CDXMLParser.h

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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 <GraphMol/RWMol.h>
 
#include <RDGeneral/types.h>
#include <string>
#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;
  bool parseQueries = false;
  bool strictQueryParsing = false;
 
  CDXMLParserParams() = default;
  CDXMLParserParams(bool sanitize, bool removeHs, CDXMLFormat format,
                    bool parseQueries = false, bool strictQueryParsing = false)
     : sanitize(sanitize),
       removeHs(removeHs),
       format(format),
       parseQueries(parseQueries),
       strictQueryParsing(strictQueryParsing) {}
};
 
//! \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 &params = 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 &params = 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 &params =
        CDXMLParserParams(true, true, v2::CDXMLParser::CDXMLFormat::Auto));
 
//! \brief write a CDX or CDXML block from a molecule
//! The RDKit is optionally built with the Revvity ChemDraw parser
//! If this is available, CDX and CDXML can be written
//!   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 unavailable, an exception will be thrown
//!  please use the support function hasChemDrawCDXSupport() to check
//!  whether ChemDraw writing support is enabled.
//! Note: For CDXML the contents of the std::string are UTF-8
//!       For CDX they are the binary bytes.
/*!
 *   \param mol - Molecule to write
 *   \param format - CDXMLFormat to use, CDX or CDXML (default)
 */
RDKIT_FILEPARSERS_EXPORT std::string MolToCDXMLBlock(
    const RWMol &mol,
    CDXMLFormat format = CDXMLFormat::CDXML);
}  // 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