Classes
class	ForwardSDMolSupplier

class	MolSupplier

class	SDMolSupplier

struct	SmartsParserParams

class	SmilesMolSupplier
	lazy file parser for Smiles tables More...

struct	SmilesParserParams

class	TDTMolSupplier
	lazy file parser for TDT files More...

Functions
ChemicalReaction *	RxnBlockToChemicalReaction (const std::string &rxnBlock, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
	Parse a text block in MDL rxn format into a ChemicalReaction.

ChemicalReaction *	RxnFileToChemicalReaction (const std::string &fileName, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
	Parse a file in MDL rxn format into a ChemicalReaction.

ChemicalReaction *	RxnDataStreamToChemicalReaction (std::istream &rxnStream, unsigned int &line, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
	Parse a text stream in MDL rxn format into a ChemicalReaction.

ChemicalReaction *	PNGStreamToChemicalReaction (std::istream &pngStream)
	constructs a ChemicalReaction from the metadata in a PNG stream

ChemicalReaction *	PNGStringToChemicalReaction (const std::string &data)
	constructs a ChemicalReaction from the metadata in a PNG string See `PNGStreamToChemicalReaction()` for more details

ChemicalReaction *	PNGFileToChemicalReaction (const std::string &fname)
	constructs a ChemicalReaction from the metadata in a PNG file See `PNGStreamToChemicalReaction()` for more details

std::vector< std::unique_ptr< RWMol > >	CDXMLDataStreamToMols (std::istream &inStream, bool sanitize=true, bool removeHs=true)
	construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

std::vector< std::unique_ptr< RWMol > >	CDXMLFileToMols (const std::string &filename, bool sanitize=true, bool removeHs=true)
	construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

std::vector< std::unique_ptr< RWMol > >	CDXMLToMols (const std::string &cdxml, bool sanitize=true, bool removeHs=true)
	construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

RWMol *	MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)

RWMol *	MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)

RWMol *	MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)

RWMol *	MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)

RWMol *	TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
	translate TPL data (BioCad format) into a multi-conf molecule

RWMol *	TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false)
	construct a multi-conf molecule from a TPL (BioCad format) file

RWMol *	Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)

RWMol *	Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)

RWMol *	Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)

RWMol *	Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)

RWMol *	XYZDataStreamToMol (std::istream &inStream)

RWMol *	XYZBlockToMol (const std::string &xyzBlock)

RWMol *	XYZFileToMol (const std::string &fName)

RWMol *	PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)

RWMol *	PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)

RWMol *	PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)

RWMol *	PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)

RWMol *	PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)

bool	MrvFileIsReaction (const std::string &fname)

bool	MrvDataStreamIsReaction (std::istream *inStream)

bool	MrvDataStreamIsReaction (std::istream &inStream)

bool	MrvBlockIsReaction (const std::string &molmrvText)

RWMol *	MrvDataStreamToMol (std::istream *inStream, bool sanitize=false, bool removeHs=false)

RWMol *	MrvDataStreamToMol (std::istream &inStream, bool sanitize=false, bool removeHs=false)

RWMol *	MrvBlockToMol (const std::string &molmrvText, bool sanitize=false, bool removeHs=false)

RWMol *	MrvFileToMol (const std::string &fName, bool sanitize=false, bool removeHs=false)

ChemicalReaction *	MrvDataStreamToChemicalReaction (std::istream *inStream, bool sanitize=false, bool removeHs=false)

ChemicalReaction *	MrvDataStreamToChemicalReaction (std::istream &inStream, bool sanitize=false, bool removeHs=false)

ChemicalReaction *	MrvBlockToChemicalReaction (const std::string &molmrvText, bool sanitize=false, bool removeHs=false)

ChemicalReaction *	MrvFileToChemicalReaction (const std::string &fName, bool sanitize=false, bool removeHs=false)

RDKit::RWMol *	SmilesToMol (const std::string &smi, const SmilesParserParams &ps)

Atom *	SmilesToAtom (const std::string &smi)

Bond *	SmilesToBond (const std::string &smi)

RWMol *	SmilesToMol (const std::string &smi, int debugParse=0, bool sanitize=true, std::map< std::string, std::string > *replacements=nullptr)
	Construct a molecule from a SMILES string.

