mirror of
https://github.com/rdkit/rdkit.git
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199 lines
8.7 KiB
C++
199 lines
8.7 KiB
C++
//
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// Copyright (C) 2016 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/Wrap.h>
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#include <DataStructs/FPBReader.h>
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#include <DataStructs/MultiFPBReader.h>
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#include <RDBoost/PySequenceHolder.h>
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#include "wrap_helpers.h"
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namespace python = boost::python;
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using namespace RDKit;
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namespace {
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python::tuple taniNbrHelper(const FPBReader *self, const std::string &bytes,
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double threshold) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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std::vector<std::pair<double, unsigned int>> nbrs =
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self->getTanimotoNeighbors(bv, threshold);
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python::list result;
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for (auto &nbr : nbrs) {
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result.append(python::make_tuple(nbr.first, nbr.second));
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}
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return python::tuple(result);
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}
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python::tuple tverskyNbrHelper(const FPBReader *self, const std::string &bytes,
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double ca, double cb, double threshold) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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std::vector<std::pair<double, unsigned int>> nbrs =
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self->getTverskyNeighbors(bv, ca, cb, threshold);
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python::list result;
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for (auto &nbr : nbrs) {
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result.append(python::make_tuple(nbr.first, nbr.second));
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}
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return python::tuple(result);
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}
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python::tuple containingNbrHelper(const FPBReader *self,
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const std::string &bytes) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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std::vector<unsigned int> nbrs = self->getContainingNeighbors(bv);
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python::list result;
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for (auto &nbr : nbrs) {
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result.append(nbr);
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}
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return python::tuple(result);
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}
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python::tuple multiTaniNbrHelper(const MultiFPBReader *self,
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const std::string &bytes, double threshold,
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unsigned int numThreads) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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std::vector<MultiFPBReader::ResultTuple> nbrs =
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self->getTanimotoNeighbors(bv, threshold, numThreads);
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python::list result;
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for (auto &nbr : nbrs) {
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result.append(python::make_tuple(std::get<0>(nbr), std::get<1>(nbr),
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std::get<2>(nbr)));
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}
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return python::tuple(result);
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}
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python::tuple multiTverskyNbrHelper(const MultiFPBReader *self,
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const std::string &bytes, double ca,
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double cb, double threshold,
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unsigned int numThreads) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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std::vector<MultiFPBReader::ResultTuple> nbrs =
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self->getTverskyNeighbors(bv, ca, cb, threshold, numThreads);
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python::list result;
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for (auto &nbr : nbrs) {
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result.append(python::make_tuple(std::get<0>(nbr), std::get<1>(nbr),
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std::get<2>(nbr)));
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}
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return python::tuple(result);
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}
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python::tuple multiContainingNbrHelper(const MultiFPBReader *self,
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const std::string &bytes,
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unsigned int numThreads) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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std::vector<std::pair<unsigned int, unsigned int>> nbrs =
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self->getContainingNeighbors(bv, numThreads);
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python::list result;
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for (auto &nbr : nbrs) {
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result.append(python::make_tuple(nbr.first, nbr.second));
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}
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return python::tuple(result);
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}
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python::object getBytesHelper(const FPBReader *self, unsigned int which) {
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boost::shared_array<std::uint8_t> bv = self->getBytes(which);
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python::object retval =
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python::object(python::handle<>(PyBytes_FromStringAndSize(
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reinterpret_cast<const char *>(bv.get()), self->nBits() / 8)));
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return retval;
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}
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double getTaniHelper(const FPBReader *self, unsigned int which,
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const std::string &bytes) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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return self->getTanimoto(which, bv);
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}
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python::tuple getItemHelper(const FPBReader *self, unsigned int which) {
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std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> v = (*self)[which];
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return python::make_tuple(v.first, v.second);
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}
