#include <star_parser.hh>

Inherited by ChemdictParser, ChemdictParser, MMCifReader, and MMCifReader.

Public Member Functions
	StarParser (std::istream &stream, bool items_as_row=false)

	StarParser (const String &filename, bool items_as_row=false)

virtual	~StarParser ()

virtual bool	OnBeginLoop (const StarLoopDesc &header)

virtual void	OnEndLoop ()

virtual void	OnDataRow (const StarLoopDesc &header, const std::vector< StringRef > &columns)

virtual void	OnDataItem (const StarDataItem &item)

virtual bool	OnBeginData (const StringRef &data_name)

virtual void	OnEndData ()

Real	TryGetReal (const StringRef &data, const String &name) const

Real	GetRealOrDefault (const StringRef &data, const String &name, Real alt, bool(*is_default)(StringRef)) const

float	TryGetFloat (const StringRef &data, const String &name) const

std::pair< bool, float >	TryGetFloat (const StringRef &data, const String &name, bool may_fail) const

int	TryGetInt (const StringRef &data, const String &name) const

std::pair< bool, int >	TryGetInt (const StringRef &data, const String &name, bool may_fail) const

bool	TryGetBool (const StringRef &data, const String &name) const

String	FormatDiagnostic (StarDiagType type, const String &message, int line=-1) const

void	SetFilename (const String &filename)

int	GetCurrentLinenum () const

void	Parse ()

	StarParser (std::istream &stream, bool items_as_row=false)

	StarParser (const String &filename, bool items_as_row=false)

virtual	~StarParser ()

virtual bool	OnBeginLoop (const StarLoopDesc &header)

virtual void	OnEndLoop ()

virtual void	OnDataRow (const StarLoopDesc &header, const std::vector< StringRef > &columns)

virtual void	OnDataItem (const StarDataItem &item)

virtual bool	OnBeginData (const StringRef &data_name)

virtual void	OnEndData ()

Real	TryGetReal (const StringRef &data, const String &name) const

Real	GetRealOrDefault (const StringRef &data, const String &name, Real alt, bool(*is_default)(StringRef)) const

float	TryGetFloat (const StringRef &data, const String &name) const

std::pair< bool, float >	TryGetFloat (const StringRef &data, const String &name, bool may_fail) const

int	TryGetInt (const StringRef &data, const String &name) const

std::pair< bool, int >	TryGetInt (const StringRef &data, const String &name, bool may_fail) const

bool	TryGetBool (const StringRef &data, const String &name) const

String	FormatDiagnostic (StarDiagType type, const String &message, int line=-1) const

void	SetFilename (const String &filename)

int	GetCurrentLinenum () const

void	Parse ()

Static Public Member Functions
static bool	SplitLine (const StringRef &line, std::vector< StringRef > &parts, bool clear=true)

static bool	IsUndefined (StringRef value)

static bool	SplitLine (const StringRef &line, std::vector< StringRef > &parts, bool clear=true)

static bool	IsUndefined (StringRef value)

Detailed Description

parser for the STAR file format

STAR format description

In essence, STAR files are structured text files. A few simple control structures control the interpretation of the content.

Commented lines start with a '#'.
a data section starts with data_<id> and ends, whenever another data block starts or at the end of the file.
data-items consist of a name-value pair. Names start with an underscore and are made up of a category and an identifier. The category and the identifier are separated by a '.'. The name is followed by a simple or quoted value.
lists of data items are specified using the loop_ keyword, followed by a list of column names and values.

Definition at line 114 of file star_parser.hh.

Constructor & Destructor Documentation

◆ StarParser() [1/4]

StarParser	(	std::istream &	stream,
		bool	items_as_row = `false`
	)

explicit

create a StarParser

Parameters

stream	input stream
items_as_row	if true, data-items are first gathered (identifier as header, values as row) and then parsed like a loop (OnBeginLoop(), OnDataRow(), OnEndLoop())

◆ StarParser() [2/4]

StarParser	(	const String &	filename,
		bool	items_as_row = `false`
	)

explicit

◆ ~StarParser() [1/2]

virtual ~StarParser ( )

inlinevirtual

Definition at line 124 of file star_parser.hh.

◆ StarParser() [3/4]

StarParser	(	std::istream &	stream,
		bool	items_as_row = `false`
	)

explicit

create a StarParser

Parameters

stream	input stream
items_as_row	if true, data-items are first gathered (identifier as header, values as row) and then parsed like a loop (OnBeginLoop(), OnDataRow(), OnEndLoop())

◆ StarParser() [4/4]

StarParser	(	const String &	filename,
		bool	items_as_row = `false`
	)

explicit

◆ ~StarParser() [2/2]

virtual ~StarParser ( )

inlinevirtual

Definition at line 124 of file star_parser.hh.

