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12929849f5
* allow MaeWriter to throw * update tests * throw ValueErrorException * add note on backward incompatible change of behavior
245 lines
11 KiB
C++
245 lines
11 KiB
C++
//
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// Copyright (C) 2002-2024 Greg Landrum and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef RD_FILEWRITERS_H
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#define RD_FILEWRITERS_H
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#include <RDGeneral/types.h>
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#include <GraphMol/RDKitBase.h>
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#include <string>
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namespace RDKit {
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struct RDKIT_FILEPARSERS_EXPORT MolWriterParams {
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bool includeStereo = true; /**< toggles inclusion of stereochemistry
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information*/
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bool kekulize = true; /**< triggers kekulization of the molecule before
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it is written*/
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bool forceV3000 = false; /**< force generation a V3000 mol block (happens
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automatically with more than 999 atoms or
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bond or if the magnitude of the coordinates
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are too large)*/
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unsigned int precision = 6; /**< precision of coordinates (only available in
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V3000)*/
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};
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// \brief generates an MDL mol block for a molecule
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/*!
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* \param mol - the molecule in question
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* \param MolWriterParams - parmeter struct with write options
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* \param confId - selects the conformer to be used
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* (default=-1 - find first in mol)
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*/
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RDKIT_FILEPARSERS_EXPORT std::string MolToMolBlock(
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const ROMol &mol, const MolWriterParams ¶ms, int confId = -1);
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// \brief generates an MDL mol block for a molecule
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/*!
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* \param mol - the molecule in question
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* \param includeStereo - toggles inclusion of stereochemistry information
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* (default=true)
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* \param confId - selects the conformer to be used
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* (default=-1 - find first in mol)
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* \param kekulize - triggers kekulization
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* of the molecule before it is written (default=true)
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* \param forceV3000 - force generation a V3000 mol block (happens
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* automatically with more than 999 atoms or
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* bonds)(default=false)
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*/
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inline std::string MolToMolBlock(const ROMol &mol, bool includeStereo = true,
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int confId = -1, bool kekulize = true,
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bool forceV3000 = false) {
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MolWriterParams params{includeStereo, kekulize, forceV3000};
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return MolToMolBlock(mol, params, confId);
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}
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// \brief generates an MDL v3000 mol block for a molecule
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/*!
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* \param mol - the molecule in question
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* \param MolWriterParams - parameter struct with write options
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* \param confId - selects the conformer to be used
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* (default=-1 - find first in mol)
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*/
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inline std::string MolToV3KMolBlock(const ROMol &mol,
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const MolWriterParams ¶ms,
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int confId = -1) {
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// have to set forceV300, prefer copy over mutable params argument
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MolWriterParams v3KParams{params};
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v3KParams.forceV3000 = true;
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return MolToMolBlock(mol, v3KParams, confId);
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}
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// \brief generates an MDL v3000 mol block for a molecule
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/*!
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* \param mol - the molecule in question
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* \param includeStereo - toggles inclusion of stereochemistry information
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* \param confId - selects the conformer to be used
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* (default=-1 - find first in mol)
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* \param kekulize - triggers kekulization of the molecule before it is
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* - written
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*/
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inline std::string MolToV3KMolBlock(const ROMol &mol, bool includeStereo = true,
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int confId = -1, bool kekulize = true) {
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MolWriterParams params{includeStereo, kekulize, true};
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return MolToMolBlock(mol, params, confId);
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}
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// \brief generates an MDL v2000 mol block for a molecule
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/*!
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* \param mol - the molecule in question
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* \param MolWriterParams - parameter struct with write options
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* \param confId - selects the conformer to be used
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* (default=-1 - find first in mol)
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*
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* \note This function will throw a ValueError exception if the molecule has
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* more than 999 atoms, bonds, or SGroups.
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*/
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RDKIT_FILEPARSERS_EXPORT std::string MolToV2KMolBlock(
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const ROMol &mol, const MolWriterParams ¶ms = MolWriterParams(),
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int confId = -1);
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// \brief Writes a molecule to an MDL mol file
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/*!
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* \param mol - the molecule in question
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* \param fName - the name of the file to use
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* \param MolWriterParams - parameter struct with write options
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* \param confId - selects the conformer to be used
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*/
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RDKIT_FILEPARSERS_EXPORT void MolToMolFile(const ROMol &mol,
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const std::string &fName,
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const MolWriterParams ¶ms,
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int confId = -1);
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// \brief Writes a molecule to an MDL mol file
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/*!