RWMol *	SmartsToMol (const std::string &sma, const SmartsParserParams &ps)

RWMol *	SmartsToMol (const std::string &sma, int debugParse=0, bool mergeHs=false, std::map< std::string, std::string > *replacements=nullptr)
	Construct a molecule from a SMARTS string.

Atom *	SmartsToAtom (const std::string &sma)

Bond *	SmartsToBond (const std::string &sma)

Reaction SMARTS/SMILES Support
ChemicalReaction *	RxnSmartsToChemicalReaction (const std::string &text, std::map< std::string, std::string > *replacements=nullptr, bool useSmiles=false, bool allowCXSMILES=true)
	Parse a string containing "Reaction SMARTS" into a ChemicalReaction.

Function Documentation

◆ CDXMLDataStreamToMols()

std::vector< std::unique_ptr< RWMol > > RDKit::v1::CDXMLDataStreamToMols	(	std::istream &	inStream,
		bool	sanitize = `true`,
		bool	removeHs = `true`
	)

inline

construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

Parameters

inStream	- string containing the mol block
sanitize	- toggles sanitization and stereochemistry perception of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized correctness of the contents.

Definition at line 82 of file CDXMLParser.h.

◆ CDXMLFileToMols()

std::vector< std::unique_ptr< RWMol > > RDKit::v1::CDXMLFileToMols	(	const std::string &	filename,
		bool	sanitize = `true`,
		bool	removeHs = `true`
	)

inline

construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

Parameters

fileName	- cdxml fileName
sanitize	- toggles sanitization and stereochemistry perception of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized correctness of the contents.

Definition at line 102 of file CDXMLParser.h.

◆ CDXMLToMols()

std::vector< std::unique_ptr< RWMol > > RDKit::v1::CDXMLToMols	(	const std::string &	cdxml,
		bool	sanitize = `true`,
		bool	removeHs = `true`
	)

inline

construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

Parameters

cdxml	- string containing the mol block
sanitize	- toggles sanitization and stereochemistry perception of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized correctness of the contents.

Definition at line 122 of file CDXMLParser.h.

◆ Mol2BlockToMol()

RWMol * RDKit::v1::Mol2BlockToMol	(	const std::string &	molBlock,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		Mol2Type	variant = `Mol2Type::CORINA`,
		bool	cleanupSubstructures = `true`
	)

inline

Parameters

molBlock	- string containing the mol block
sanitize	- toggles sanitization of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
variant	- the atom type definitions to use
cleanupSubstructures	- toggles recognition and cleanup of common substructures

Definition at line 310 of file FileParsers.h.

◆ Mol2DataStreamToMol() [1/2]

RWMol * RDKit::v1::Mol2DataStreamToMol	(	std::istream &	inStream,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		Mol2Type	variant = `Mol2Type::CORINA`,
		bool	cleanupSubstructures = `true`
	)

inline

Parameters

inStream	- stream containing the data
sanitize	- toggles sanitization of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
variant	- the atom type definitions to use
cleanupSubstructures	- toggles recognition and cleanup of common substructures

Definition at line 280 of file FileParsers.h.

◆ Mol2DataStreamToMol() [2/2]

RWMol * RDKit::v1::Mol2DataStreamToMol	(	std::istream *	inStream,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		Mol2Type	variant = `Mol2Type::CORINA`,
		bool	cleanupSubstructures = `true`
	)

inline

Definition at line 292 of file FileParsers.h.

