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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_THREADSAFE_SSS
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <string>
// ours
#include <GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/FileParseException.h>
#include "MolSupplier.h"
#include "MultithreadedMolSupplier.h"
namespace python = boost::python;
namespace RDKit {
std::string multiSmilesMolSupplierClassDoc =
"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 = MultithreadedSmilesMolSupplier('in.smi')\n\
>>> for mol in suppl:\n\
... if(mol):\n\
... mol.GetNumAtoms()\n\
\n\
2) Lazy evaluation 2:\n\n\
>>> suppl = MultithreadedSmilesMolSupplier('in.smi')\n\
>>> while (!suppl.atEnd()):\n\
... mol = next(mol)\n\
... if(mol):\n\
... mol.GetNumAtoms()\n\
\n";
std::string multiSmsDocStr =
"Constructor\n\n\
ARGUMENTS: \n\
\n\
- fileName: name of the file to be read\n\
\n\
- delimiter: (optional) text delimiter (a string). Defauts to ' \t'.\n\
\n\
- smilesColumn: (optional) index of the column containing the SMILES\n\
data. Defaults to 0.\n\
\n\
- nameColumn: (optional) index of the column containing molecule names.\n\
Defaults to 1.\n\
\n\
- titleLine: (optional) set this toggle if the file contains a title line.\n\
Defaults to true.\n\
\n\
- sanitize: (optional) toggles sanitization of molecules as they are read.\n\
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";
struct multiSmiMolSup_wrap {
static void wrap() {
python::class_<MultithreadedSmilesMolSupplier, boost::noncopyable>(
"MultithreadedSmilesMolSupplier",
multiSmilesMolSupplierClassDoc.c_str(), python::init<>())
.def(python::init<std::string, std::string, int, int, bool, bool,
unsigned int, size_t, size_t>(
(python::arg("fileName"), python::arg("delimiter") = " \t",
python::arg("smilesColumn") = 0, python::arg("nameColumn") = 1,
python::arg("titleLine") = true, python::arg("sanitize") = true,
python::arg("numWriterThreads") = 1,
python::arg("sizeInputQueue") = 5,
python::arg("sizeOutputQueue") = 5),
multiSmsDocStr.c_str()))
.def("__iter__",
(MultithreadedSmilesMolSupplier *
(*)(MultithreadedSmilesMolSupplier *)) &
MTMolSupplIter,
python::return_internal_reference<1>())
.def("__next__",
(ROMol * (*)(MultithreadedSmilesMolSupplier *)) &
MolForwardSupplNext,
"Returns the next molecule in the file. Raises _StopIteration_ "
"on EOF.\n",
python::return_value_policy<python::manage_new_object>())
.def("atEnd", &MultithreadedSmilesMolSupplier::atEnd,
"Returns true if we have read all records else false.\n")
.def("GetLastRecordId",
(unsigned int (*)(MultithreadedSmilesMolSupplier *)) &
MTMolSupplLastId,
"Returns the record id for the last extracted item.\n")
.def("GetLastItemText",
(std::string(*)(MultithreadedSmilesMolSupplier *)) &
MTMolSupplLastItem,
"Returns the text for the last extracted item.\n");
};
};
} // namespace RDKit
void wrap_multiSmiSupplier() { RDKit::multiSmiMolSup_wrap::wrap(); }
#endif
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