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//
// Copyright (C) 2018-2021 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/AtomPairGenerator.h>
#include <RDBoost/Wrap.h>
using namespace RDKit;
using namespace RDKit::AtomPair;
namespace python = boost::python;
namespace RDKit {
namespace AtomPairWrapper {
template <typename OutputType>
FingerprintGenerator<OutputType> *getAtomPairGenerator(
unsigned int minDistance, unsigned int maxDistance, bool includeChirality,
bool use2D, bool countSimulation, python::object &py_countBounds,
std::uint32_t fpSize, python::object &py_atomInvGen) {
AtomInvariantsGenerator *atomInvariantsGenerator = nullptr;
python::extract<AtomInvariantsGenerator *> atomInvGen(py_atomInvGen);
if (atomInvGen.check() && atomInvGen()) {
atomInvariantsGenerator = atomInvGen()->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 AtomPair::getAtomPairGenerator<OutputType>(
minDistance, maxDistance, includeChirality, use2D,
atomInvariantsGenerator, countSimulation, fpSize, countBounds, true);
}
AtomInvariantsGenerator *getAtomPairAtomInvGen(const bool includeChirality) {
return new AtomPairAtomInvGenerator(includeChirality);
}
void exportAtompair() {
python::class_<AtomPair::AtomPairArguments,
python::bases<FingerprintArguments>, boost::noncopyable>(
"AtomPairFingerprintOptions", python::no_init)
.def_readwrite("use2D", &AtomPair::AtomPairArguments::df_use2D,
"use 2D distances")
.def_readwrite("minDistance", &AtomPair::AtomPairArguments::d_minDistance,
"minimum distance to be included")
.def_readwrite("maxDistance", &AtomPair::AtomPairArguments::d_maxDistance,
"maximum distance to be included");
python::def(
"GetAtomPairGenerator", &getAtomPairGenerator<std::uint64_t>,
(python::arg("minDistance") = 1,
python::arg("maxDistance") = AtomPair::maxPathLen - 1,
python::arg("includeChirality") = false, python::arg("use2D") = true,
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"
" - minDistance: minimum distance between atoms to be considered in a "
"pair, default is 1 bond\n"
" - maxDistance: maximum distance between atoms to be considered in a "
"pair, default is maxPathLen-1 bonds\n"
" - includeChirality: if set, chirality will be used in the atom "
"invariants, this is ignored if atomInvariantsGenerator is provided\n"
" - use2D: if set, the 2D (topological) distance matrix will be "
"used\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"
" - bitInfoMap: map from bitId to (atomId, radius) pairs\n\n"
" RETURNS: FingerprintGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
python::def("GetAtomPairAtomInvGen", &getAtomPairAtomInvGen,
(python::arg("includeChirality") = false),
"Get an atom pair atom-invariant generator\n\n"
" ARGUMENTS:\n"
" - includeChirality: if set, chirality will be taken into "
"account for invariants\n"
" RETURNS: AtomInvariantsGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
return;
}
} // namespace AtomPairWrapper
} // namespace RDKit
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