BALL::MOL2File Class Reference

#include <BALL/FORMAT/MOL2File.h>

Inheritance diagram for BALL::MOL2File:

Classes
struct	AtomStruct
struct	BondStruct
struct	CommentStruct
struct	MoleculeStruct
struct	SetStruct
	A class used for storing TRIPOS sets. More...
struct	SubstructureStruct

Public Member Functions
Constructors and Destructors
	MOL2File ()
	MOL2File (const String &filename, File::OpenMode open_mode=std::ios::in)
virtual	~MOL2File ()
	Destructor. More...
Reading and Writing of Kernel Datastructures
virtual bool	write (const System &system)
virtual bool	read (System &system)
virtual Molecule *	read ()
virtual bool	write (const Molecule &molecule)
const MOL2File &	operator= (const MOL2File &file)
Size	getNumberOfSets () const
	Return the number of TRIPOS-Sets defined in this instance. More...
SetStruct &	getSet (Position i)
	Return the i-th TRIPOS set. NOTE: no range checking is performed. More...
const SetStruct &	getSet (Position i) const
	Return the i-th TRIPOS set, const version. NOTE: no range checking is performed. More...
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

Static Public Attributes
Constants
static const String	TRIPOS
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
void	readAtomSection_ ()
void	readBondSection_ ()
void	readMoleculeSection_ ()
void	readSetSection_ ()
void	readSubstructureSection_ ()
void	readCommentSection_ ()
String	getSybylType_ (const Atom &atom) const
bool	nextLine_ ()
void	clear_ ()
bool	buildAll_ (Molecule &molecule)
bool	containsAtomChilds_ (AtomContainerConstIterator &frag_it)
Protected Member Functions inherited from BALL::GenericMolFile
virtual void	initRead_ ()
virtual void	initWrite_ ()

Protected Attributes
vector< AtomStruct >	atoms_
vector< BondStruct >	bonds_
vector< SetStruct >	sets_
vector< SubstructureStruct >	substructures_
vector< CommentStruct >	comments_
MoleculeStruct	molecule_
Size	number_of_lines_
char	buffer_ [4096]
String	line_
bool	found_next_header_
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_

Static Protected Attributes
static const Size	MAX_LENGTH_
Static Protected Attributes inherited from BALL::File
static HashSet< String >	created_temp_filenames_
static TransformationManager	transformation_manager_
static Size	transformation_methods_

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)

Detailed Description

SYBYL MOL2 file class. This class is used to read and write SYBYL MOL2 files (Tripos).

Definition at line 30 of file MOL2File.h.

Constructor & Destructor Documentation

BALL::MOL2File::MOL2File

(

)

Default constructor

BALL::MOL2File::MOL2File	(	const String &	filename,
		File::OpenMode	open_mode = std::ios::in
	)

Detailed constructor

Exceptions

Exception::FileNotFound

if the file could not be opened

virtual BALL::MOL2File::~MOL2File ( )

virtual

Destructor.

Member Function Documentation

bool BALL::MOL2File::buildAll_ ( Molecule &  molecule )

protected

void BALL::MOL2File::clear_ ( )

protected

bool BALL::MOL2File::containsAtomChilds_ ( AtomContainerConstIterator &  frag_it )

protected

Size BALL::MOL2File::getNumberOfSets ( ) const

inline

Return the number of TRIPOS-Sets defined in this instance.

Definition at line 105 of file MOL2File.h.

SetStruct& BALL::MOL2File::getSet ( Position  i )

inline

Return the i-th TRIPOS set. NOTE: no range checking is performed.

Definition at line 108 of file MOL2File.h.

const SetStruct& BALL::MOL2File::getSet ( Position  i ) const

inline

Return the i-th TRIPOS set, const version. NOTE: no range checking is performed.

Definition at line 111 of file MOL2File.h.

String BALL::MOL2File::getSybylType_ ( const Atom &  atom ) const

protected

bool BALL::MOL2File::nextLine_ ( )

protected

const MOL2File& BALL::MOL2File::operator=

(

const MOL2File &

file

)

virtual bool BALL::MOL2File::read ( System &  system )

virtual

Read a system from the MOL2 file

Exceptions

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

virtual Molecule* BALL::MOL2File::read ( )

virtual

Read a molecule from the MOL2 file

Exceptions

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

void BALL::MOL2File::readAtomSection_ ( )

protected

void BALL::MOL2File::readBondSection_ ( )

protected

void BALL::MOL2File::readCommentSection_ ( )

protected

void BALL::MOL2File::readMoleculeSection_ ( )

protected

void BALL::MOL2File::readSetSection_ ( )

protected

void BALL::MOL2File::readSubstructureSection_ ( )

protected

virtual bool BALL::MOL2File::write ( const System &  system )

virtual

Write a system to the MOL2 file

Exceptions

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::MOL2File::write ( const Molecule &  molecule )

virtual

Write a molecule to a HIN file.

Exceptions

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

Member Data Documentation

vector<AtomStruct> BALL::MOL2File::atoms_

protected

Definition at line 188 of file MOL2File.h.

vector<BondStruct> BALL::MOL2File::bonds_

protected

Definition at line 189 of file MOL2File.h.

char BALL::MOL2File::buffer_[4096]

protected

Definition at line 197 of file MOL2File.h.

vector<CommentStruct> BALL::MOL2File::comments_

protected

Definition at line 192 of file MOL2File.h.

bool BALL::MOL2File::found_next_header_

protected

Definition at line 199 of file MOL2File.h.

String BALL::MOL2File::line_

protected

Definition at line 198 of file MOL2File.h.

const Size BALL::MOL2File::MAX_LENGTH_

staticprotected

Definition at line 196 of file MOL2File.h.

MoleculeStruct BALL::MOL2File::molecule_

protected

Definition at line 193 of file MOL2File.h.

Size BALL::MOL2File::number_of_lines_

protected

Definition at line 195 of file MOL2File.h.

vector<SetStruct> BALL::MOL2File::sets_

protected

Definition at line 190 of file MOL2File.h.

vector<SubstructureStruct> BALL::MOL2File::substructures_

protected

Definition at line 191 of file MOL2File.h.

const String BALL::MOL2File::TRIPOS

static

Tripos Record Type Identifier (RTI)

Definition at line 56 of file MOL2File.h.