BALL::GAMESSLogFile Class Reference

#include <BALL/FORMAT/GAMESSLogFile.h>

Inheritance diagram for BALL::GAMESSLogFile:

Classes
struct	State

Public Member Functions
Constructors and Destructors
	GAMESSLogFile ()
	GAMESSLogFile (const GAMESSLogFile &file)
	GAMESSLogFile (const String &filename, File::OpenMode open_mode=std::ios::in)
virtual	~GAMESSLogFile ()
Assignment.
const GAMESSLogFile &	operator= (const GAMESSLogFile &rhs)
Reading and Writing of Kernel Logastructures
virtual bool	write (const Molecule &molecule)
virtual bool	write (const System &molecule)
virtual Molecule *	read ()
virtual bool	read (System &system)
Accessors
void	newMolecule ()
void	setMoleculeName (char *name)
void	insertAtom (const String &element, float charge, float x, float y, float z)
void	insertBond (Index a1, Index a2)
void	clearBonds ()
void	setCurrentCharge (float charge)
void	setUnitConversionFactor (float factor)
void	addCoefficient (float coefficient)
void	initializeBasisSet ()
QMBasisSet &	getBasisSet ()
const QMBasisSet &	getBasisSet () const
void	addBasisOption (const String &key, const String &value)
String	getBasisOption (const String &key)
Public Member Functions inherited from BALL::GenericMolFile
	GenericMolFile ()
	GenericMolFile (const String &filename, File::OpenMode open_mode=std::ios::in)
virtual	~GenericMolFile ()
virtual void	close ()
const GenericMolFile &	operator= (const GenericMolFile &rhs)
void	defineInputAsTemporary (bool b=true)
void	enableOutputCompression (String zipped_filename)
bool	isCompressedFile ()
virtual GenericMolFile &	operator>> (System &system)
virtual GenericMolFile &	operator<< (const System &system)
virtual GenericMolFile &	operator>> (Molecule &molecule)
virtual GenericMolFile &	operator<< (const Molecule &molecule)
Public Member Functions inherited from BALL::LineBasedFile
	LineBasedFile ()
	Default constructor. More...
	LineBasedFile (const String &filename, File::OpenMode open_mode=std::ios::in, bool trim_whitespaces=false)
void	clear ()
bool	operator== (const LineBasedFile &f)
bool	operator!= (const LineBasedFile &f)
const LineBasedFile &	operator= (const LineBasedFile &file)
Position	getLineNumber () const
	Get the last line number in the file. More...
const String &	getLine () const
	Return the current line. More...
String &	getLine ()
	Return the current line. More...
bool	readLine ()
bool	skipLines (Size number=1)
bool	search (const String &text, bool return_to_start=false)
bool	search (const String &text, const String &stop, bool return_to_start=false)
bool	gotoLine (Position line_number)
void	rewind ()
void	test (const char *file, int line, bool condition, const String &msg) const
String	getField (Index pos=0, const String &quotes="", const String &delimiters=String::CHARACTER_CLASS__WHITESPACE) const
bool	startsWith (const String &text) const
	Test if the current line starts with text. More...
bool	has (const String &text) const
	Return true if the current line contains text. More...
Index	switchString (const std::vector< String > &data) const
bool	parseColumnFormat (const char *format, Position index, Size length, void *arg)
void	enableTrimWhitespaces (bool state)
	Set wheter leading and trailing whitespaces in lines shall be removed. More...
bool	trimWhiteSpacesEnabled () const
Public Member Functions inherited from BALL::File
	File ()
	File (const String &name, OpenMode open_mode=std::ios::in)
virtual	~File ()
bool	isValid () const
bool	open (const String &name, File::OpenMode open_mode=std::ios::in)
bool	reopen ()
bool	reopen (File::OpenMode open_mode)
void	close ()
const String &	getName () const
void	setName (const String &name)
const String &	getOriginalName () const
Size	getSize ()
File::OpenMode	getOpenMode () const
Type	getType (bool trace_link) const
bool	copyTo (const String &destination_name, Size buffer_size=4096)
bool	moveTo (const String &destination_name)
bool	remove ()
bool	renameTo (const String &new_path)
bool	truncate (Size size=0)
std::fstream &	getFileStream ()
TransformationManager &	getTransformationManager ()
const TransformationManager &	getTransformationManager () const
bool	operator== (const File &file) const
bool	operator!= (const File &file) const
bool	isOpen () const
bool	isClosed () const
bool	isAccessible () const
bool	isCanonized () const
bool	isReadable () const
bool	isWritable () const
bool	isExecutable () const

