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MultithreadedMolSupplier.h
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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
#ifndef MULTITHREADED_MOL_SUPPLIER
#define MULTITHREADED_MOL_SUPPLIER
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/ConcurrentQueue.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/RDThreads.h>
#include <RDGeneral/StreamOps.h>
#include <atomic>
#include <boost/tokenizer.hpp>
#include "FileParsers.h"
#include "MolSupplier.h"
typedef boost::tokenizer<boost::char_separator<char>> tokenizer;
namespace RDKit {
class RDKIT_FILEPARSERS_EXPORT MultithreadedMolSupplier : public MolSupplier {
//! this is an abstract base class to concurrently supply molecules one at a
//! time
public:
MultithreadedMolSupplier() {}
~MultithreadedMolSupplier() override;
//! pop elements from the output queue
ROMol *next() override;
//! returns true when all records have been read from the supplier
bool atEnd() override;
//! included for the interface, always returns false
bool getEOFHitOnRead() const { return false; }
//! returns the record id of the last extracted item
//! Note: d_LastRecordId = 0, initially therefore the value 0 is returned
//! if and only if the function is called before extracting the first
//! record
unsigned int getLastRecordId() const;
//! returns the text block for the last extracted item
std::string getLastItemText() const;
protected:
//! starts reader and writer threads
void startThreads();
private:
//! reads lines from input stream to populate the input queue
void reader();
//! parses lines from the input queue converting them to ROMol objects
//! populating the output queue
void writer();
//! finalizes the reader and writer threads
void endThreads();
//! disable automatic copy constructors and assignment operators
//! for this class and its subclasses. They will likely be
//! carrying around stream pointers and copying those is a recipe
//! for disaster.
MultithreadedMolSupplier(const MultithreadedMolSupplier &);
MultithreadedMolSupplier &operator=(const MultithreadedMolSupplier &);
//! not yet implemented
void reset() override;
void init() override = 0;
virtual bool getEnd() const = 0;
//! extracts next record from the input file or stream
virtual bool extractNextRecord(std::string &record, unsigned int &lineNum,
unsigned int &index) = 0;
//! processes the record into an ROMol object
virtual ROMol *processMoleculeRecord(const std::string &record,
unsigned int lineNum) = 0;
private:
std::atomic<unsigned int> d_threadCounter{1}; //!< thread counter
std::vector<std::thread> d_writerThreads; //!< vector writer threads
std::thread d_readerThread; //!< single reader thread
protected:
std::atomic<unsigned int> d_lastRecordId =
0; //!< stores last extracted record id
std::string d_lastItemText; //!< stores last extracted record
const unsigned int d_numReaderThread = 1; //!< number of reader thread
unsigned int d_numWriterThreads; //!< number of writer threads
size_t d_sizeInputQueue; //!< size of input queue
size_t d_sizeOutputQueue; //!< size of output queue
ConcurrentQueue<std::tuple<std::string, unsigned int, unsigned int>>
*d_inputQueue; //!< concurrent input queue
ConcurrentQueue<std::tuple<ROMol *, std::string, unsigned int>>
*d_outputQueue; //!< concurrent output queue
};
} // namespace RDKit
#endif
#endif
BadFileException.h
ConcurrentQueue.h
FileParseException.h
FileParsers.h
tokenizer
boost::tokenizer< boost::char_separator< char > > tokenizer
Definition LinkNode.h:18
MolSupplier.h
RDLog.h
RDThreads.h
SmilesParse.h
StreamOps.h
RDKIT_FILEPARSERS_EXPORT
#define RDKIT_FILEPARSERS_EXPORT
Definition export.h:161
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::rdvalue_is
bool rdvalue_is(const RDValue_cast_t)
Definition RDValue-doublemagic.h:372