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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_SD_MOL_SUPPLIER
#define MULTITHREADED_SD_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 MultithreadedSDMolSupplier
: public MultithreadedMolSupplier {
public:
explicit MultithreadedSDMolSupplier(
const std::string &fileName, const Parameters ¶ms = Parameters(),
const MolFileParserParams &parseParams = MolFileParserParams());
explicit MultithreadedSDMolSupplier(
std::istream *inStream, bool takeOwnership = true,
const Parameters ¶ms = Parameters(),
const MolFileParserParams &parseParams = MolFileParserParams());
MultithreadedSDMolSupplier();
~MultithreadedSDMolSupplier() override;
void init() override {}
void checkForEnd();
bool getEnd() const override;
void setProcessPropertyLists(bool val) { df_processPropertyLists = val; }
bool getProcessPropertyLists() const { return df_processPropertyLists; }
bool getEOFHitOnRead() const { return df_eofHitOnRead; }
//! reads next record and returns whether or not EOF was hit
bool extractNextRecord(std::string &record, unsigned int &lineNum,
unsigned int &index) override;
void readMolProps(RWMol &mol, std::istringstream &inStream);
//! parses the record and returns the resulting molecule
RWMol *processMoleculeRecord(const std::string &record,
unsigned int lineNum) override;
private:
void initFromSettings(bool takeOwnership, const Parameters ¶ms,
const MolFileParserParams &parseParams);
bool df_end = false; //!< have we reached the end of the file?
int d_line = 0; //!< line number we are currently on
bool df_processPropertyLists = true;
bool df_eofHitOnRead = false;
unsigned int d_currentRecordId = 1; //!< current record id
MolFileParserParams d_parseParams;
};
} // namespace FileParsers
} // namespace v2
inline namespace v1 {
class RDKIT_FILEPARSERS_EXPORT MultithreadedSDMolSupplier : public MolSupplier {
//! this is an abstract base class to concurrently supply molecules one at a
//! time
public:
using ContainedType = v2::FileParsers::MultithreadedSDMolSupplier;
MultithreadedSDMolSupplier() {}
explicit MultithreadedSDMolSupplier(
const std::string &fileName, bool sanitize = true, bool removeHs = true,
bool strictParsing = true, unsigned int numWriterThreads = 1,
size_t sizeInputQueue = 5, size_t sizeOutputQueue = 5) {
v2::FileParsers::MultithreadedSDMolSupplier::Parameters params;
params.numWriterThreads = numWriterThreads;
params.sizeInputQueue = sizeInputQueue;
params.sizeOutputQueue = sizeOutputQueue;
v2::FileParsers::MolFileParserParams parseParams;
parseParams.sanitize = sanitize;
parseParams.removeHs = removeHs;
parseParams.strictParsing = strictParsing;
dp_supplier.reset(new v2::FileParsers::MultithreadedSDMolSupplier(
fileName, params, parseParams));
}
explicit MultithreadedSDMolSupplier(
std::istream *inStream, bool takeOwnership = true, bool sanitize = true,
bool removeHs = true, bool strictParsing = true,
unsigned int numWriterThreads = 1, size_t sizeInputQueue = 5,
size_t sizeOutputQueue = 5) {
v2::FileParsers::MultithreadedSDMolSupplier::Parameters params;
params.numWriterThreads = numWriterThreads;
params.sizeInputQueue = sizeInputQueue;
params.sizeOutputQueue = sizeOutputQueue;
v2::FileParsers::MolFileParserParams parseParams;
parseParams.sanitize = sanitize;
parseParams.removeHs = removeHs;
parseParams.strictParsing = strictParsing;
dp_supplier.reset(new v2::FileParsers::MultithreadedSDMolSupplier(
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();
}
void setProcessPropertyLists(bool val) {
PRECONDITION(dp_supplier, "no supplier");
static_cast<ContainedType *>(dp_supplier.get())
->setProcessPropertyLists(val);
}
bool getProcessPropertyLists() const {
PRECONDITION(dp_supplier, "no supplier");
return static_cast<ContainedType *>(dp_supplier.get())
->getProcessPropertyLists();
}
};
} // namespace v1
} // namespace RDKit
#endif
#endif
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