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//
// Copyright (C) 2018 Boran Adas, Google Summer of Code
//
// @@ 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/MorganGenerator.h>
using namespace RDKit;
namespace python = boost::python;
namespace RDKit {
namespace MorganWrapper {
template <typename OutputType>
FingerprintGenerator<OutputType> *getMorganGenerator(
const unsigned int radius, const bool countSimulation,
const bool includeChirality, const bool useBondTypes,
const bool onlyNonzeroInvariants, const bool includeRingMembership,
python::object &py_countBounds, const std::uint32_t fpSize,
python::object &py_atomInvGen, python::object &py_bondInvGen) {
AtomInvariantsGenerator *atomInvariantsGenerator = nullptr;
BondInvariantsGenerator *bondInvariantsGenerator = nullptr;
python::extract<AtomInvariantsGenerator *> atomInvGen(py_atomInvGen);
if (atomInvGen.check() && atomInvGen()) {
atomInvariantsGenerator = atomInvGen()->clone();
}
python::extract<BondInvariantsGenerator *> bondInvGen(py_bondInvGen);
if (bondInvGen.check() && bondInvGen()) {
bondInvariantsGenerator = bondInvGen()->clone();
}
std::vector<std::uint32_t> countBounds = {1, 2, 4, 8};
python::extract<std::vector<std::uint32_t>> countBoundsE(py_countBounds);
if (countBoundsE.check() && !countBoundsE().empty()) {
countBounds = countBoundsE();
}
const std::vector<std::uint32_t> countBoundsC = countBounds;
return MorganFingerprint::getMorganGenerator<OutputType>(
radius, countSimulation, includeChirality, useBondTypes,
onlyNonzeroInvariants, atomInvariantsGenerator, bondInvariantsGenerator,
fpSize, countBounds, true, true);
}
AtomInvariantsGenerator *getMorganAtomInvGen(const bool includeRingMembership) {
return new MorganFingerprint::MorganAtomInvGenerator(includeRingMembership);
}
AtomInvariantsGenerator *getMorganFeatureAtomInvGen(
python::object &py_patterns) {
std::vector<const ROMol *> patterns;
python::extract<std::vector<const ROMol *>> patternsE(py_patterns);
if (patternsE.check()) {
patterns = patternsE();
return new MorganFingerprint::MorganFeatureAtomInvGenerator(&patterns);
} else {
return new MorganFingerprint::MorganFeatureAtomInvGenerator(nullptr);
}
}
BondInvariantsGenerator *getMorganBondInvGen(const bool useBondTypes,
const bool useChirality) {
return new MorganFingerprint::MorganBondInvGenerator(useBondTypes,
useChirality);
}
void exportMorgan() {
/*python::def(
"GetMorganGenerator32", getMorganGenerator<std::uint32_t>,
(python::arg("radius") = 3, python::arg("useCountSimulation") = true,
python::arg("includeChirality") = false,
python::arg("useBondTypes") = true,
python::arg("onlyNonzeroInvariants") = false,
python::arg("includeRingMembership") = true,
python::arg("countBounds") = python::object(),
python::arg("fpSize") = 2048,
python::arg("atomInvariantsGenerator") = python::object(),
python::arg("bondInvariantsGenerator") = python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());*/
python::def(
"GetMorganGenerator", getMorganGenerator<std::uint64_t>,
(python::arg("radius") = 3, python::arg("useCountSimulation") = true,
python::arg("includeChirality") = false,
python::arg("useBondTypes") = true,
python::arg("onlyNonzeroInvariants") = false,
python::arg("includeRingMembership") = true,
python::arg("countBounds") = python::object(),
python::arg("fpSize") = 2048,
python::arg("atomInvariantsGenerator") = python::object(),
python::arg("bondInvariantsGenerator") = python::object()),
"Get a morgan fingerprint generator\n\n"
" ARGUMENTS:\n"
" - radius: the number of iterations to grow the fingerprint\n"
" - useCountSimulation: if set, use count simulation while generating "
"the fingerprint\n"
" - includeChirality: if set, chirality information will be added to "
"the generated fingerprint\n"
" - useBondTypes: if set, bond types will be included as a part of "
"the default bond invariants\n"
" - useCountSimulation: 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"
" RETURNS: FingerprintGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
python::def("GetMorganAtomInvGen", &getMorganAtomInvGen,
(python::arg("includeRingMembership") = false),
"Get a morgan atom invariants generator\n\n"
" ARGUMENTS:\n"
" - includeRingMembership: if set, whether or not the atom is "
"in a ring will be used in the invariant list\n\n"
" RETURNS: AtomInvariantsGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
python::def(
"GetMorganFeatureAtomInvGen", &getMorganFeatureAtomInvGen,
(python::arg("patterns") = python::object()),
"Get a morgan feature atom invariants generator\n\n"
" ARGUMENTS:\n"
" - patterns: if provided should contain the queries used to assign "
"atom-types. if not provided, feature definitions adapted from "
"reference: Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998) will "
"be used for Donor, Acceptor, Aromatic, Halogen, Basic, Acidic.\n\n"
" RETURNS: AtomInvariantsGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
python::def(
"GetMorganBondInvGen", &getMorganBondInvGen,
(python::arg("useBondTypes") = true, python::arg("useChirality") = false),
"Get a morgan bond invariants generator\n\n"
" ARGUMENTS:\n"
" - useBondTypes: if set, bond types will be included as a part of "
"the bond invariants\n"
" - useChirality: if set, chirality information will be included as a "
"part of the bond invariants\n\n"
" RETURNS: BondInvariantsGenerator\n\n",
python::return_value_policy<python::manage_new_object>());
return;
}
} // namespace MorganWrapper
} // namespace RDKit
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