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MultithreadedSmilesMolSupplier.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_SMILES_MOL_SUPPLIER
#define MULTITHREADED_SMILES_MOL_SUPPLIER
#include "MultithreadedMolSupplier.h"
namespace RDKit {
//! This class is still a bit experimental and the public API may change
//! in future releases.
class RDKIT_FILEPARSERS_EXPORT MultithreadedSmilesMolSupplier
: public MultithreadedMolSupplier {
public:
explicit MultithreadedSmilesMolSupplier(
const std::string &fileName, const std::string &delimiter = " \t",
int smilesColumn = 0, int nameColumn = 1, bool titleLine = true,
bool sanitize = true, unsigned int numWriterThreads = 1,
size_t sizeInputQueue = 5, size_t sizeOutputQueue = 5);
explicit MultithreadedSmilesMolSupplier(
std::istream *inStream, bool takeOwnership = true,
const std::string &delimiter = " \t", int smilesColumn = 0,
int nameColumn = 1, bool titleLine = true, bool sanitize = true,
unsigned int numWriterThreads = 1, size_t sizeInputQueue = 5,
size_t sizeOutputQueue = 5);
MultithreadedSmilesMolSupplier();
~MultithreadedSmilesMolSupplier() override;
void init() override {}
//! returns df_end
bool getEnd() const override;
//! reads and processes the title line
void processTitleLine();
//! reads next record and returns whether or not EOF was hit
bool extractNextRecord(std::string &record, unsigned int &lineNum,
unsigned int &index) override;
//! parses the record and returns the resulting molecule
ROMol *processMoleculeRecord(const std::string &record,
unsigned int lineNum) override;
private:
void initFromSettings(bool takeOwnership, const std::string &delimiter,
int smilesColumn, int nameColumn, bool titleLine,
bool sanitize, unsigned int numWriterThreads,
size_t sizeInputQueue, size_t sizeOutputQueue);
private:
bool df_end = false; //!< have we reached the end of the file?
int d_line = 0; //!< line number we are currently on
std::string d_delim; //!< the delimiter string
bool df_sanitize = true; //!< sanitize molecules before returning them?
STR_VECT d_props; //!< vector of property names
bool df_title = true; //!< do we have a title line?
int d_smi = 0; //!< column id for the smile string
int d_name = 1; //!< column id for the name
unsigned int d_currentRecordId = 1; //!< current record id
};
} // namespace RDKit
#endif
#endif
MultithreadedMolSupplier.h
RDKIT_FILEPARSERS_EXPORT
#define RDKIT_FILEPARSERS_EXPORT
Definition export.h:161
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::STR_VECT
std::vector< std::string > STR_VECT
Definition Dict.h:29
RDKit::rdvalue_is
bool rdvalue_is(const RDValue_cast_t)
Definition RDValue-doublemagic.h:372