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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 {
namespace v2 {
namespace FileParsers {
//! 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 Parameters &params = Parameters(),
const SmilesMolSupplierParams &parseParams = SmilesMolSupplierParams());
explicit MultithreadedSmilesMolSupplier(
std::istream *inStream, bool takeOwnership = true,
const Parameters &params = Parameters(),
const SmilesMolSupplierParams &parseParams = SmilesMolSupplierParams());
MultithreadedSmilesMolSupplier();
virtual ~MultithreadedSmilesMolSupplier() {close();};
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
RWMol *processMoleculeRecord(const std::string &record,
unsigned int lineNum) override;
protected:
void closeStreams() override;
private:
void initFromSettings(
bool takeOwnership, const Parameters &params,
const SmilesMolSupplierParams &parseParams = SmilesMolSupplierParams());
private:
bool df_end = false; //!< have we reached the end of the file?
int d_line = 0; //!< line number we are currently on
STR_VECT d_props; //!< vector of property names
unsigned int d_currentRecordId = 1; //!< current record id
SmilesMolSupplierParams d_parseParams;
};
} // namespace FileParsers
} // namespace v2
inline namespace v1 {
class RDKIT_FILEPARSERS_EXPORT MultithreadedSmilesMolSupplier
: public MolSupplier {
//! this is an abstract base class to concurrently supply molecules one at a
//! time
public:
using ContainedType = v2::FileParsers::MultithreadedSmilesMolSupplier;
MultithreadedSmilesMolSupplier() {}
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) {
v2::FileParsers::MultithreadedSmilesMolSupplier::Parameters params;
params.numWriterThreads = numWriterThreads;
params.sizeInputQueue = sizeInputQueue;
params.sizeOutputQueue = sizeOutputQueue;
v2::FileParsers::SmilesMolSupplierParams parseParams;
parseParams.delimiter = delimiter;
parseParams.smilesColumn = smilesColumn;
parseParams.nameColumn = nameColumn;
parseParams.titleLine = titleLine;
parseParams.parseParameters.sanitize = sanitize;
dp_supplier.reset(new v2::FileParsers::MultithreadedSmilesMolSupplier(
fileName, params, parseParams));
}
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) {
v2::FileParsers::MultithreadedSmilesMolSupplier::Parameters params;
params.numWriterThreads = numWriterThreads;
params.sizeInputQueue = sizeInputQueue;
params.sizeOutputQueue = sizeOutputQueue;
v2::FileParsers::SmilesMolSupplierParams parseParams;
parseParams.delimiter = delimiter;
parseParams.smilesColumn = smilesColumn;
parseParams.nameColumn = nameColumn;
parseParams.titleLine = titleLine;
parseParams.parseParameters.sanitize = sanitize;
dp_supplier.reset(new v2::FileParsers::MultithreadedSmilesMolSupplier(
inStream, takeOwnership, params, parseParams));
}
//! included for the interface, always returns false
bool getEOFHitOnRead() const {
if (dp_supplier) {
return static_cast<ContainedType *>(dp_supplier.get())->getEOFHitOnRead();
}
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 {
PRECONDITION(dp_supplier, "no supplier");
return static_cast<ContainedType *>(dp_supplier.get())->getLastRecordId();
}
//! returns the text block for the last extracted item
std::string getLastItemText() const {
PRECONDITION(dp_supplier, "no supplier");
return static_cast<ContainedType *>(dp_supplier.get())->getLastItemText();
}
};
} // namespace v1
} // namespace RDKit
#endif
#endif
PRECONDITION
#define PRECONDITION(expr, mess)
Definition Invariant.h:108
MultithreadedMolSupplier.h
RDKit::v1::MolSupplier
Definition MolSupplier.v1API.h:36
RDKit::v1::MolSupplier::reset
void reset()
Definition MolSupplier.v1API.h:46
RDKIT_FILEPARSERS_EXPORT
#define RDKIT_FILEPARSERS_EXPORT
Definition export.h:177
RDKit::v1
Definition ReactionParser.h:91
RDKit::v2::FileParsers
Definition FileParsers.h:30
RDKit::v2
Definition ReactionParser.h:71
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::STR_VECT
std::vector< std::string > STR_VECT
Definition Dict.h:29