Member Function Documentation

◆ FormatDiagnostic() [1/2]

String FormatDiagnostic	(	StarDiagType	type,
		const String &	message,
		int	line = `-1`
	)		const

format diagnostic and returns it as a string.

◆ FormatDiagnostic() [2/2]

String FormatDiagnostic	(	StarDiagType	type,
		const String &	message,
		int	line = `-1`
	)		const

format diagnostic and returns it as a string.

◆ GetCurrentLinenum() [1/2]

int GetCurrentLinenum ( ) const

inline

retrieve the line, the parser is currently working on

Definition at line 232 of file star_parser.hh.

◆ GetCurrentLinenum() [2/2]

int GetCurrentLinenum ( ) const

inline

retrieve the line, the parser is currently working on

Definition at line 232 of file star_parser.hh.

◆ GetRealOrDefault() [1/2]

Real GetRealOrDefault	(	const StringRef &	data,
		const String &	name,
		Real	alt,
		bool(*)(StringRef)	is_default
	)		const

try to convert a value to Real, on failure return default value.

Parameters

data	value to be converted
name	to be included in the message
alt	value
is_default	a function to check if data is a default value.

Returns: converted or alt value

◆ GetRealOrDefault() [2/2]

Real GetRealOrDefault	(	const StringRef &	data,
		const String &	name,
		Real	alt,
		bool(*)(StringRef)	is_default
	)		const

try to convert a value to Real, on failure return default value.

Parameters

data	value to be converted
name	to be included in the message
alt	value
is_default	a function to check if data is a default value.

Returns: converted or alt value

◆ IsUndefined() [1/2]

static bool IsUndefined ( StringRef value )

inlinestatic

Definition at line 242 of file star_parser.hh.

◆ IsUndefined() [2/2]

static bool IsUndefined ( StringRef value )

inlinestatic

Definition at line 242 of file star_parser.hh.

◆ OnBeginData() [1/2]

virtual bool OnBeginData ( const StringRef & data_name )

inlinevirtual

invoked when a new data control structure is encountered

Returns: When true, for each data-item belonging to the data block, OnDataItem() is invoked. For every loop, OnBeginLoop() is called.

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 149 of file star_parser.hh.

◆ OnBeginData() [2/2]

virtual bool OnBeginData ( const StringRef & data_name )

inlinevirtual

invoked when a new data control structure is encountered

Returns: When true, for each data-item belonging to the data block, OnDataItem() is invoked. For every loop, OnBeginLoop() is called.

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 149 of file star_parser.hh.

◆ OnBeginLoop() [1/2]

virtual bool OnBeginLoop ( const StarLoopDesc & header )

inlinevirtual

called when a loop is encountered

Returns: When true, for each row in the loop, OnDataRow() is returned. If false, the loop is skipped.

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 131 of file star_parser.hh.

◆ OnBeginLoop() [2/2]

virtual bool OnBeginLoop ( const StarLoopDesc & header )

inlinevirtual

called when a loop is encountered

Returns: When true, for each row in the loop, OnDataRow() is returned. If false, the loop is skipped.

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 131 of file star_parser.hh.

◆ OnDataItem() [1/2]

virtual void OnDataItem ( const StarDataItem & item )

inlinevirtual

invoked when a data item is encountered

Reimplemented in ChemdictParser, and ChemdictParser.

Definition at line 144 of file star_parser.hh.

◆ OnDataItem() [2/2]

virtual void OnDataItem ( const StarDataItem & item )

inlinevirtual

invoked when a data item is encountered

Reimplemented in ChemdictParser, and ChemdictParser.

Definition at line 144 of file star_parser.hh.

◆ OnDataRow() [1/2]

virtual void OnDataRow	(	const StarLoopDesc &	header,
		const std::vector< StringRef > &	columns
	)

inlinevirtual

invoked when a data row in a loop is encountered.

Parameters

header	describes the row format
columns	contains the data columns

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 139 of file star_parser.hh.

◆ OnDataRow() [2/2]

virtual void OnDataRow	(	const StarLoopDesc &	header,
		const std::vector< StringRef > &	columns
	)

inlinevirtual

invoked when a data row in a loop is encountered.

Parameters

header	describes the row format
columns	contains the data columns

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 139 of file star_parser.hh.

◆ OnEndData() [1/2]

virtual void OnEndData ( )

inlinevirtual

called when leaving a datasection. Will only be invoked when OnBeginData() returned true.

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 153 of file star_parser.hh.

◆ OnEndData() [2/2]

virtual void OnEndData ( )

inlinevirtual

called when leaving a datasection. Will only be invoked when OnBeginData() returned true.

Reimplemented in MMCifReader, ChemdictParser, MMCifReader, and ChemdictParser.

Definition at line 153 of file star_parser.hh.

◆ OnEndLoop() [1/2]

virtual void OnEndLoop ( )

inlinevirtual

invoked when leaving a loop

OnEndLoop() is only invoked, when OnBeginLoop() returned true.

