MarvinParser.h

Go to the documentation of this file.

//
//  Copyright (C) 2022-2023 Tad Hurst, Greg Landrum and other RDKit contributors
//
//   @@ 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_MARVINPARSER_H
#define RD_MARVINPARSER_H
 
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ChemReactions/Reaction.h>
 
#include <string>
#include <iostream>
 
namespace RDKit {
namespace v2 {
namespace MarvinParser {
RDKIT_MARVINPARSER_EXPORT bool MrvFileIsReaction(const std::string &fname);
RDKIT_MARVINPARSER_EXPORT bool MrvDataStreamIsReaction(std::istream &inStream);
RDKIT_MARVINPARSER_EXPORT bool MrvBlockIsReaction(
    const std::string &molmrvText);
 
struct RDKIT_MARVINPARSER_EXPORT MrvParserParams {
  bool sanitize = true; /**< sanitize the molecule after building it */
  bool removeHs = true; /**< remove Hs after constructing the molecule */
};
 
RDKIT_MARVINPARSER_EXPORT std::unique_ptr<RWMol> MolFromMrvDataStream(
    std::istream &inStream, const MrvParserParams &params = MrvParserParams());
RDKIT_MARVINPARSER_EXPORT std::unique_ptr<RWMol> MolFromMrvBlock(
    const std::string &molmrvText,
    const MrvParserParams &params = MrvParserParams());
RDKIT_MARVINPARSER_EXPORT std::unique_ptr<RWMol> MolFromMrvFile(
    const std::string &fName,
    const MrvParserParams &params = MrvParserParams());
 
RDKIT_MARVINPARSER_EXPORT std::unique_ptr<ChemicalReaction>
ReactionFromMrvDataStream(std::istream &inStream,
                          const MrvParserParams &params = MrvParserParams());
RDKIT_MARVINPARSER_EXPORT std::unique_ptr<ChemicalReaction>
ReactionFromMrvBlock(const std::string &molmrvText,
                     const MrvParserParams &params = MrvParserParams());
RDKIT_MARVINPARSER_EXPORT std::unique_ptr<ChemicalReaction> ReactionFromMrvFile(
    const std::string &fName,
    const MrvParserParams &params = MrvParserParams());
}  // namespace MarvinParser
}  // namespace v2
 
inline namespace v1 {
inline bool MrvFileIsReaction(const std::string &fname) {
  return v2::MarvinParser::MrvFileIsReaction(fname);
}
inline bool MrvDataStreamIsReaction(std::istream *inStream) {
  return v2::MarvinParser::MrvDataStreamIsReaction(*inStream);
}
 
inline bool MrvDataStreamIsReaction(std::istream &inStream) {
  return v2::MarvinParser::MrvDataStreamIsReaction(inStream);
}
inline bool MrvBlockIsReaction(const std::string &molmrvText) {
  return v2::MarvinParser::MrvBlockIsReaction(molmrvText);
}
 
inline RWMol *MrvDataStreamToMol(std::istream *inStream, bool sanitize = false,
                                 bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::MolFromMrvDataStream(*inStream, params).release();
}
inline RWMol *MrvDataStreamToMol(std::istream &inStream, bool sanitize = false,
                                 bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::MolFromMrvDataStream(inStream, params).release();
}
inline RWMol *MrvBlockToMol(const std::string &molmrvText,
                            bool sanitize = false, bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::MolFromMrvBlock(molmrvText, params).release();
}
inline RWMol *MrvFileToMol(const std::string &fName, bool sanitize = false,
                           bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::MolFromMrvFile(fName, params).release();
}
 
inline ChemicalReaction *MrvDataStreamToChemicalReaction(
    std::istream *inStream, bool sanitize = false, bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::ReactionFromMrvDataStream(*inStream, params)
      .release();
}
inline ChemicalReaction *MrvDataStreamToChemicalReaction(
    std::istream &inStream, bool sanitize = false, bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::ReactionFromMrvDataStream(inStream, params)
      .release();
}
inline ChemicalReaction *MrvBlockToChemicalReaction(
    const std::string &molmrvText, bool sanitize = false,
    bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::ReactionFromMrvBlock(molmrvText, params).release();
}
inline ChemicalReaction *MrvFileToChemicalReaction(const std::string &fName,
                                                   bool sanitize = false,
                                                   bool removeHs = false) {
  v2::MarvinParser::MrvParserParams params;
  params.sanitize = sanitize;
  params.removeHs = removeHs;
  return v2::MarvinParser::ReactionFromMrvFile(fName, params).release();
}
}  // namespace v1
 
struct RDKIT_MARVINPARSER_EXPORT MrvWriterParams {
  bool includeStereo = true;  /**< toggles inclusion of stereochemical */
  bool kekulize = true;       /**< triggers kekulization of the molecule before it's written */
  bool prettyPrint = false;   /**< makes the output more human readable */
  unsigned int precision = 6; /**< precision of the coordinates */
};
 
// \brief Writes a Marvin (MRV) file for a molecule
/*!
 *     \param mol           - the molecule
 *     \param fName         - the file to write to
 *     \param params        - marvin write params
 *     \param confId        - selects which conformation to output
 */
RDKIT_MARVINPARSER_EXPORT void MolToMrvFile(
    const ROMol &mol, const std::string &fName, const MrvWriterParams &params, int confId = -1);
 
// \brief Writes a Marvin (MRV) file for a molecule
/*!
 *     \param mol           - the molecule
 *     \param fName         - the file to write to
 *     \param includeStereo - toggles inclusion of stereochemical information in the output
 *     \param confId        - selects which conformation to output
 *     \param kekulize      - triggers kekulization of the molecule before it's written
 *     \param prettyPrint   - makes the output more human readable
 */
inline void MolToMrvFile(
    const ROMol &mol, const std::string &fName, bool includeStereo = true,
    int confId = -1, bool kekulize = true, bool prettyPrint = false) {
  MrvWriterParams params{includeStereo, kekulize, prettyPrint};
  MolToMrvFile(mol, fName, params, confId);
}
 
// \brief Returns a Marvin (Mrv) Mol block for a molecule
/*!
 *     \param mol           - the molecule
 *     \param params        - marvin write params
 *     \param confId        - selects which conformation to output
 */
RDKIT_MARVINPARSER_EXPORT std::string MolToMrvBlock(const ROMol &mol,
                                                    const MrvWriterParams &params,
                                                    int confId = -1);
 
// \brief Returns a Marvin (Mrv) Mol block for a molecule
/*!
 *     \param mol           - the molecule
 *     \param includeStereo - toggles inclusion of stereochemical information in the output
 *     \param confId        - selects which conformation to output
 *     \param kekulize      - triggers kekulization of the molecule before it's written
 *     \param prettyPrint   - makes the output more human readable
 */
inline std::string MolToMrvBlock(const ROMol &mol,
                                 bool includeStereo = true,
                                 int confId = -1,
                                 bool kekulize = true,
                                 bool prettyPrint = false) {
  MrvWriterParams params{includeStereo, kekulize, prettyPrint};
  return MolToMrvBlock(mol, params, confId);
}
 
RDKIT_MARVINPARSER_EXPORT std::string ChemicalReactionToMrvBlock(
    const ChemicalReaction &rxn, bool prettyPrint = false);
 
RDKIT_MARVINPARSER_EXPORT void ChemicalReactionToMrvFile(
    const ChemicalReaction &rxn, const std::string &fName,
    bool prettyPrint = false);
}  // namespace RDKit
 
#endif