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https://github.com/rdkit/rdkit.git
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131 lines
4.9 KiB
C++
131 lines
4.9 KiB
C++
//
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// Copyright (C) 2020 Shrey Aryan
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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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#ifdef RDK_BUILD_THREADSAFE_SSS
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#define NO_IMPORT_ARRAY
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#include <RDBoost/python.h>
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#include <fstream>
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#include <string>
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// ours
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#include <GraphMol/FileParsers/MultithreadedSDMolSupplier.h>
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#include <GraphMol/Wrap/ContextManagers.h>
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#include <GraphMol/RDKitBase.h>
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#include <RDGeneral/FileParseException.h>
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#include "MolSupplier.h"
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#include "MultithreadedMolSupplier.h"
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namespace python = boost::python;
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using boost_adaptbx::python::streambuf;
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namespace RDKit {
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std::string multiSDMolSupplierClassDoc =
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"A class which concurrently supplies molecules from a text file.\n\
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Please note that this class is still a bit experimental and the API may\n\
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change in future releases.\n\
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\n\
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Usage examples:\n\
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\n\
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1) Lazy evaluation: the molecules might not be constructed until we ask for them:\n\n\
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>>> suppl = MultithreadedSDMolSupplier('in.sdf')\n\
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>>> for mol in suppl:\n\
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... if(mol):\n\
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... mol.GetNumAtoms()\n\
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\n\
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2) Lazy evaluation 2:\n\n\
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>>> suppl = MultithreadedSDMolSupplier('in.sdf')\n\
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>>> while (!suppl.atEnd()):\n\
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... mol = next(mol)\n\
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... if(mol):\n\
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... mol.GetNumAtoms()\n\
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\n";
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std::string multiSdsDocStr =
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"Constructor\n\n\
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ARGUMENTS: \n\
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\n\
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- fileName: name of the file to be read\n\
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\n\
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- sanitize: (optional) toggles sanitization of molecules as they are read.\n\
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Defaults to true.\n\
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\n\
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- removeHs: (optional) removes Hs. Defaults to true.\n\
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\n\
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- strictParsing: (optional) allows strict or lax parsing. Defaults to true.\n\
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\n\
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- numWriterThreads: (optional) number of writer threads. Defaults to 1.\n\
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\n\
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- sizeInputQueue: (optional) size of input/reader queue. Defaults to 5.\n\
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\n\
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- sizeOutputQueue: (optional) size of output/writer queue. Defaults to 5.\n\
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\n";
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struct multiSDMolSup_wrap {
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static void wrap() {
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python::class_<MultithreadedSDMolSupplier, boost::noncopyable>(
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"MultithreadedSDMolSupplier", multiSDMolSupplierClassDoc.c_str(),
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python::init<>(python::args("self")))
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.def(python::init<std::string, bool, bool, bool, unsigned int, size_t,
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size_t>(
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(python::arg("self"), python::arg("fileName"),
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python::arg("sanitize") = true, python::arg("removeHs") = true,
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python::arg("strictParsing") = true,
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python::arg("numWriterThreads") = 1,
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python::arg("sizeInputQueue") = 5,
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python::arg("sizeOutputQueue") = 5),
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multiSdsDocStr.c_str()))
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.def("__iter__",
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(MultithreadedSDMolSupplier * (*)(MultithreadedSDMolSupplier *)) &
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MTMolSupplIter,
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python::return_internal_reference<1>(), python::args("self"))
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.def("__enter__",
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(MultithreadedSDMolSupplier * (*)(MultithreadedSDMolSupplier *)) &
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MolIOEnter,
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python::return_internal_reference<>())
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.def("__exit__", (bool (*)(MultithreadedSDMolSupplier *, python::object,
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python::object, python::object)) &
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MolIOExit)
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.def("__next__",
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(ROMol * (*)(MultithreadedSDMolSupplier *)) & MolForwardSupplNext,
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"Returns the next molecule in the file. Raises _StopIteration_ "
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"on EOF.\n",
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python::return_value_policy<python::manage_new_object>(),
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python::args("self"))
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.def("atEnd", &MultithreadedSDMolSupplier::atEnd, python::args("self"),
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"Returns true if we have read all records else false.\n")
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.def(
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"GetLastRecordId",
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(unsigned int (*)(MultithreadedSDMolSupplier *)) & MTMolSupplLastId,
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python::args("self"),
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"Returns the record id for the last extracted item.\n")
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.def(
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"GetLastItemText",
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(std::string(*)(MultithreadedSDMolSupplier *)) & MTMolSupplLastItem,
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python::args("self"),
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"Returns the text for the last extracted item.\n")
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.def("GetProcessPropertyLists",
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&MultithreadedSDMolSupplier::getProcessPropertyLists,
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python::args("self"),
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"returns whether or not any property lists that are present will "
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"be processed when reading molecules")
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.def("SetProcessPropertyLists",
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&MultithreadedSDMolSupplier::setProcessPropertyLists,
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python::args("self", "val"),
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"sets whether or not any property lists that are present will be "
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"processed when reading molecules");
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};
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};
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} // namespace RDKit
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void wrap_multiSDSupplier() { RDKit::multiSDMolSup_wrap::wrap(); }
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#endif
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