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//
// Copyright (C) 2020 Shrey Aryan
//
// @@ 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.
//
#ifdef RDK_BUILD_THREADSAFE_SSS
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <fstream>
#include <string>
// ours
#include <GraphMol/FileParsers/MultithreadedSDMolSupplier.h>
#include <GraphMol/Wrap/ContextManagers.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/FileParseException.h>
#include "MolSupplier.h"
#include "MultithreadedMolSupplier.h"
namespace python = boost::python;
using boost_adaptbx::python::streambuf;
namespace RDKit {
std::string multiSDMolSupplierClassDoc =
"A class which concurrently supplies molecules from a text file.\n\
Please note that this class is still a bit experimental and the API may\n\
change in future releases.\n\
\n\
Usage examples:\n\
\n\
1) Lazy evaluation: the molecules might not be constructed until we ask for them:\n\n\
>>> suppl = MultithreadedSDMolSupplier('in.sdf')\n\
>>> for mol in suppl:\n\
... if(mol):\n\
... mol.GetNumAtoms()\n\
\n\
2) Lazy evaluation 2:\n\n\
>>> suppl = MultithreadedSDMolSupplier('in.sdf')\n\
>>> while (!suppl.atEnd()):\n\
... mol = next(mol)\n\
... if(mol):\n\
... mol.GetNumAtoms()\n\
\n";
std::string multiSdsDocStr =
"Constructor\n\n\
ARGUMENTS: \n\
\n\
- fileName: name of the file to be read\n\
\n\
- sanitize: (optional) toggles sanitization of molecules as they are read.\n\
Defaults to true.\n\
\n\
- removeHs: (optional) removes Hs. Defaults to true.\n\
\n\
- strictParsing: (optional) allows strict or lax parsing. Defaults to true.\n\
\n\
- numWriterThreads: (optional) number of writer threads. Defaults to 1.\n\
\n\
- sizeInputQueue: (optional) size of input/reader queue. Defaults to 5.\n\
\n\
- sizeOutputQueue: (optional) size of output/writer queue. Defaults to 5.\n\
\n";
#if 0
// FIX: disabled until we figure out how to make this stable
MultithreadedSDMolSupplier* MTMolSupplStream(
python::object& input, bool sanitize = true, bool removeHs = true,
bool strictParsing = true, unsigned int numWriterThreads = 1,
size_t sizeInputQueue = 5, size_t sizeOutputQueue = 5) {
auto* sb = new streambuf(input, 'b');
auto* inStream = new streambuf::istream(*sb);
MultithreadedSDMolSupplier* sup = new MultithreadedSDMolSupplier(
inStream, true, sanitize, removeHs, strictParsing, numWriterThreads,
sizeInputQueue, sizeOutputQueue);
return sup;
}
#endif
struct multiSDMolSup_wrap {
static void wrap() {
#if 0
// FIX: disabled until we make it stable and figure out an API that we're happy with
python::def(
"SDMolSupplierFromStream", MTMolSupplStream,
"Returns MultithreadedSDMolSupplier object constructed from a file object or stream",
(python::arg("fileobj"), python::arg("sanitize") = true,
python::arg("removeHs") = true, python::arg("strictParsing") = true,
python::arg("numWriterThreads") = 1, python::arg("sizeInputQueue") = 5,
python::arg("sizeOutputQueue") = 5),
python::with_custodian_and_ward_postcall<
0, 1, python::return_value_policy<python::manage_new_object>>());
#endif
python::class_<MultithreadedSDMolSupplier, boost::noncopyable>(
"MultithreadedSDMolSupplier", multiSDMolSupplierClassDoc.c_str(),
python::init<>())
.def(python::init<std::string, bool, bool, bool, unsigned int, size_t,
size_t>(
(python::arg("fileName"), python::arg("sanitize") = true,
python::arg("removeHs") = true,
python::arg("strictParsing") = true,
python::arg("numWriterThreads") = 1,
python::arg("sizeInputQueue") = 5,
python::arg("sizeOutputQueue") = 5),
multiSdsDocStr.c_str()))
.def("__iter__",
(MultithreadedSDMolSupplier * (*)(MultithreadedSDMolSupplier *)) &
MTMolSupplIter,
python::return_internal_reference<1>())
.def("__enter__",
(MultithreadedSDMolSupplier * (*)(MultithreadedSDMolSupplier *)) &
MolIOEnter,
python::return_internal_reference<>())
.def("__exit__", (bool (*)(MultithreadedSDMolSupplier *, python::object,
python::object, python::object)) &
MolIOExit)
.def("__next__",
(ROMol * (*)(MultithreadedSDMolSupplier *)) & MolForwardSupplNext,
"Returns the next molecule in the file. Raises _StopIteration_ "
"on EOF.\n",
python::return_value_policy<python::manage_new_object>())
.def("atEnd", &MultithreadedSDMolSupplier::atEnd,
"Returns true if we have read all records else false.\n")
.def(
"GetLastRecordId",
(unsigned int (*)(MultithreadedSDMolSupplier *)) & MTMolSupplLastId,
"Returns the record id for the last extracted item.\n")
.def(
"GetLastItemText",
(std::string(*)(MultithreadedSDMolSupplier *)) & MTMolSupplLastItem,
"Returns the text for the last extracted item.\n")
.def("GetProcessPropertyLists",
&MultithreadedSDMolSupplier::getProcessPropertyLists,
"returns whether or not any property lists that are present will "
"be processed when reading molecules")
.def("SetProcessPropertyLists",
&MultithreadedSDMolSupplier::setProcessPropertyLists,
"sets whether or not any property lists that are present will be "
"processed when reading molecules");
};
};
} // namespace RDKit
void wrap_multiSDSupplier() { RDKit::multiSDMolSup_wrap::wrap(); }
#endif
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