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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
109 lines
4.5 KiB
C++
109 lines
4.5 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/AtomPairGenerator.h>
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#include <RDBoost/Wrap.h>
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using namespace RDKit;
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using namespace RDKit::AtomPair;
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namespace python = boost::python;
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namespace RDKit {
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namespace AtomPairWrapper {
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template <typename OutputType>
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FingerprintGenerator<OutputType> *getAtomPairGenerator(
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unsigned int minDistance, unsigned int maxDistance, bool includeChirality,
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bool use2D, bool countSimulation, python::object &py_countBounds,
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std::uint32_t fpSize, 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 AtomPair::getAtomPairGenerator<OutputType>(
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minDistance, maxDistance, includeChirality, use2D,
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atomInvariantsGenerator, countSimulation, fpSize, countBounds, true);
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}
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AtomInvariantsGenerator *getAtomPairAtomInvGen(const bool includeChirality) {
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return new AtomPairAtomInvGenerator(includeChirality);
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}
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void exportAtompair() {
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python::class_<AtomPair::AtomPairArguments,
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python::bases<FingerprintArguments>, boost::noncopyable>(
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"AtomPairFingerprintOptions", python::no_init)
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.def_readwrite("use2D", &AtomPair::AtomPairArguments::df_use2D,
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"use 2D distances")
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.def_readwrite("minDistance", &AtomPair::AtomPairArguments::d_minDistance,
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"minimum distance to be included")
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.def_readwrite("maxDistance", &AtomPair::AtomPairArguments::d_maxDistance,
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"maximum distance to be included");
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python::def(
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"GetAtomPairGenerator", &getAtomPairGenerator<std::uint64_t>,
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(python::arg("minDistance") = 1,
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python::arg("maxDistance") = AtomPair::maxPathLen - 1,
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python::arg("includeChirality") = false, python::arg("use2D") = true,
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python::arg("countSimulation") = true,
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python::arg("countBounds") = python::object(),
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python::arg("fpSize") = 2048,
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python::arg("atomInvariantsGenerator") = python::object()),
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"Get an atom pair fingerprint generator\n\n"
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" ARGUMENTS:\n"
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" - minDistance: minimum distance between atoms to be considered in a "
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"pair, default is 1 bond\n"
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" - maxDistance: maximum distance between atoms to be considered in a "
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"pair, default is maxPathLen-1 bonds\n"
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" - includeChirality: if set, chirality will be used in the atom "
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"invariants, this is ignored if atomInvariantsGenerator is provided\n"
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" - use2D: if set, the 2D (topological) distance matrix will be "
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"used\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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" - 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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" - bitInfoMap: map from bitId to (atomId, radius) pairs\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("GetAtomPairAtomInvGen", &getAtomPairAtomInvGen,
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(python::arg("includeChirality") = false),
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"Get an atom pair atom-invariant generator\n\n"
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" ARGUMENTS:\n"
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" - includeChirality: if set, chirality will be taken into "
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"account for invariants\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 AtomPairWrapper
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} // namespace RDKit
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