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//
// Copyright (C) 2018-2022 Boran Adas 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 <boost/python.hpp>
#include <GraphMol/Fingerprints/FingerprintGenerator.h>
#include <GraphMol/Fingerprints/TopologicalTorsionGenerator.h>
#include <RDBoost/Wrap.h>
using namespace RDKit;
namespace python = boost::python;
namespace RDKit {
namespace TopologicalTorsionWrapper {
template <typename OutputType>
FingerprintGenerator<OutputType> *getTopologicalTorsionFPGenerator(
const bool includeChirality, const uint32_t torsionAtomCount,
const bool countSimulation, python::object &py_countBounds,
const std::uint32_t fpSize, python::object &py_atomInvGen) {
AtomInvariantsGenerator *atomInvariantsGenerator = nullptr;
python::extract<AtomInvariantsGenerator *> atomInvGen(py_atomInvGen);
if (atomInvGen.check() && atomInvGen()) {
atomInvariantsGenerator = atomInvGen();
atomInvariantsGenerator = atomInvariantsGenerator->clone();
}
std::vector<std::uint32_t> countBounds = {1, 2, 4, 8};
if (py_countBounds) {
auto tmp = pythonObjectToVect<std::uint32_t>(py_countBounds);
countBounds = *tmp;
}
return TopologicalTorsion::getTopologicalTorsionGenerator<OutputType>(
includeChirality, torsionAtomCount, atomInvariantsGenerator,
countSimulation, fpSize, countBounds, false);
}
void exportTopologicalTorsion() {
// Topological torsion fingerprint does not support 32 bit output yet
python::class_<TopologicalTorsion::TopologicalTorsionArguments,
python::bases<FingerprintArguments>, boost::noncopyable>(
"TopologicalTorsionFingerprintOptions", python::no_init)
.def_readwrite(
"torsionAtomCount",
&TopologicalTorsion::TopologicalTorsionArguments::d_torsionAtomCount,
"number of atoms to be included in the paths")
.def_readwrite(
"onlyShortestPaths",
&TopologicalTorsion::TopologicalTorsionArguments::
df_onlyShortestPaths,
"whether or not to only include paths which are the shortest path between the start and end atoms");
python::def(
"GetTopologicalTorsionGenerator",
&getTopologicalTorsionFPGenerator<std::uint64_t>,
(python::arg("includeChirality") = false,
python::arg("torsionAtomCount") = 4,
python::arg("countSimulation") = true,
python::arg("countBounds") = python::object(),
python::arg("fpSize") = 2048,
python::arg("atomInvariantsGenerator") = python::object()),
"Get an atom pair fingerprint generator\n\n"
" ARGUMENTS:\n"
" - includeChirality: includeChirality argument for both the default "
"atom invariants generator and the fingerprint arguments\n"
" - torsionAtomCount: the number of atoms to include in the "
"\"torsions\"\n"
" - countSimulation: if set, use count simulation while "
"generating the fingerprint\n"
" - countBounds: boundaries for count simulation, corresponding bit "
"will be set if the count is higher than the number provided for that "
"spot\n"
" - fpSize: size of the generated fingerprint, does not affect the "
"sparse versions\n"
" - atomInvariantsGenerator: atom invariants to be used during "
"fingerprint generation\n\n"
"This generator supports the following AdditionalOutput types:\n"
" - atomToBits: which bits each atom is involved in\n"
" - atomCounts: how many bits each atom sets\n"
" - bitPaths: map from bitId to vectors of atom indices\n\n"
" RETURNS: FingerprintGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
return;
}
} // namespace TopologicalTorsionWrapper
} // namespace RDKit
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