◆ Mol2FileToMol()

RWMol * RDKit::v1::Mol2FileToMol	(	const std::string &	fName,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		Mol2Type	variant = `Mol2Type::CORINA`,
		bool	cleanupSubstructures = `true`
	)

inline

Parameters

fName	- string containing the file name
sanitize	- toggles sanitization of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
variant	- the atom type definitions to use
cleanupSubstructures	- toggles recognition and cleanup of common substructures

Definition at line 258 of file FileParsers.h.

◆ MolBlockToMol()

RWMol * RDKit::v1::MolBlockToMol	(	const std::string &	molBlock,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		bool	strictParsing = `true`
	)

inline

Parameters

molBlock	- string containing the mol block
sanitize	- toggles sanitization and stereochemistry perception of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
strictParsing	- if set to false, the parser is more lax about correctness of the contents.

Definition at line 112 of file FileParsers.h.

◆ MolDataStreamToMol() [1/2]

RWMol * RDKit::v1::MolDataStreamToMol	(	std::istream &	inStream,
		unsigned int &	line,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		bool	strictParsing = `true`
	)

inline

Definition at line 97 of file FileParsers.h.

◆ MolDataStreamToMol() [2/2]

RWMol * RDKit::v1::MolDataStreamToMol	(	std::istream *	inStream,
		unsigned int &	line,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		bool	strictParsing = `true`
	)

inline

Parameters

inStream	- stream containing the data
line	- current line number (used for error reporting)
sanitize	- toggles sanitization and stereochemistry perception of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
line	- current line number (used for error reporting)
strictParsing	- if set to false, the parser is more lax about correctness of the contents.

Definition at line 87 of file FileParsers.h.

◆ MolFileToMol()

RWMol * RDKit::v1::MolFileToMol	(	const std::string &	fName,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		bool	strictParsing = `true`
	)

inline

Parameters

fName	- string containing the file name
sanitize	- toggles sanitization and stereochemistry perception of the molecule
removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
strictParsing	- if set to false, the parser is more lax about correctness of the contents.

Definition at line 131 of file FileParsers.h.

◆ MrvBlockIsReaction()

bool RDKit::v1::MrvBlockIsReaction ( const std::string & molmrvText )

inline

Definition at line 67 of file MarvinParser.h.

◆ MrvBlockToChemicalReaction()

ChemicalReaction * RDKit::v1::MrvBlockToChemicalReaction	(	const std::string &	molmrvText,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 116 of file MarvinParser.h.

◆ MrvBlockToMol()

RWMol * RDKit::v1::MrvBlockToMol	(	const std::string &	molmrvText,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 85 of file MarvinParser.h.

◆ MrvDataStreamIsReaction() [1/2]

bool RDKit::v1::MrvDataStreamIsReaction ( std::istream & inStream )

inline

Definition at line 64 of file MarvinParser.h.

◆ MrvDataStreamIsReaction() [2/2]

bool RDKit::v1::MrvDataStreamIsReaction ( std::istream * inStream )

inline

Definition at line 60 of file MarvinParser.h.

◆ MrvDataStreamToChemicalReaction() [1/2]

ChemicalReaction * RDKit::v1::MrvDataStreamToChemicalReaction	(	std::istream &	inStream,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 108 of file MarvinParser.h.

◆ MrvDataStreamToChemicalReaction() [2/2]

ChemicalReaction * RDKit::v1::MrvDataStreamToChemicalReaction	(	std::istream *	inStream,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 100 of file MarvinParser.h.

◆ MrvDataStreamToMol() [1/2]

RWMol * RDKit::v1::MrvDataStreamToMol	(	std::istream &	inStream,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 78 of file MarvinParser.h.

◆ MrvDataStreamToMol() [2/2]

RWMol * RDKit::v1::MrvDataStreamToMol	(	std::istream *	inStream,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 71 of file MarvinParser.h.

◆ MrvFileIsReaction()

bool RDKit::v1::MrvFileIsReaction ( const std::string & fname )

inline

Definition at line 57 of file MarvinParser.h.

