GeneralFileReader.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.
//
#ifndef GENERAL_FILE_READER_H
#define GENERAL_FILE_READER_H
#include <RDGeneral/BadFileException.h>
#include <RDStreams/streams.h>
#include <boost/algorithm/string.hpp>
#include <iostream>
#include <memory>
#include <string>
#include <vector>
#include "MolSupplier.h"
#include "MultithreadedSDMolSupplier.h"
#include "MultithreadedSmilesMolSupplier.h"
namespace RDKit {
namespace GeneralMolSupplier {
struct SupplierOptions {
bool takeOwnership = true;
bool sanitize = true;
bool removeHs = true;
bool strictParsing = true;
std::string delimiter = "\t";
int smilesColumn = 0;
int nameColumn = 1;
bool titleLine = true;
std::string nameRecord = "";
int confId2D = -1;
int confId3D = 0;
unsigned int numWriterThreads = 0;
};
//! current supported file formats
const std::vector<std::string> supportedFileFormats{
"sdf", "mae", "maegz", "sdfgz", "smi", "csv", "txt", "tsv", "tdt"};
//! current supported compression formats
const std::vector<std::string> supportedCompressionFormats{"gz"};
//! given file path determines the file and compression format
//! returns true on success, otherwise false
//! Note: Error handeling is done in the getSupplier method
void determineFormat(const std::string path, std::string& fileFormat,
std::string& compressionFormat) {
//! filename without compression format
std::string basename;
//! Special case maegz.
//! NOTE: also supporting case-insensitive filesystems
if (boost::algorithm::iends_with(path, ".maegz")) {
fileFormat = "mae";
compressionFormat = "gz";
return;
} else if (boost::algorithm::iends_with(path, ".sdfgz")) {
fileFormat = "sdf";
compressionFormat = "gz";
return;
} else if (boost::algorithm::iends_with(path, ".gz")) {
compressionFormat = "gz";
basename = path.substr(0, path.size() - 3);
} else if (boost::algorithm::iends_with(path, ".zst") ||
boost::algorithm::iends_with(path, ".bz2") ||
boost::algorithm::iends_with(path, ".7z")) {
throw BadFileException(
"Unsupported compression extension (.zst, .bz2, .7z) given path: " +
path);
} else {
basename = path;
compressionFormat = "";
}
for (auto const& suffix : supportedFileFormats) {
if (boost::algorithm::iends_with(basename, "." + suffix)) {
fileFormat = suffix;
return;
}
}
throw BadFileException(
"Unsupported structure or compression extension given path: " + path);
}
//! returns a new MolSupplier object based on the file name instantiated
//! with the relevant options provided in the SupplierOptions struct
/*!
<b>Note:</b>
- the caller owns the memory and therefore the pointer must be deleted
*/
std::unique_ptr<MolSupplier> getSupplier(const std::string& path,
const struct SupplierOptions& opt) {
std::string fileFormat = "";
std::string compressionFormat = "";
//! get the file and compression format form the path
determineFormat(path, fileFormat, compressionFormat);
std::istream* strm;
if (compressionFormat.empty()) {
strm = new std::ifstream(path.c_str(), std::ios::in | std::ios::binary);
} else {
strm = new gzstream(path);
}
//! Dispatch to the appropriate supplier
if (fileFormat == "sdf") {
#ifdef RDK_THREADSAFE_SSS
if (opt.numWriterThreads > 0) {
MultithreadedSDMolSupplier* sdsup = new MultithreadedSDMolSupplier(
strm, true, opt.sanitize, opt.removeHs, opt.strictParsing,
opt.numWriterThreads);
std::unique_ptr<MolSupplier> p(sdsup);
return p;
}
#endif
ForwardSDMolSupplier* sdsup = new ForwardSDMolSupplier(
strm, true, opt.sanitize, opt.removeHs, opt.strictParsing);
std::unique_ptr<MolSupplier> p(sdsup);
return p;
}
else if (fileFormat == "smi" || fileFormat == "csv" || fileFormat == "txt" ||
fileFormat == "tsv") {
