RDKit::v2::FileParsers Namespace Reference

Classes
class	MolFileUnhandledFeatureException
struct	MolFileParserParams
struct	MolFromSCSRParams
struct	TPLParserParams
struct	Mol2ParserParams
struct	PDBParserParams
class	MolSupplier
class	ForwardSDMolSupplier
class	SDMolSupplier
struct	SmilesMolSupplierParams
class	SmilesMolSupplier
	lazy file parser for Smiles tables More...
struct	TDTMolSupplierParams
class	TDTMolSupplier
	lazy file parser for TDT files More...

Enumerations
enum class	SCSRTemplateNames { AsEntered , UseFirstName , UseSecondName }
enum class	SCSRBaseHbondOptions { Ignore , UseSapAll , UseSapOne , Auto }
enum	Mol2Type { CORINA = 0 }

Functions
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromMolDataStream (std::istream &inStream, unsigned int &line, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromMolBlock (const std::string &molBlock, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromMolFile (const std::string &fName, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol >	MolFromSCSRDataStream (std::istream &inStream, unsigned int &line, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol >	MolFromSCSRBlock (const std::string &molBlock, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol >	MolFromSCSRFile (const std::string &fName, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromTPLDataStream (std::istream &inStream, unsigned int &line, const TPLParserParams &params=TPLParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromTPLFile (const std::string &fName, const TPLParserParams &params=TPLParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromMol2DataStream (std::istream &inStream, const Mol2ParserParams &params=Mol2ParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromMol2Block (const std::string &molBlock, const Mol2ParserParams &params=Mol2ParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromMol2File (const std::string &fName, const Mol2ParserParams &params=Mol2ParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromXYZDataStream (std::istream &inStream)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromXYZBlock (const std::string &xyzBlock)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromXYZFile (const std::string &fName)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromPDBDataStream (std::istream &inStream, const PDBParserParams &params=PDBParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromPDBFile (const std::string &fname, const PDBParserParams &params=PDBParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol >	MolFromPDBBlock (const std::string &str, const PDBParserParams &params=PDBParserParams())

Enumeration Type Documentation

Mol2Type

enum RDKit::v2::FileParsers::Mol2Type

Enumerator
CORINA	supports output from Corina and some dbtranslate output

Definition at line 264 of file FileParsers.h.

SCSRBaseHbondOptions

enum class RDKit::v2::FileParsers::SCSRBaseHbondOptions

strong

Enumerator
Ignore
UseSapAll
UseSapOne
Auto

Definition at line 65 of file FileParsers.h.

SCSRTemplateNames

enum class RDKit::v2::FileParsers::SCSRTemplateNames

strong

Enumerator
AsEntered
UseFirstName
UseSecondName

Definition at line 57 of file FileParsers.h.

Function Documentation

MolFromMol2Block()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromMol2Block	(	const std::string &	molBlock,
		const Mol2ParserParams &	params = Mol2ParserParams() )

References MolFromMol2Block(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromMol2Block(), and RDKit::operator""_mol2().

MolFromMol2DataStream()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromMol2DataStream	(	std::istream &	inStream,
		const Mol2ParserParams &	params = Mol2ParserParams() )

References MolFromMol2DataStream(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromMol2DataStream().

MolFromMol2File()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromMol2File	(	const std::string &	fName,
		const Mol2ParserParams &	params = Mol2ParserParams() )

References MolFromMol2File(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromMol2File().

MolFromMolBlock()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromMolBlock	(	const std::string &	molBlock,
		const MolFileParserParams &	params = MolFileParserParams() )

References MolFromMolBlock(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromMolBlock(), and RDKit::operator""_ctab().

MolFromMolDataStream()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromMolDataStream	(	std::istream &	inStream,
		unsigned int &	line,
		const MolFileParserParams &	params = MolFileParserParams() )

References MolFromMolDataStream(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromMolDataStream().

MolFromMolFile()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromMolFile	(	const std::string &	fName,
		const MolFileParserParams &	params = MolFileParserParams() )

References MolFromMolFile(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromMolFile().

MolFromPDBBlock()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromPDBBlock	(	const std::string &	str,
		const PDBParserParams &	params = PDBParserParams() )

References MolFromPDBBlock(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromPDBBlock(), and RDKit::operator""_pdb().

MolFromPDBDataStream()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromPDBDataStream	(	std::istream &	inStream,
		const PDBParserParams &	params = PDBParserParams() )

References MolFromPDBDataStream(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromPDBDataStream().

MolFromPDBFile()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromPDBFile	(	const std::string &	fname,
		const PDBParserParams &	params = PDBParserParams() )

References MolFromPDBFile(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromPDBFile().

MolFromSCSRBlock()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol > RDKit::v2::FileParsers::MolFromSCSRBlock	(	const std::string &	molBlock,
		const MolFileParserParams &	molFileParserParams = MolFileParserParams(),
		const MolFromSCSRParams &	molFromSCSRParams = MolFromSCSRParams() )

References MolFromSCSRBlock(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromSCSRBlock().

MolFromSCSRDataStream()

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() )

References MolFromSCSRDataStream(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromSCSRDataStream().

MolFromSCSRFile()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol > RDKit::v2::FileParsers::MolFromSCSRFile	(	const std::string &	fName,
		const MolFileParserParams &	molFileParserParams = MolFileParserParams(),
		const MolFromSCSRParams &	molFromSCSRParams = MolFromSCSRParams() )

References MolFromSCSRFile(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromSCSRFile().

MolFromTPLDataStream()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromTPLDataStream	(	std::istream &	inStream,
		unsigned int &	line,
		const TPLParserParams &	params = TPLParserParams() )

References MolFromTPLDataStream(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromTPLDataStream().

MolFromTPLFile()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromTPLFile	(	const std::string &	fName,
		const TPLParserParams &	params = TPLParserParams() )

References MolFromTPLFile(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromTPLFile().

MolFromXYZBlock()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromXYZBlock

(

const std::string &

xyzBlock

)

Parameters

xyzBlock

- string containing the xyz block

References MolFromXYZBlock(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromXYZBlock().

MolFromXYZDataStream()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromXYZDataStream

(

std::istream &

inStream

)

References MolFromXYZDataStream(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromXYZDataStream().

MolFromXYZFile()

RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > RDKit::v2::FileParsers::MolFromXYZFile

(

const std::string &

fName

)

Parameters

fName

- string containing the file name

References MolFromXYZFile(), and RDKIT_FILEPARSERS_EXPORT.

Referenced by MolFromXYZFile().