mirror of
https://github.com/rdkit/rdkit.git
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db93262a3e
* add safeSetattr to varios params objects * added safeSetattr to further params / options
99 lines
4.0 KiB
C++
99 lines
4.0 KiB
C++
//
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// Copyright (C) 2024 Greg Landrum 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 <RDBoost/python.h>
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#include <RDBoost/Wrap.h>
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#include <GraphMol/MolProcessing/MolProcessing.h>
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#include <GraphMol/FileParsers/GeneralFileReader.h>
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namespace python = boost::python;
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using namespace RDKit;
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namespace {
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template <typename OutputType>
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python::tuple getFingerprintsHelper(
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const std::string &fileName, python::object pyGenerator,
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const GeneralMolSupplier::SupplierOptions &options) {
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FingerprintGenerator<OutputType> *generator = nullptr;
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if (pyGenerator) {
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generator =
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python::extract<FingerprintGenerator<OutputType> *>(pyGenerator);
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}
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std::vector<std::unique_ptr<ExplicitBitVect>> fps;
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{
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NOGIL gil;
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fps = MolProcessing::getFingerprintsForMolsInFile(fileName, options,
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generator);
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}
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python::list pyFingerprints;
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boost::python::manage_new_object::apply<ExplicitBitVect *>::type converter;
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for (auto &fp : fps) {
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// transfer ownership to python
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python::handle<> handle(converter(fp.release()));
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pyFingerprints.append(handle);
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}
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return python::tuple(pyFingerprints);
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}
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} // namespace
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BOOST_PYTHON_MODULE(rdMolProcessing) {
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python::scope().attr("__doc__") =
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"Module containing functions for working with groups of molecules";
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python::class_<GeneralMolSupplier::SupplierOptions>(
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"SupplierOptions", "Supplier Options", python::init<>())
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.def_readwrite("numThreads",
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&GeneralMolSupplier::SupplierOptions::numWriterThreads,
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"the number of threads to use while working")
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.def_readwrite("sanitize", &GeneralMolSupplier::SupplierOptions::sanitize)
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.def_readwrite("removeHs", &GeneralMolSupplier::SupplierOptions::removeHs)
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.def_readwrite("strictParsing",
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&GeneralMolSupplier::SupplierOptions::strictParsing)
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.def_readwrite("delimiter",
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&GeneralMolSupplier::SupplierOptions::delimiter,
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"used for SMILES files")
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.def_readwrite("smilesColumn",
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&GeneralMolSupplier::SupplierOptions::smilesColumn,
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"used for SMILES files")
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.def_readwrite("nameColumn",
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&GeneralMolSupplier::SupplierOptions::nameColumn,
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"used for SMILES files")
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.def_readwrite("titleLine",
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&GeneralMolSupplier::SupplierOptions::titleLine,
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"used for SMILES files")
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.def_readwrite("nameRecord",
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&GeneralMolSupplier::SupplierOptions::nameRecord,
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"used for TDT files")
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.def_readwrite("confId2D", &GeneralMolSupplier::SupplierOptions::confId2D,
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"used for TDT files")
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.def_readwrite("confId3D", &GeneralMolSupplier::SupplierOptions::confId3D,
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"used for TDT files")
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.def("__setattr__", &safeSetattr);
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python::def(
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"GetFingerprintsForMolsInFile",
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(python::tuple(*)(const std::string &, python::object,
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const GeneralMolSupplier::SupplierOptions &))
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getFingerprintsHelper<std::uint32_t>,
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(python::arg("filename"), python::arg("generator") = python::object(),
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python::arg("options") = GeneralMolSupplier::SupplierOptions()),
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"returns the fingerprints for the molecules in a file (32 bit version)");
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python::def(
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"GetFingerprintsForMolsInFile",
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(python::tuple(*)(const std::string &, python::object,
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const GeneralMolSupplier::SupplierOptions &))
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getFingerprintsHelper<std::uint64_t>,
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(python::arg("filename"), python::arg("generator") = python::object(),
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python::arg("options") = GeneralMolSupplier::SupplierOptions()),
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"returns the fingerprints for the molecules in a file (64 bit version)");
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}
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