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