Public Attributes
Index	current_atom
Index	current_set
Index	current_coefficient_line
Size	basis_size
bool	molecule_already_defined
System *	system

Static Public Attributes
static State	state
Static Public Attributes inherited from BALL::File
static const OpenMode	MODE_IN
	Open for input (default) More...
static const OpenMode	MODE_OUT
	Open for output. More...
static const OpenMode	MODE_APP
	Append. Seek to end before each write operation. More...
static const OpenMode	MODE_BINARY
	Binary mode. More...
static const OpenMode	MODE_ATE
	Seek to end directly after opening. More...
static const OpenMode	MODE_TRUNC
	Truncate an existing file. More...
static const String	TRANSFORMATION_EXEC_PREFIX
	Prefix for filenames that are created through the execution of commands "exec:". More...
static const String	TRANSFORMATION_FILE_PREFIX
	Prefix for files (to mimick URL-like behavior) "file:". More...
static const String	TRANSFORMATION_FTP_PREFIX
	Prefix for FTP-transfers "ftp://". More...
static const String	TRANSFORMATION_HTTP_PREFIX
	Prefix for HTTP-transfer "http://". More...

Protected Member Functions
virtual void	initRead_ ()
Protected Member Functions inherited from BALL::GenericMolFile
virtual void	initWrite_ ()

Protected Attributes
Molecule *	molecule_
float	factor_
splitValenceSet	qmbs_
StringHashMap< String >	basis_options_
Protected Attributes inherited from BALL::GenericMolFile
bool	input_is_temporary_
bool	compress_output_
bool	gmf_is_closed_
String	zipped_filename_
Protected Attributes inherited from BALL::LineBasedFile
String	line_
	buffer for the line in use More...
Position	line_number_
	line number in the file More...
bool	trim_whitespaces_
vector< char >	col_buffer_
	buffer for column parsing More...
Protected Attributes inherited from BALL::File
String	name_
String	original_name_
OpenMode	open_mode_
bool	is_open_
bool	is_temporary_

Additional Inherited Members
Public Types inherited from BALL::File
typedef std::ios::openmode	OpenMode
enum	Transformation { TRANSFORMATION__EXEC = 1, TRANSFORMATION__FILTER = 2, TRANSFORMATION__URL = 3 }
enum	Type {   TYPE__UNKNOWN = 0, TYPE__DIRECTORY = 1, TYPE__CHAR_SPECIAL_FILE = 2, TYPE__BLOCK_SPECIAL_FILE = 3,   TYPE__REGULAR_FILE = 4, TYPE__SYMBOLIC_LINK = 5, TYPE__SOCKET = 6, TYPE__FIFO_SPECIAL_FILE = 7 }
Static Public Member Functions inherited from BALL::File
static Size	getSize (String name)
static Type	getType (String name, bool trace_link)
static bool	copy (String source_name, String destination_name, Size buffer_size=4096)
static bool	move (const String &source_name, const String &destination_name)
static bool	remove (String name)
static bool	rename (String old_path, String new_path)
static bool	truncate (String path, Size size=0)
static bool	createTemporaryFilename (String &temporary, const String &suffix=".TMP")
static void	enableTransformation (Transformation transformation)
static void	disableTransformation (Transformation transformation)
static bool	isTransformationEnabled (Transformation transformation)
static void	registerTransformation (const String &pattern, const String &exec)
static void	unregisterTransformation (const String &pattern)
static bool	isAccessible (String name)
static bool	isReadable (String name)
static bool	isWritable (String name)
static bool	isExecutable (String name)
Static Protected Attributes inherited from BALL::File
static HashSet< String >	created_temp_filenames_
static TransformationManager	transformation_manager_
static Size	transformation_methods_

Detailed Description

GAMESSLog file class. This class enables BALL to read and write input and output .log files for the GAMESS quantum chemistry application.

Definition at line 28 of file GAMESSLogFile.h.

