mirror of
https://github.com/rdkit/rdkit.git
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3866d3c419
* add test making sure that multiple bits per feature works with other fp types * simplification * expose base options class * remove redundant df_includeChirality from TT generator * expose the fingerprint arguments (i.e. options) to python * typo
115 lines
4.8 KiB
C++
115 lines
4.8 KiB
C++
//
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// Copyright (C) 2018-2021 Boran Adas and other RDKit contributors
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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 <boost/python.hpp>
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#include <GraphMol/Fingerprints/FingerprintGenerator.h>
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#include <GraphMol/Fingerprints/RDKitFPGenerator.h>
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#include <RDBoost/Wrap.h>
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using namespace RDKit;
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namespace python = boost::python;
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namespace RDKit {
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namespace RDKitFPWrapper {
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template <typename OutputType>
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FingerprintGenerator<OutputType> *getRDKitFPGenerator(
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unsigned int minPath, unsigned int maxPath, bool useHs, bool branchedPaths,
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bool useBondOrder, bool countSimulation, python::object &py_countBounds,
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std::uint32_t fpSize, std::uint32_t numBitsPerFeature,
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python::object &py_atomInvGen) {
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AtomInvariantsGenerator *atomInvariantsGenerator = nullptr;
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python::extract<AtomInvariantsGenerator *> atomInvGen(py_atomInvGen);
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if (atomInvGen.check() && atomInvGen()) {
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atomInvariantsGenerator = atomInvGen()->clone();
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}
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std::vector<std::uint32_t> countBounds = {1, 2, 4, 8};
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if (py_countBounds) {
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auto tmp = pythonObjectToVect<std::uint32_t>(py_countBounds);
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countBounds = *tmp;
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}
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return RDKitFP::getRDKitFPGenerator<OutputType>(
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minPath, maxPath, useHs, branchedPaths, useBondOrder,
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atomInvariantsGenerator, countSimulation, countBounds, fpSize,
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numBitsPerFeature, true);
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}
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AtomInvariantsGenerator *getRDKitAtomInvGen() {
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return new RDKitFP::RDKitFPAtomInvGenerator();
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}
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void exportRDKit() {
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python::class_<RDKitFP::RDKitFPArguments, python::bases<FingerprintArguments>,
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boost::noncopyable>("RDKitFingerprintOptions", python::no_init)
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.def_readwrite("minPath", &RDKitFP::RDKitFPArguments::d_minPath,
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"minimum path length (in bonds) to be included")
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.def_readwrite("maxPath", &RDKitFP::RDKitFPArguments::d_maxPath,
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"maximum path length (in bonds) to be included")
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.def_readwrite(
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"useHs", &RDKitFP::RDKitFPArguments::df_useHs,
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"use explicit Hs in the paths (if molecule has explicit Hs)")
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.def_readwrite("branchedPaths",
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&RDKitFP::RDKitFPArguments::df_branchedPaths,
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"generate branched subgraphs, not just linear ones")
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.def_readwrite("useBondOrder",
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&RDKitFP::RDKitFPArguments::df_useBondOrder,
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"include bond orders in the path hashes");
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python::def(
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"GetRDKitFPGenerator", &getRDKitFPGenerator<std::uint64_t>,
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(python::arg("minPath") = 1, python::arg("maxPath") = 7,
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python::arg("useHs") = true, python::arg("branchedPaths") = true,
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python::arg("useBondOrder") = true,
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python::arg("countSimulation") = false,
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python::arg("countBounds") = python::object(),
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python::arg("fpSize") = 2048, python::arg("numBitsPerFeature") = 2,
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python::arg("atomInvariantsGenerator") = python::object()),
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"Get an RDKit fingerprint generator\n\n"
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" ARGUMENTS:\n"
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" - minPath: the minimum path length (in bonds) to be included\n"
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" - maxPath: the maximum path length (in bonds) to be included\n"
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" - useHs: toggles inclusion of Hs in paths (if the molecule has "
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"explicit Hs)\n"
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" - branchedPaths: toggles generation of branched subgraphs, not just "
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"linear paths\n"
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" - useBondOrder: toggles inclusion of bond orders in the path "
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"hashes\n"
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" - countSimulation: if set, use count simulation while "
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"generating the fingerprint\n"
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" - countBounds: boundaries for count simulation, corresponding bit "
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"will be set if the count is higher than the number provided for that "
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"spot\n"
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" - fpSize: size of the generated fingerprint, does not affect the "
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"sparse versions\n"
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" - numBitsPerFeature: the number of bits set per path/subgraph "
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"found\n"
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" - atomInvariantsGenerator: atom invariants to be used during "
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"fingerprint generation\n\n"
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"This generator supports the following AdditionalOutput types:\n"
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" - atomToBits: which bits each atom is involved in\n"
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" - atomCounts: how many bits each atom sets\n"
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" - bitPaths: map from bitId to vectors of bond indices for the "
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"individual subgraphs\n\n"
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" RETURNS: FingerprintGenerator\n\n",
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python::return_value_policy<python::manage_new_object>());
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python::def("GetRDKitAtomInvGen", &getRDKitAtomInvGen,
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"Get an RDKit atom invariants generator\n\n"
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" RETURNS: AtomInvariantsGenerator\n\n",
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python::return_value_policy<python::manage_new_object>());
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return;
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}
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} // namespace RDKitFPWrapper
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} // namespace RDKit
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