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//
// Copyright (c) 2022 Brian P Kelley
// 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.
//
#include <RDGeneral/export.h>
#ifndef RD_CDXML_FILEPARSERS_H
#define RD_CDXML_FILEPARSERS_H
#include <RDGeneral/types.h>
#include <string>
#include <iostream>
#include <vector>
namespace RDKit {
class RWMol;
namespace v2 {
namespace CDXMLParser {
enum class CDXMLFormat {
CDXML = 0,
CDX = 1,
Auto = 2
};
//! \brief Returns true if the RDKit was build with ChemDraw CDX support
RDKIT_FILEPARSERS_EXPORT bool hasChemDrawCDXSupport();
struct RDKIT_FILEPARSERS_EXPORT CDXMLParserParams {
bool sanitize = true;
bool removeHs = true;
CDXMLFormat format = CDXMLFormat::Auto;
CDXMLParserParams() = default;
CDXMLParserParams(bool sanitize, bool removeHs, CDXMLFormat format) :
sanitize(sanitize), removeHs(removeHs), format(format) {}
};
//! \brief construct molecules from a CDXML file
//! The RDKit is optionally built with the Revvity ChemDraw parser
//! If this is available, CDX and CDXML can be read, see CDXMLParserParams
//! Note that the CDXML format is large and complex, the RDKit doesn't
//! support full functionality, just the base ones required for molecule and
//! reaction parsing.
//! Note: If the ChemDraw extensions are available, this auto detects between
//! CDXML and CDX
/*!
* \param inStream - string containing the mol block
* \param params - parameters controlling the parsing and post-processing
*/
RDKIT_FILEPARSERS_EXPORT std::vector<std::unique_ptr<RWMol>>
MolsFromCDXMLDataStream(std::istream &inStream,
const CDXMLParserParams ¶ms = CDXMLParserParams());
//! \brief construct molecules from a CDXML file
//! The RDKit is optionally built with the Revvity ChemDraw parser
//! If this is available, CDX and CDXML can be read, see CDXMLParserParams
//! Note that the CDXML format is large and complex, the RDKit doesn't
//! support full functionality, just the base ones required for molecule and
//! reaction parsing.
/*!
* \param fileName - cdxml fileName
* \param params - parameters controlling the parsing and post-processing
*/
RDKIT_FILEPARSERS_EXPORT std::vector<std::unique_ptr<RWMol>> MolsFromCDXMLFile(
const std::string &filename,
const CDXMLParserParams ¶ms = CDXMLParserParams(true, true, CDXMLFormat::Auto));
//! \brief construct molecules from a CDXML block
//! The RDKit is optionally built with the Revvity ChemDraw parser
//! If this is available, CDX and CDXML can be read, see CDXMLParserParams
//! Note that the CDXML format is large and complex, the RDKit doesn't
//! support full functionality, just the base ones required for molecule and
//! reaction parsing.
//! Note: If the ChemDraw extensions are available,
//! CDXMLFormat::Auto attempts to see if the input string is CDXML or CDX
/*!
* \param cdxml - string containing the mol block
* \param params - parameters controlling the parsing and post-processing
*/
RDKIT_FILEPARSERS_EXPORT std::vector<std::unique_ptr<RWMol>> MolsFromCDXML(
const std::string &cdxml,
const CDXMLParserParams ¶ms = CDXMLParserParams(true, true, v2::CDXMLParser::CDXMLFormat::Auto));
} // namespace CDXMLParser
} // namespace v2
inline namespace v1 {
//! \brief construct molecules from a CDXML file
//! Note that the CDXML format is large and complex, the RDKit doesn't support
//! full functionality, just the base ones required for molecule and
//! reaction parsing.
//! Note: If the ChemDraw extensions are available, this auto detects between
//! CDXML and CDX
/*!
* \param inStream - string containing the mol block
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* correctness of the contents.
*/
inline std::vector<std::unique_ptr<RWMol>> CDXMLDataStreamToMols(
std::istream &inStream, bool sanitize = true, bool removeHs = true) {
v2::CDXMLParser::CDXMLParserParams params(
sanitize, removeHs, v2::CDXMLParser::CDXMLFormat::Auto);
return v2::CDXMLParser::MolsFromCDXMLDataStream(inStream, params);
}
//! \brief construct molecules from a CDXML file
//! Note that the CDXML format is large and complex, the RDKit doesn't support
//! full functionality, just the base ones required for molecule and
//! reaction parsing.
//! Note: If the ChemDraw extensions are available,
//! This function uses the file extension to determine the file type, .cdx or .cdxml
//! If not, it defaults to CDXML
/*!
* \param fileName - cdxml fileName
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* correctness of the contents.
*/
inline std::vector<std::unique_ptr<RWMol>> CDXMLFileToMols(
const std::string &filename, bool sanitize = true, bool removeHs = true) {
v2::CDXMLParser::CDXMLParserParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
params.format = v2::CDXMLParser::CDXMLFormat::Auto;
return v2::CDXMLParser::MolsFromCDXMLFile(filename, params);
}
//! \brief construct molecules from a CDXML block
//! Note that the CDXML format is large and complex, the RDKit doesn't support
//! full functionality, just the base ones required for molecule and
//! reaction parsing.
//! Note: to parse CDX files see the CDXParserParams variant of this function
/*!
* \param cdxml - string containing the mol block
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* correctness of the contents.
*/
inline std::vector<std::unique_ptr<RWMol>> CDXMLToMols(const std::string &cdxml,
bool sanitize = true,
bool removeHs = true) {
v2::CDXMLParser::CDXMLParserParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
params.format = v2::CDXMLParser::CDXMLFormat::Auto;
return v2::CDXMLParser::MolsFromCDXML(cdxml, params);
}
} // namespace v1
} // namespace RDKit
#endif // RD_CDXML_FILEPARSERS_H
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