Definition at line 135 of file star_parser.hh.

◆ OnEndLoop() [2/2]

virtual void OnEndLoop ( )

inlinevirtual

invoked when leaving a loop

OnEndLoop() is only invoked, when OnBeginLoop() returned true.

Definition at line 135 of file star_parser.hh.

◆ Parse() [1/2]

void Parse ( )

◆ Parse() [2/2]

void Parse ( )

◆ SetFilename() [1/2]

void SetFilename ( const String & filename )

inline

Definition at line 226 of file star_parser.hh.

◆ SetFilename() [2/2]

void SetFilename ( const String & filename )

inline

Definition at line 226 of file star_parser.hh.

◆ SplitLine() [1/2]

static bool SplitLine	(	const StringRef &	line,
		std::vector< StringRef > &	parts,
		bool	clear = `true`
	)

static

◆ SplitLine() [2/2]

static bool SplitLine	(	const StringRef &	line,
		std::vector< StringRef > &	parts,
		bool	clear = `true`
	)

static

◆ TryGetBool() [1/2]

bool TryGetBool	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to bool, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

◆ TryGetBool() [2/2]

bool TryGetBool	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to bool, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

◆ TryGetFloat() [1/4]

float TryGetFloat	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to float, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

◆ TryGetFloat() [2/4]

float TryGetFloat	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to float, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

◆ TryGetFloat() [3/4]

std::pair<bool, float> TryGetFloat	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)		const

try to convert a value to float, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message
may_fail	decides if an exception is raised (false) or not (true)

Returns: converted value

◆ TryGetFloat() [4/4]

std::pair<bool, float> TryGetFloat	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)		const

try to convert a value to float, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message
may_fail	decides if an exception is raised (false) or not (true)

Returns: converted value

◆ TryGetInt() [1/4]

int TryGetInt	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to integer, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

◆ TryGetInt() [2/4]

int TryGetInt	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to integer, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

◆ TryGetInt() [3/4]

std::pair<bool, int> TryGetInt	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)		const

try to convert a value to integer, exception can be turned off.

Parameters

data	value to be converted
name	to be included in the message
may_fail	decides if an exception is raised (false) or not (true)

Returns: pair with value and indicator if conversion worked

◆ TryGetInt() [4/4]

std::pair<bool, int> TryGetInt	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)		const

try to convert a value to integer, exception can be turned off.

Parameters

data	value to be converted
name	to be included in the message
may_fail	decides if an exception is raised (false) or not (true)

Returns: pair with value and indicator if conversion worked

◆ TryGetReal() [1/2]

Real TryGetReal	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to Real, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

◆ TryGetReal() [2/2]

Real TryGetReal	(	const StringRef &	data,
		const String &	name
	)		const

try to convert a value to Real, on failure raise an exception.

Parameters

data	value to be converted
name	to be included in the message

Returns: converted value

The documentation for this class was generated from the following file:

build-2.9.0-doc/stage/include/ost/io/mol/star_parser.hh

Public Member Functions

Static Public Member Functions

Detailed Description

STAR format description

Constructor & Destructor Documentation

◆ StarParser() [1/4]

◆ StarParser() [2/4]

◆ ~StarParser() [1/2]

◆ StarParser() [3/4]

◆ StarParser() [4/4]

◆ ~StarParser() [2/2]

Member Function Documentation

◆ FormatDiagnostic() [1/2]

◆ FormatDiagnostic() [2/2]

◆ GetCurrentLinenum() [1/2]

◆ GetCurrentLinenum() [2/2]

◆ GetRealOrDefault() [1/2]

◆ GetRealOrDefault() [2/2]

◆ IsUndefined() [1/2]

◆ IsUndefined() [2/2]

◆ OnBeginData() [1/2]

◆ OnBeginData() [2/2]

◆ OnBeginLoop() [1/2]

◆ OnBeginLoop() [2/2]

◆ OnDataItem() [1/2]

◆ OnDataItem() [2/2]

◆ OnDataRow() [1/2]

◆ OnDataRow() [2/2]

◆ OnEndData() [1/2]

◆ OnEndData() [2/2]

◆ OnEndLoop() [1/2]

◆ OnEndLoop() [2/2]

◆ Parse() [1/2]

◆ Parse() [2/2]

◆ SetFilename() [1/2]

◆ SetFilename() [2/2]

◆ SplitLine() [1/2]

◆ SplitLine() [2/2]

◆ TryGetBool() [1/2]

◆ TryGetBool() [2/2]

◆ TryGetFloat() [1/4]

◆ TryGetFloat() [2/4]

◆ TryGetFloat() [3/4]

◆ TryGetFloat() [4/4]

◆ TryGetInt() [1/4]

◆ TryGetInt() [2/4]

◆ TryGetInt() [3/4]

◆ TryGetInt() [4/4]

◆ TryGetReal() [1/2]

◆ TryGetReal() [2/2]