◆ MrvFileToChemicalReaction()

ChemicalReaction * RDKit::v1::MrvFileToChemicalReaction	(	const std::string &	fName,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 124 of file MarvinParser.h.

◆ MrvFileToMol()

RWMol * RDKit::v1::MrvFileToMol	(	const std::string &	fName,
		bool	sanitize = `false`,
		bool	removeHs = `false`
	)

inline

Definition at line 92 of file MarvinParser.h.

◆ PDBBlockToMol() [1/2]

RWMol * RDKit::v1::PDBBlockToMol	(	const char *	str,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		unsigned int	flavor = `0`,
		bool	proximityBonding = `true`
	)

inline

Definition at line 395 of file FileParsers.h.

◆ PDBBlockToMol() [2/2]

RWMol * RDKit::v1::PDBBlockToMol	(	const std::string &	str,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		unsigned int	flavor = `0`,
		bool	proximityBonding = `true`
	)

inline

Definition at line 385 of file FileParsers.h.

◆ PDBDataStreamToMol() [1/2]

RWMol * RDKit::v1::PDBDataStreamToMol	(	std::istream &	inStream,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		unsigned int	flavor = `0`,
		bool	proximityBonding = `true`
	)

inline

Definition at line 411 of file FileParsers.h.

◆ PDBDataStreamToMol() [2/2]

RWMol * RDKit::v1::PDBDataStreamToMol	(	std::istream *	inStream,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		unsigned int	flavor = `0`,
		bool	proximityBonding = `true`
	)

inline

Definition at line 421 of file FileParsers.h.

◆ PDBFileToMol()

RWMol * RDKit::v1::PDBFileToMol	(	const std::string &	fname,
		bool	sanitize = `true`,
		bool	removeHs = `true`,
		unsigned int	flavor = `0`,
		bool	proximityBonding = `true`
	)

inline

Definition at line 401 of file FileParsers.h.

◆ PNGFileToChemicalReaction()

ChemicalReaction * RDKit::v1::PNGFileToChemicalReaction ( const std::string & fname )

inline

constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction() for more details

Definition at line 324 of file ReactionParser.h.

◆ PNGStreamToChemicalReaction()

ChemicalReaction * RDKit::v1::PNGStreamToChemicalReaction ( std::istream & pngStream )

inline

constructs a ChemicalReaction from the metadata in a PNG stream

Looks through the metadata in the PNG to find the first tag that matches one of the tags in RDKit::PNGData. A reaction is constructed from this chunk.

Throws a FileParseException if no suitable tag is found.

The caller is responsible for the returned pointer.

Definition at line 314 of file ReactionParser.h.

◆ PNGStringToChemicalReaction()

ChemicalReaction * RDKit::v1::PNGStringToChemicalReaction ( const std::string & data )

inline

constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction() for more details

Definition at line 319 of file ReactionParser.h.

◆ RxnBlockToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnBlockToChemicalReaction	(	const std::string &	rxnBlock,
		bool	sanitize = `false`,
		bool	removeHs = `false`,
		bool	strictParsing = `true`
	)

inline

Parse a text block in MDL rxn format into a ChemicalReaction.

Definition at line 196 of file ReactionParser.h.

◆ RxnDataStreamToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnDataStreamToChemicalReaction	(	std::istream &	rxnStream,
		unsigned int &	line,
		bool	sanitize = `false`,
		bool	removeHs = `false`,
		bool	strictParsing = `true`
	)

inline

Parse a text stream in MDL rxn format into a ChemicalReaction.

Definition at line 218 of file ReactionParser.h.

◆ RxnFileToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnFileToChemicalReaction	(	const std::string &	fileName,
		bool	sanitize = `false`,
		bool	removeHs = `false`,
		bool	strictParsing = `true`
	)

inline

Parse a file in MDL rxn format into a ChemicalReaction.

Definition at line 207 of file ReactionParser.h.