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double getTverskyHelper(const FPBReader *self, unsigned int which,
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const std::string &bytes, double ca, double cb) {
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const auto *bv = reinterpret_cast<const std::uint8_t *>(bytes.c_str());
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return self->getTversky(which, bv, ca, cb);
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}
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} // namespace
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struct FPB_wrapper {
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static void wrap() {
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std::string FPBReaderClassDoc =
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"A class for reading and searching FPB files from Andrew Dalke's chemfp.\n\
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Note that this functionality is still experimental and the API may\n\
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change in future releases.\n";
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python::class_<FPBReader, boost::noncopyable>(
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"FPBReader", FPBReaderClassDoc.c_str(),
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python::init<std::string, python::optional<bool>>(
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(python::arg("filename"), python::arg("lazy") = false),
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"docstring"))
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.def("Init", &FPBReader::init,
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"Read the fingerprints from the file. This can take a while.\n")
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.def("__len__", &FPBReader::length)
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.def("__getitem__", &getItemHelper)
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.def("GetNumBits", &FPBReader::nBits,
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"returns the number of bits in a fingerprint")
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.def("GetFP", &FPBReader::getFP,
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"returns a particular fingerprint as an ExplicitBitVect")
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.def("GetBytes", &getBytesHelper,
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"returns a particular fingerprint as bytes")
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.def("GetId", &FPBReader::getId,
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"returns the id of a particular fingerprint")
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.def("GetTanimoto", &getTaniHelper,
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"return the tanimoto similarity of a particular fingerprint to "
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"the bytes provided")
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.def("GetTanimotoNeighbors", &taniNbrHelper,
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(python::arg("bv"), python::arg("threshold") = 0.7),
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"returns tanimoto similarities to and indices of all neighbors "
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"above the specified threshold")
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.def("GetTversky", &getTverskyHelper,
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"return the Tverksy similarity of a particular fingerprint to "
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"the bytes provided")
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.def("GetTverskyNeighbors", &tverskyNbrHelper,
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(python::arg("bv"), python::arg("ca"), python::arg("cb"),
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python::arg("threshold") = 0.7),
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"returns Tversky similarities to and indices of all neighbors "
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"above the specified threshold")
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.def(
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"GetContainingNeighbors", &containingNbrHelper, (python::arg("bv")),
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"returns indices of neighbors that contain this fingerprint (where "
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"all bits from this fingerprint are also set)");
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std::string MultiFPBReaderClassDoc =
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"A class for reading and searching multiple FPB files from Andrew Dalke's chemfp.\n\
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Note that this functionality is still experimental and the API may\n\
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change in future releases.\n";
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python::class_<MultiFPBReader, boost::noncopyable>(
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"MultiFPBReader", MultiFPBReaderClassDoc.c_str(),
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python::init<python::optional<bool>>(
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(python::arg("initOnSearch") = false), "docstring"))
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.def("Init", &MultiFPBReader::init,
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"Call Init() on each of our children. This can take a while.\n")
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.def("__len__", &MultiFPBReader::length)
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.def("GetNumBits", &MultiFPBReader::nBits,
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"returns the number of bits in a fingerprint")
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.def("AddReader", &MultiFPBReader::addReader,
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python::with_custodian_and_ward<1, 2>(),
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"adds an FPBReader to our set of readers")
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.def("GetReader", &MultiFPBReader::getReader,
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python::return_value_policy<python::reference_existing_object>(),
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"returns one of our readers")
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.def("GetTanimotoNeighbors", &multiTaniNbrHelper,
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(python::arg("bv"), python::arg("threshold") = 0.7,
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python::arg("numThreads") = 1),
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"returns tanimoto similarities to and indices of all neighbors "
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"above the specified threshold")
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.def("GetTverskyNeighbors", &multiTverskyNbrHelper,
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(python::arg("bv"), python::arg("ca"), python::arg("cb"),
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python::arg("threshold") = 0.7, python::arg("numThreads") = 1),
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"returns Tversky similarities to and indices of all neighbors "
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"above the specified threshold")
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.def(
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"GetContainingNeighbors", &multiContainingNbrHelper,
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(python::arg("bv"), python::arg("numThreads") = 1),
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"returns indices of neighbors that contain this fingerprint (where "
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"all bits from this fingerprint are also set)");
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}
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};
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void wrap_FPB() { FPB_wrapper::wrap(); }
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