#ifdef RDK_THREADSAFE_SSS
if (opt.numWriterThreads > 0) {
MultithreadedSmilesMolSupplier* smsup =
new MultithreadedSmilesMolSupplier(
strm, true, opt.delimiter, opt.smilesColumn, opt.nameColumn,
opt.titleLine, opt.sanitize, opt.numWriterThreads);
std::unique_ptr<MolSupplier> p(smsup);
return p;
}
#endif
SmilesMolSupplier* smsup =
new SmilesMolSupplier(strm, true, opt.delimiter, opt.smilesColumn,
opt.nameColumn, opt.titleLine, opt.sanitize);
std::unique_ptr<MolSupplier> p(smsup);
return p;
}
#ifdef RDK_BUILD_MAEPARSER_SUPPORT
else if (fileFormat == "mae") {
MaeMolSupplier* maesup =
new MaeMolSupplier(strm, true, opt.sanitize, opt.removeHs);
std::unique_ptr<MolSupplier> p(maesup);
return p;
}
#endif
else if (fileFormat == "tdt") {
TDTMolSupplier* tdtsup = new TDTMolSupplier(
strm, true, opt.nameRecord, opt.confId2D, opt.confId3D, opt.sanitize);
std::unique_ptr<MolSupplier> p(tdtsup);
return p;
}
throw BadFileException("Unsupported fileFormat: " + fileFormat);
}
} // namespace GeneralMolSupplier
} // namespace RDKit
#endif
BadFileException.h
MolSupplier.h
MultithreadedSDMolSupplier.h
MultithreadedSmilesMolSupplier.h
RDKit::BadFileException
used by various file parsing classes to indicate a bad file
Definition: BadFileException.h:22
RDKit::ForwardSDMolSupplier
Definition: MolSupplier.h:119
RDKit::SmilesMolSupplier
lazy file parser for Smiles tables
Definition: MolSupplier.h:230
RDKit::TDTMolSupplier
lazy file parser for TDT files
Definition: MolSupplier.h:313
RDKit::GeneralMolSupplier::supportedCompressionFormats
const std::vector< std::string > supportedCompressionFormats
current supported compression formats
Definition: GeneralFileReader.h:48
RDKit::GeneralMolSupplier::supportedFileFormats
const std::vector< std::string > supportedFileFormats
current supported file formats
Definition: GeneralFileReader.h:45
RDKit::GeneralMolSupplier::determineFormat
void determineFormat(const std::string path, std::string &fileFormat, std::string &compressionFormat)
Definition: GeneralFileReader.h:54
RDKit::GeneralMolSupplier::getSupplier
std::unique_ptr< MolSupplier > getSupplier(const std::string &path, const struct SupplierOptions &opt)
Definition: GeneralFileReader.h:98
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::GeneralMolSupplier::SupplierOptions
Definition: GeneralFileReader.h:27
RDKit::GeneralMolSupplier::SupplierOptions::nameColumn
int nameColumn
Definition: GeneralFileReader.h:35
RDKit::GeneralMolSupplier::SupplierOptions::strictParsing
bool strictParsing
Definition: GeneralFileReader.h:31
RDKit::GeneralMolSupplier::SupplierOptions::smilesColumn
int smilesColumn
Definition: GeneralFileReader.h:34
RDKit::GeneralMolSupplier::SupplierOptions::confId3D
int confId3D
Definition: GeneralFileReader.h:40
RDKit::GeneralMolSupplier::SupplierOptions::sanitize
bool sanitize
Definition: GeneralFileReader.h:29
RDKit::GeneralMolSupplier::SupplierOptions::titleLine
bool titleLine
Definition: GeneralFileReader.h:36
RDKit::GeneralMolSupplier::SupplierOptions::numWriterThreads
unsigned int numWriterThreads
Definition: GeneralFileReader.h:42
RDKit::GeneralMolSupplier::SupplierOptions::nameRecord
std::string nameRecord
Definition: GeneralFileReader.h:38
RDKit::GeneralMolSupplier::SupplierOptions::takeOwnership
bool takeOwnership
Definition: GeneralFileReader.h:28
RDKit::GeneralMolSupplier::SupplierOptions::delimiter
std::string delimiter
Definition: GeneralFileReader.h:33
RDKit::GeneralMolSupplier::SupplierOptions::removeHs
bool removeHs
Definition: GeneralFileReader.h:30
RDKit::GeneralMolSupplier::SupplierOptions::confId2D
int confId2D
Definition: GeneralFileReader.h:39