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//
// Copyright (C) 2002-2024 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_FILEWRITERS_H
#define RD_FILEWRITERS_H
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include <string>
namespace RDKit {
struct RDKIT_FILEPARSERS_EXPORT MolWriterParams {
bool includeStereo = true; /**< toggles inclusion of stereochemistry
information*/
bool kekulize = true; /**< triggers kekulization of the molecule before
it is written*/
bool forceV3000 = false; /**< force generation a V3000 mol block (happens
automatically with more than 999 atoms or
bond or if the magnitude of the coordinates
are too large)*/
unsigned int precision = 6; /**< precision of coordinates (only available in
V3000)*/
};
// \brief generates an MDL mol block for a molecule
/*!
* \param mol - the molecule in question
* \param MolWriterParams - parmeter struct with write options
* \param confId - selects the conformer to be used
* (default=-1 - find first in mol)
*/
RDKIT_FILEPARSERS_EXPORT std::string MolToMolBlock(
const ROMol &mol, const MolWriterParams ¶ms, int confId = -1);
// \brief generates an MDL mol block for a molecule
/*!
* \param mol - the molecule in question
* \param includeStereo - toggles inclusion of stereochemistry information
* (default=true)
* \param confId - selects the conformer to be used
* (default=-1 - find first in mol)
* \param kekulize - triggers kekulization
* of the molecule before it is written (default=true)
* \param forceV3000 - force generation a V3000 mol block (happens
* automatically with more than 999 atoms or
* bonds)(default=false)
*/
inline std::string MolToMolBlock(const ROMol &mol, bool includeStereo = true,
int confId = -1, bool kekulize = true,
bool forceV3000 = false) {
MolWriterParams params{includeStereo, kekulize, forceV3000};
return MolToMolBlock(mol, params, confId);
}
// \brief generates an MDL v3000 mol block for a molecule
/*!
* \param mol - the molecule in question
* \param MolWriterParams - parameter struct with write options
* \param confId - selects the conformer to be used
* (default=-1 - find first in mol)
*/
inline std::string MolToV3KMolBlock(const ROMol &mol,
const MolWriterParams ¶ms,
int confId = -1) {
// have to set forceV300, prefer copy over mutable params argument
MolWriterParams v3KParams{params};
v3KParams.forceV3000 = true;
return MolToMolBlock(mol, v3KParams, confId);
}
// \brief generates an MDL v3000 mol block for a molecule
/*!
* \param mol - the molecule in question
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* (default=-1 - find first in mol)
* \param kekulize - triggers kekulization of the molecule before it is
* - written
*/
inline std::string MolToV3KMolBlock(const ROMol &mol, bool includeStereo = true,
int confId = -1, bool kekulize = true) {
MolWriterParams params{includeStereo, kekulize, true};
return MolToMolBlock(mol, params, confId);
}
// \brief generates an MDL v2000 mol block for a molecule
/*!
* \param mol - the molecule in question
* \param MolWriterParams - parameter struct with write options
* \param confId - selects the conformer to be used
* (default=-1 - find first in mol)
*
* \note This function will throw a ValueError exception if the molecule has
* more than 999 atoms, bonds, or SGroups.
