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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/RDKitFPGenerator.h>
#include <RDBoost/Wrap.h>
using namespace RDKit;
namespace python = boost::python;
namespace RDKit {
namespace RDKitFPWrapper {
template <typename OutputType>
FingerprintGenerator<OutputType> *getRDKitFPGenerator(
unsigned int minPath, unsigned int maxPath, bool useHs, bool branchedPaths,
bool useBondOrder, bool countSimulation, python::object &py_countBounds,
std::uint32_t fpSize, std::uint32_t numBitsPerFeature,
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 RDKitFP::getRDKitFPGenerator<OutputType>(
minPath, maxPath, useHs, branchedPaths, useBondOrder,
atomInvariantsGenerator, countSimulation, countBounds, fpSize,
numBitsPerFeature, true);
}
AtomInvariantsGenerator *getRDKitAtomInvGen() {
return new RDKitFP::RDKitFPAtomInvGenerator();
}
void exportRDKit() {
python::def(
"GetRDKitFPGenerator", &getRDKitFPGenerator<std::uint64_t>,
(python::arg("minPath") = 1, python::arg("maxPath") = 7,
python::arg("useHs") = true, python::arg("branchedPaths") = true,
python::arg("useBondOrder") = true,
python::arg("countSimulation") = false,
python::arg("countBounds") = python::object(),
python::arg("fpSize") = 2048, python::arg("numBitsPerFeature") = 2,
python::arg("atomInvariantsGenerator") = python::object()),
"Get an RDKit fingerprint generator\n\n"
" ARGUMENTS:\n"
" - minPath: the minimum path length (in bonds) to be included\n"
" - maxPath: the maximum path length (in bonds) to be included\n"
" - useHs: toggles inclusion of Hs in paths (if the molecule has "
"explicit Hs)\n"
" - branchedPaths: toggles generation of branched subgraphs, not just "
"linear paths\n"
" - useBondOrder: toggles inclusion of bond orders in the path "
"hashes\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"
" - numBitsPerFeature: the number of bits set per path/subgraph "
"found\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 bond indices for the "
"individual subgraphs\n\n"
" RETURNS: FingerprintGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
python::def("GetRDKitAtomInvGen", &getRDKitAtomInvGen,
"Get an RDKit atom invariants generator\n\n"
" RETURNS: AtomInvariantsGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
return;
}
} // namespace RDKitFPWrapper
} // namespace RDKit
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