FileParsers.h File Reference

#include <RDGeneral/export.h>
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileWriters.h>
#include "CDXMLParser.h"
#include <string>
#include <string_view>
#include <vector>
#include <exception>
#include <boost/shared_ptr.hpp>

Go to the source code of this file.

Classes
class	RDKit::v2::FileParsers::MolFileUnhandledFeatureException
struct	RDKit::v2::FileParsers::MolFileParserParams
struct	RDKit::v2::FileParsers::MolFromSCSRParams
struct	RDKit::v2::FileParsers::TPLParserParams
struct	RDKit::v2::FileParsers::Mol2ParserParams
struct	RDKit::v2::FileParsers::PDBParserParams
class	RDKit::v1::MolFileUnhandledFeatureException
struct	RDKit::v1::PDBParserParams

Namespaces
namespace	RDKit
	Std stuff.
namespace	RDKit::v2
namespace	RDKit::v2::FileParsers
namespace	RDKit::v1

Enumerations
enum class	RDKit::v2::FileParsers::SCSRTemplateNames { RDKit::v2::FileParsers::AsEntered , RDKit::v2::FileParsers::UseFirstName , RDKit::v2::FileParsers::UseSecondName }
enum class	RDKit::v2::FileParsers::SCSRBaseHbondOptions { RDKit::v2::FileParsers::Ignore , RDKit::v2::FileParsers::UseSapAll , RDKit::v2::FileParsers::UseSapOne , RDKit::v2::FileParsers::Auto }
enum	RDKit::v2::FileParsers::Mol2Type { RDKit::v2::FileParsers::CORINA = 0 }
enum	RDKit::v1::Mol2Type

Functions
RDKIT_FILEPARSERS_EXPORT std::string	RDKit::strip (const std::string &orig)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromMolDataStream (std::istream &inStream, unsigned int &line, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromMolBlock (const std::string &molBlock, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromMolFile (const std::string &fName, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol >	RDKit::v2::FileParsers::MolFromSCSRDataStream (std::istream &inStream, unsigned int &line, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol >	RDKit::v2::FileParsers::MolFromSCSRBlock (const std::string &molBlock, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol >	RDKit::v2::FileParsers::MolFromSCSRFile (const std::string &fName, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RWMol *	RDKit::v1::MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol *	RDKit::v1::MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol *	RDKit::v1::MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol *	RDKit::v1::MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromTPLDataStream (std::istream &inStream, unsigned int &line, const TPLParserParams &params=TPLParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromTPLFile (const std::string &fName, const TPLParserParams &params=TPLParserParams())
RWMol *	RDKit::v1::TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
	translate TPL data (BioCad format) into a multi-conf molecule
RWMol *	RDKit::v1::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::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromMol2DataStream (std::istream &inStream, const Mol2ParserParams &params=Mol2ParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromMol2Block (const std::string &molBlock, const Mol2ParserParams &params=Mol2ParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromMol2File (const std::string &fName, const Mol2ParserParams &params=Mol2ParserParams())
RWMol *	RDKit::v1::Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol *	RDKit::v1::Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol *	RDKit::v1::Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol *	RDKit::v1::Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromXYZDataStream (std::istream &inStream)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromXYZBlock (const std::string &xyzBlock)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromXYZFile (const std::string &fName)
RWMol *	RDKit::v1::XYZDataStreamToMol (std::istream &inStream)
RWMol *	RDKit::v1::XYZBlockToMol (const std::string &xyzBlock)
RWMol *	RDKit::v1::XYZFileToMol (const std::string &fName)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromPDBDataStream (std::istream &inStream, const PDBParserParams &params=PDBParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromPDBFile (const std::string &fname, const PDBParserParams &params=PDBParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	RDKit::v2::FileParsers::MolFromPDBBlock (const std::string &str, const PDBParserParams &params=PDBParserParams())
RWMol *	RDKit::v1::PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	RDKit::v1::PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	RDKit::v1::PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	RDKit::v1::PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol *	RDKit::v1::PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RDKIT_FILEPARSERS_EXPORT RWMol *	RDKit::RDKitSVGToMol (const std::string &svg, bool sanitize=true, bool removeHs=true)
RDKIT_FILEPARSERS_EXPORT RWMol *	RDKit::RDKitSVGToMol (std::istream *instream, bool sanitize=true, bool removeHs=true)
std::unique_ptr< RDKit::RWMol >	RDKit::operator""_ctab (const char *text, size_t len)
std::unique_ptr< RDKit::RWMol >	RDKit::operator""_mol2 (const char *text, size_t len)
std::unique_ptr< RDKit::RWMol >	RDKit::operator""_pdb (const char *text, size_t len)