*/
RDKIT_FILEPARSERS_EXPORT std::string MolToV2KMolBlock(
const ROMol &mol, const MolWriterParams ¶ms = MolWriterParams(),
int confId = -1);
// \brief Writes a molecule to an MDL mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param MolWriterParams - parameter struct with write options
* \param confId - selects the conformer to be used
*/
RDKIT_FILEPARSERS_EXPORT void MolToMolFile(const ROMol &mol,
const std::string &fName,
const MolWriterParams ¶ms,
int confId = -1);
// \brief Writes a molecule to an MDL mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is
* written
* \param forceV3000 - force generation a V3000 mol block (happens
* automatically with
* more than 999 atoms or bonds)
*/
inline void MolToMolFile(const ROMol &mol, const std::string &fName,
bool includeStereo = true, int confId = -1,
bool kekulize = true, bool forceV3000 = false) {
MolWriterParams params{includeStereo, kekulize, forceV3000};
MolToMolFile(mol, fName, params, confId);
}
// \brief Writes a molecule to an MDL V3000 mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param MolWriterParams - parameter struct with write options
* \param confId - selects the conformer to be used
*/
inline void MolToV3KMolFile(const ROMol &mol, const std::string &fName,
const MolWriterParams ¶ms, int confId = -1) {
// have to set forceV300, prefer copy over mutable params argument
MolWriterParams v3KParams{params};
v3KParams.forceV3000 = true;
MolToMolFile(mol, fName, v3KParams, confId);
}
// \brief Writes a molecule to an MDL V3000 mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is
* written
*/
inline void MolToV3KMolFile(const ROMol &mol, const std::string &fName,
bool includeStereo = true, int confId = -1,
bool kekulize = true) {
MolWriterParams params{includeStereo, kekulize, true};
MolToMolFile(mol, fName, params, confId);
}
RDKIT_FILEPARSERS_EXPORT std::string MolToCMLBlock(const ROMol &mol,
int confId = -1,
bool kekulize = true);
RDKIT_FILEPARSERS_EXPORT void MolToCMLFile(const ROMol &mol,
const std::string &fName,
int confId = -1,
bool kekulize = true);
// \brief Writes a molecule to an XYZ block
/*!
* \param mol - the molecule in question
* \param confId - selects which conformation to output
* \param precision - precision of the coordinates
*/
RDKIT_FILEPARSERS_EXPORT std::string MolToXYZBlock(const ROMol &mol,
int confId = -1,
unsigned int precision = 6);
// \brief Writes a molecule to an XYZ block
/*!
* \param mol - the molecule in question
* \param fName - the file to write to
* \param confId - selects which conformation to output
* \param precision - precision of the coordinates
*/
RDKIT_FILEPARSERS_EXPORT void MolToXYZFile(const ROMol &mol,
const std::string &fName,
int confId = -1,
unsigned int precision = 6);
RDKIT_FILEPARSERS_EXPORT std::string MolToTPLText(
const ROMol &mol, const std::string &partialChargeProp = "_GasteigerCharge",
bool writeFirstConfTwice = false);
RDKIT_FILEPARSERS_EXPORT void MolToTPLFile(
const ROMol &mol, const std::string &fName,
const std::string &partialChargeProp = "_GasteigerCharge",
bool writeFirstConfTwice = false);
// \brief generates an PDB block for a molecule
/*!
* \param mol - the molecule in question
* \param confId - selects the conformer to be used
* \param flavor - controls what gets written:
* flavor & 1 : Write MODEL/ENDMDL lines around each record
* flavor & 2 : Don't write single CONECT records
* flavor & 4 : Write CONECT records in both directions
* flavor & 8 : Don't use multiple CONECTs to encode bond order
* flavor & 16 : Write MASTER record
* flavor & 32 : Write TER record
*/
RDKIT_FILEPARSERS_EXPORT std::string MolToPDBBlock(const ROMol &mol,
int confId = -1,
unsigned int flavor = 0);
// \brief Writes a molecule to an MDL mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param confId - selects the conformer to be used
* \param flavor - controls what gets written:
* flavor & 1 : Write MODEL/ENDMDL lines around each record
* flavor & 2 : Don't write single CONECT records
* flavor & 4 : Write CONECT records in both directions
* flavor & 8 : Don't use multiple CONECTs to encode bond order
* flavor & 16 : Write MASTER record
* flavor & 32 : Write TER record
*/
RDKIT_FILEPARSERS_EXPORT void MolToPDBFile(const ROMol &mol,
const std::string &fname,
int confId = -1,
unsigned int flavor = 0);
} // namespace RDKit
#endif
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