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* \param mol - the molecule in question
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* \param fName - the name of the file to use
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* \param includeStereo - toggles inclusion of stereochemistry information
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* \param confId - selects the conformer to be used
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* \param kekulize - triggers kekulization of the molecule before it is
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* written
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* \param forceV3000 - force generation a V3000 mol block (happens
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* automatically with
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* more than 999 atoms or bonds)
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*/
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inline void MolToMolFile(const ROMol &mol, const std::string &fName,
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bool includeStereo = true, int confId = -1,
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bool kekulize = true, bool forceV3000 = false) {
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MolWriterParams params{includeStereo, kekulize, forceV3000};
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MolToMolFile(mol, fName, params, confId);
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}
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// \brief Writes a molecule to an MDL V3000 mol file
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/*!
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* \param mol - the molecule in question
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* \param fName - the name of the file to use
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* \param MolWriterParams - parameter struct with write options
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* \param confId - selects the conformer to be used
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*/
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inline void MolToV3KMolFile(const ROMol &mol, const std::string &fName,
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const MolWriterParams ¶ms, int confId = -1) {
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// have to set forceV300, prefer copy over mutable params argument
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MolWriterParams v3KParams{params};
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v3KParams.forceV3000 = true;
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MolToMolFile(mol, fName, v3KParams, confId);
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}
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// \brief Writes a molecule to an MDL V3000 mol file
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/*!
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* \param mol - the molecule in question
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* \param fName - the name of the file to use
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* \param includeStereo - toggles inclusion of stereochemistry information
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* \param confId - selects the conformer to be used
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* \param kekulize - triggers kekulization of the molecule before it is
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* written
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*/
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inline void MolToV3KMolFile(const ROMol &mol, const std::string &fName,
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bool includeStereo = true, int confId = -1,
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bool kekulize = true) {
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MolWriterParams params{includeStereo, kekulize, true};
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MolToMolFile(mol, fName, params, confId);
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}
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RDKIT_FILEPARSERS_EXPORT std::string MolToCMLBlock(const ROMol &mol,
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int confId = -1,
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bool kekulize = true);
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RDKIT_FILEPARSERS_EXPORT void MolToCMLFile(const ROMol &mol,
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const std::string &fName,
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int confId = -1,
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bool kekulize = true);
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// \brief Writes a molecule to an XYZ block
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/*!
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* \param mol - the molecule in question
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* \param confId - selects which conformation to output
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* \param precision - precision of the coordinates
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*/
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RDKIT_FILEPARSERS_EXPORT std::string MolToXYZBlock(const ROMol &mol,
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int confId = -1,
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unsigned int precision = 6);
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// \brief Writes a molecule to an XYZ block
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/*!
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* \param mol - the molecule in question
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* \param fName - the file to write to
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* \param confId - selects which conformation to output
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* \param precision - precision of the coordinates
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*/
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RDKIT_FILEPARSERS_EXPORT void MolToXYZFile(const ROMol &mol,
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const std::string &fName,
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int confId = -1,
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unsigned int precision = 6);
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RDKIT_FILEPARSERS_EXPORT std::string MolToTPLText(
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const ROMol &mol, const std::string &partialChargeProp = "_GasteigerCharge",
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bool writeFirstConfTwice = false);
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RDKIT_FILEPARSERS_EXPORT void MolToTPLFile(
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const ROMol &mol, const std::string &fName,
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const std::string &partialChargeProp = "_GasteigerCharge",
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bool writeFirstConfTwice = false);
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// \brief generates an PDB block for a molecule
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/*!
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* \param mol - the molecule in question
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* \param confId - selects the conformer to be used
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* \param flavor - controls what gets written:
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* flavor & 1 : Write MODEL/ENDMDL lines around each record
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* flavor & 2 : Don't write single CONECT records
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* flavor & 4 : Write CONECT records in both directions
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* flavor & 8 : Don't use multiple CONECTs to encode bond order
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* flavor & 16 : Write MASTER record
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* flavor & 32 : Write TER record
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*/
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RDKIT_FILEPARSERS_EXPORT std::string MolToPDBBlock(const ROMol &mol,
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int confId = -1,
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unsigned int flavor = 0);
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// \brief Writes a molecule to an MDL mol file
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/*!
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* \param mol - the molecule in question
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* \param fName - the name of the file to use
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* \param confId - selects the conformer to be used
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* \param flavor - controls what gets written:
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* flavor & 1 : Write MODEL/ENDMDL lines around each record
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* flavor & 2 : Don't write single CONECT records
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* flavor & 4 : Write CONECT records in both directions
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* flavor & 8 : Don't use multiple CONECTs to encode bond order
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* flavor & 16 : Write MASTER record
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* flavor & 32 : Write TER record
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*/
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RDKIT_FILEPARSERS_EXPORT void MolToPDBFile(const ROMol &mol,
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const std::string &fname,
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int confId = -1,
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unsigned int flavor = 0);
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} // namespace RDKit
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#endif
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