RDKit
Open-source cheminformatics and machine learning.
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FileParsers.h File Reference
#include <RDGeneral/export.h>
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include "CDXMLParser.h"
#include <string>
#include <string_view>
#include <iostream>
#include <vector>
#include <exception>
#include <boost/shared_ptr.hpp>

Go to the source code of this file.

Classes

class  RDKit::MolFileUnhandledFeatureException
 

Namespaces

namespace  RDKit
 Std stuff.
 

Typedefs

typedef std::vector< RWMOL_SPTRRDKit::RWMOL_SPTR_VECT
 

Enumerations

enum  RDKit::Mol2Type { RDKit::CORINA = 0 }
 

Functions

RDKIT_FILEPARSERS_EXPORT std::string RDKit::strip (const std::string &orig)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
 
std::string RDKit::MolToV3KMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true)
 
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
 
void RDKit::MolToV3KMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true)
 
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToCMLBlock (const ROMol &mol, int confId=-1, bool kekulize=true)
 
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToCMLFile (const ROMol &mol, const std::string &fName, int confId=-1, bool kekulize=true)
 
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToXYZBlock (const ROMol &mol, int confId=-1)
 
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToXYZFile (const ROMol &mol, const std::string &fName, int confId=-1)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
 translate TPL data (BioCad format) into a multi-conf molecule
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false)
 construct a multi-conf molecule from a TPL (BioCad format) file
 
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToTPLText (const ROMol &mol, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
 
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToTPLFile (const ROMol &mol, const std::string &fName, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::XYZDataStreamToMol (std::istream &inStream)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::XYZBlockToMol (const std::string &xyzBlock)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::XYZFileToMol (const std::string &fName)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RDKIT_FILEPARSERS_EXPORT std::string RDKit::MolToPDBBlock (const ROMol &mol, int confId=-1, unsigned int flavor=0)
 
RDKIT_FILEPARSERS_EXPORT void RDKit::MolToPDBFile (const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::RDKitSVGToMol (const std::string &svg, bool sanitize=true, bool removeHs=true)
 
RDKIT_FILEPARSERS_EXPORT RWMolRDKit::RDKitSVGToMol (std::istream *instream, bool sanitize=true, bool removeHs=true)
 
std::unique_ptr< RDKit::RWMolRDKit::operator""_ctab (const char *text, size_t len)
 
std::unique_ptr< RDKit::RWMolRDKit::operator""_mol2 (const char *text, size_t len)
 
std::unique_ptr< RDKit::RWMolRDKit::operator""_pdb (const char *text, size_t len)
 

Variables

const int RDKit::MOLFILE_MAXLINE = 256