◆ RxnSmartsToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnSmartsToChemicalReaction	(	const std::string &	text,
		std::map< std::string, std::string > *	replacements = `nullptr`,
		bool	useSmiles = `false`,
		bool	allowCXSMILES = `true`
	)

inline

Parse a string containing "Reaction SMARTS" into a ChemicalReaction.

Our definition of Reaction SMARTS is something that looks a lot like reaction SMILES, except that SMARTS queries are allowed on the reactant side and that atom-map numbers are required (at least for now)

Parameters

text	the SMARTS to convert
replacements	a string->string map of replacement strings.

See also: SmilesToMol for more information about replacements

Parameters

useSmiles	if set, the SMILES parser will be used instead of the SMARTS parserfor the individual components
allowCXSMILES	if set, any CXSMILES extensions present will be parsed, otherwise it will be ignored

Definition at line 114 of file ReactionParser.h.

◆ SmartsToAtom()

Atom * RDKit::v1::SmartsToAtom ( const std::string & sma )

inline

Definition at line 229 of file SmilesParse.h.

◆ SmartsToBond()

Bond * RDKit::v1::SmartsToBond ( const std::string & sma )

inline

Definition at line 232 of file SmilesParse.h.

◆ SmartsToMol() [1/2]

RWMol * RDKit::v1::SmartsToMol	(	const std::string &	sma,
		const SmartsParserParams &	ps
	)

inline

Definition at line 189 of file SmilesParse.h.

◆ SmartsToMol() [2/2]

RWMol * RDKit::v1::SmartsToMol	(	const std::string &	sma,
		int	debugParse = `0`,
		bool	mergeHs = `false`,
		std::map< std::string, std::string > *	replacements = `nullptr`
	)

inline

Construct a molecule from a SMARTS string.

Parameters

sma	the SMARTS to convert
debugParse	toggles verbose debugging information from the parser
mergeHs	toggles merging H atoms in the SMARTS into neighboring atoms
replacements	a string->string map of replacement strings.

See also: SmilesToMol for more information about replacements

Returns: a pointer to the new molecule; the caller is responsible for free'ing this.

Definition at line 217 of file SmilesParse.h.

◆ SmilesToAtom()

Atom * RDKit::v1::SmilesToAtom ( const std::string & smi )

inline

Definition at line 135 of file SmilesParse.h.

◆ SmilesToBond()

Bond * RDKit::v1::SmilesToBond ( const std::string & smi )

inline

Definition at line 140 of file SmilesParse.h.

◆ SmilesToMol() [1/2]

RDKit::RWMol * RDKit::v1::SmilesToMol	(	const std::string &	smi,
		const SmilesParserParams &	ps
	)

inline

Definition at line 118 of file SmilesParse.h.

◆ SmilesToMol() [2/2]

RWMol * RDKit::v1::SmilesToMol	(	const std::string &	smi,
		int	debugParse = `0`,
		bool	sanitize = `true`,
		std::map< std::string, std::string > *	replacements = `nullptr`
	)

inline

Construct a molecule from a SMILES string.

Parameters

smi	the SMILES to convert
debugParse	toggles verbose debugging information from the parser
sanitize	toggles H removal and sanitization of the molecule
replacements	a string->string map of replacement strings. See below for more information about replacements.

Returns: a pointer to the new molecule; the caller is responsible for free'ing this.

The optional replacements map can be used to do string substitution of abbreviations in the input SMILES. The set of substitutions is repeatedly looped through until the string no longer changes. It is the responsibility of the caller to make sure that substitutions results in legal and sensible SMILES.

Examples of substitutions:

CC{Q}C with {"{Q}":"OCCO"} -> CCOCCOC
C{A}C{Q}C with {"{Q}":"OCCO", "{A}":"C1(CC1)"} -> CC1(CC1)COCCOC
C{A}C{Q}C with {"{Q}":"{X}CC{X}", "{A}":"C1CC1", "{X}":"N"} -> CC1CC1CNCCNC

Definition at line 171 of file SmilesParse.h.

