndexType>::getVal,
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"Get the value at a specified location")
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.def(python::self & python::self)
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.def(python::self | python::self)
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.def(python::self - python::self)
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#ifdef __clang__
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#pragma GCC diagnostic push
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#pragma GCC diagnostic ignored "-Wself-assign-overloaded"
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#endif
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.def(python::self -=
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python::self) // clang warns incorrectly on this construct
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#ifdef __clang__
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#pragma GCC diagnostic pop
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#endif
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.def(python::self + python::self)
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.def(python::self += python::self)
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.def(python::self == python::self)
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.def(python::self != python::self)
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//.def(python::self - int())
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.def(python::self -= int())
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//.def(python::self + int())
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.def(python::self += int())
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//.def(python::self / int())
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.def(python::self /= int())
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//.def(python::self * int())
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.def(python::self *= int())
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.def("GetTotalVal", &SparseIntVect<IndexType>::getTotalVal,
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(python::args("useAbs") = false),
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"Get the sum of the values in the vector, basically L1 norm")
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.def("GetLength", &SparseIntVect<IndexType>::getLength,
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"Returns the length of the vector")
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.def("ToBinary", &SIVToBinaryText<IndexType>,
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"returns a binary (pickle) representation of the vector")
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.def("UpdateFromSequence", &pyUpdateFromSequence<IndexType>,
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"update the vector based on the values in the list or tuple")
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.def("GetNonzeroElements", &pyGetNonzeroElements<IndexType>,
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"returns a dictionary of the nonzero elements")
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.def_pickle(siv_pickle_suite<IndexType>());
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python::def(
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"DiceSimilarity", &DiceSimilarity<IndexType>,
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(python::args("siv1"), python::args("siv2"),
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python::args("returnDistance") = false, python::args("bounds") = 0.0),
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"return the Dice similarity between two vectors");
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python::def("BulkDiceSimilarity", &BulkDice<SparseIntVect<IndexType>>,
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(python::args("v1"), python::args("v2"),
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python::args("returnDistance") = false),
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"return the Dice similarities between one vector and a "
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"sequence of others");
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python::def(
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"TanimotoSimilarity", &TanimotoSimilarity<IndexType>,
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(python::args("siv1"), python::args("siv2"),
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python::args("returnDistance") = false, python::args("bounds") = 0.0),
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"return the Tanimoto similarity between two vectors");
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python::def("BulkTanimotoSimilarity",
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&BulkTanimoto<SparseIntVect<IndexType>>,
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(python::args("v1"), python::args("v2"),
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python::args("returnDistance") = false),
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"return the Tanimoto similarities between one vector and a "
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"sequence of others");
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python::def("TverskySimilarity", &TverskySimilarity<IndexType>,
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(python::args("siv1"), python::args("siv2"), python::args("a"),
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python::args("b"), python::args("returnDistance") = false,
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python::args("bounds") = 0.0),
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"return the Tversky similarity between two vectors");
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python::def("BulkTverskySimilarity", &BulkTversky<SparseIntVect<IndexType>>,
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(python::args("v1"), python::args("v2"), python::args("a"),
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python::args("b"), python::args("returnDistance") = false),
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"return the Tversky similarities between one vector and a "
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"sequence of others");
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}
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static void wrap() {
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wrapOne<std::int32_t>("IntSparseIntVect");
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wrapOne<boost::int64_t>("LongSparseIntVect");
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wrapOne<std::uint32_t>("UIntSparseIntVect");
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wrapOne<boost::uint64_t>("ULongSparseIntVect");
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}
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};
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void wrap_sparseIntVect() { sparseIntVec_wrapper::wrap(); }
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