Constructor & Destructor Documentation

BALL::GAMESSLogFile::GAMESSLogFile

(

)

Default constructor

BALL::GAMESSLogFile::GAMESSLogFile

(

const GAMESSLogFile &

file

)

Copy constructor

Exceptions

Exception::FileNotFound

if the file could not be opened

BALL::GAMESSLogFile::GAMESSLogFile	(	const String &	filename,
		File::OpenMode	open_mode = std::ios::in
	)

Detailed constructor

Exceptions

Exception::FileNotFound

if the file could not be opened

virtual BALL::GAMESSLogFile::~GAMESSLogFile ( )

virtual

Destructor

Member Function Documentation

void BALL::GAMESSLogFile::addBasisOption	(	const String &	key,
		const String &	value
	)

void BALL::GAMESSLogFile::addCoefficient

(

float

coefficient

)

void BALL::GAMESSLogFile::clearBonds

(

)

String BALL::GAMESSLogFile::getBasisOption

(

const String &

key

)

QMBasisSet& BALL::GAMESSLogFile::getBasisSet

(

)

const QMBasisSet& BALL::GAMESSLogFile::getBasisSet

(

)

const

void BALL::GAMESSLogFile::initializeBasisSet

(

)

virtual void BALL::GAMESSLogFile::initRead_ ( )

protectedvirtual

Initialize internals for read. This method is called by the default implementation of read(System& system) . Its purpose is the initialization of internal members holding, for example, header information from the file. The default implementation provided is empty.

Reimplemented from BALL::GenericMolFile.

void BALL::GAMESSLogFile::insertAtom	(	const String &	element,
		float	charge,
		float	x,
		float	y,
		float	z
	)

void BALL::GAMESSLogFile::insertBond	(	Index	a1,
		Index	a2
	)

void BALL::GAMESSLogFile::newMolecule

(

)

const GAMESSLogFile& BALL::GAMESSLogFile::operator=

(

const GAMESSLogFile &

rhs

)

Assignment operator.

Exceptions

Exception::FileNotFound

if the file could not be opened

virtual Molecule* BALL::GAMESSLogFile::read ( )

virtual

Read a Molecule from the GAMESSLogFile. If the GAMESS .log - file contains additional lines apart from the molecule itself, they are stored in this class.

Exceptions

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::GAMESSLogFile::read ( System &  system )

virtual

Read a System from the GAMESSLogFile. If the GAMESS .log - file contains additional lines apart from the molecule itself, they are stored in this class.

Exceptions

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

void BALL::GAMESSLogFile::setCurrentCharge

(

float

charge

)

void BALL::GAMESSLogFile::setMoleculeName

(

char *

name

)

void BALL::GAMESSLogFile::setUnitConversionFactor

(

float

factor

)

virtual bool BALL::GAMESSLogFile::write ( const Molecule &  molecule )

virtual

Write a molecule to a GAMESSLogFile. If additional GAMESS - keywords are stored in this class, they will be written as well.

Exceptions

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::GAMESSLogFile::write ( const System &  molecule )

virtual

Write a system to a GAMESSLogFile. If additional GAMESS - keywords are stored in this class, they will be written as well.

Exceptions

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

Member Data Documentation

StringHashMap<String> BALL::GAMESSLogFile::basis_options_

protected

Definition at line 160 of file GAMESSLogFile.h.

Size BALL::GAMESSLogFile::basis_size

Definition at line 143 of file GAMESSLogFile.h.

Index BALL::GAMESSLogFile::current_atom

Definition at line 140 of file GAMESSLogFile.h.

Index BALL::GAMESSLogFile::current_coefficient_line

Definition at line 142 of file GAMESSLogFile.h.

Index BALL::GAMESSLogFile::current_set

Definition at line 141 of file GAMESSLogFile.h.

float BALL::GAMESSLogFile::factor_

protected

Definition at line 156 of file GAMESSLogFile.h.

Molecule* BALL::GAMESSLogFile::molecule_

protected

Definition at line 155 of file GAMESSLogFile.h.

bool BALL::GAMESSLogFile::molecule_already_defined

Definition at line 144 of file GAMESSLogFile.h.

splitValenceSet BALL::GAMESSLogFile::qmbs_

protected

Definition at line 158 of file GAMESSLogFile.h.

State BALL::GAMESSLogFile::state

static

Definition at line 139 of file GAMESSLogFile.h.

System* BALL::GAMESSLogFile::system

All of this stuff should not really be placed here... we need a data structure for QM data sets that stores all the stuff here.

Definition at line 150 of file GAMESSLogFile.h.