◆ TPLDataStreamToMol()

RWMol * RDKit::v1::TPLDataStreamToMol	(	std::istream *	inStream,
		unsigned int &	line,
		bool	sanitize = `true`,
		bool	skipFirstConf = `false`
	)

inline

translate TPL data (BioCad format) into a multi-conf molecule

Parameters

inStream	the stream from which to read
line	used to track the line number of errors
sanitize	toggles sanitization and stereochemistry perception of the molecule
skipFirstConf	according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set.

Definition at line 179 of file FileParsers.h.

◆ TPLFileToMol()

RWMol * RDKit::v1::TPLFileToMol	(	const std::string &	fName,
		bool	sanitize = `true`,
		bool	skipFirstConf = `false`
	)

inline

construct a multi-conf molecule from a TPL (BioCad format) file

Parameters

fName	the name of the file from which to read
sanitize	toggles sanitization and stereochemistry perception of the molecule
skipFirstConf	according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set.

Definition at line 203 of file FileParsers.h.

◆ XYZBlockToMol()

RWMol * RDKit::v1::XYZBlockToMol ( const std::string & xyzBlock )

inline

Parameters

xyzBlock - string containing the xyz block

Definition at line 350 of file FileParsers.h.

◆ XYZDataStreamToMol()

RWMol * RDKit::v1::XYZDataStreamToMol ( std::istream & inStream )

inline

Definition at line 343 of file FileParsers.h.

◆ XYZFileToMol()

RWMol * RDKit::v1::XYZFileToMol ( const std::string & fName )

inline

Parameters

fName - string containing the file name

Definition at line 357 of file FileParsers.h.

Classes

Functions

Function Documentation

◆ CDXMLDataStreamToMols()

◆ CDXMLFileToMols()

◆ CDXMLToMols()

◆ Mol2BlockToMol()

◆ Mol2DataStreamToMol() [1/2]

◆ Mol2DataStreamToMol() [2/2]

◆ Mol2FileToMol()

◆ MolBlockToMol()

◆ MolDataStreamToMol() [1/2]

◆ MolDataStreamToMol() [2/2]

◆ MolFileToMol()

◆ MrvBlockIsReaction()

◆ MrvBlockToChemicalReaction()

◆ MrvBlockToMol()

◆ MrvDataStreamIsReaction() [1/2]

◆ MrvDataStreamIsReaction() [2/2]

◆ MrvDataStreamToChemicalReaction() [1/2]

◆ MrvDataStreamToChemicalReaction() [2/2]

◆ MrvDataStreamToMol() [1/2]

◆ MrvDataStreamToMol() [2/2]

◆ MrvFileIsReaction()

◆ MrvFileToChemicalReaction()

◆ MrvFileToMol()

◆ PDBBlockToMol() [1/2]

◆ PDBBlockToMol() [2/2]

◆ PDBDataStreamToMol() [1/2]

◆ PDBDataStreamToMol() [2/2]

◆ PDBFileToMol()

◆ PNGFileToChemicalReaction()

◆ PNGStreamToChemicalReaction()

◆ PNGStringToChemicalReaction()

◆ RxnBlockToChemicalReaction()

◆ RxnDataStreamToChemicalReaction()

◆ RxnFileToChemicalReaction()

◆ RxnSmartsToChemicalReaction()

◆ SmartsToAtom()

◆ SmartsToBond()

◆ SmartsToMol() [1/2]

◆ SmartsToMol() [2/2]

◆ SmilesToAtom()

◆ SmilesToBond()

◆ SmilesToMol() [1/2]

◆ SmilesToMol() [2/2]

◆ TPLDataStreamToMol()

◆ TPLFileToMol()

◆ XYZBlockToMol()

◆ XYZDataStreamToMol()

◆ XYZFileToMol()