#include <BALL/FORMAT/HMOFile.h>

Inheritance diagram for BALL::HMOFile:

Classes
class	HMOCharge

Public Types
Nested classes and enums
enum	ElementType { L2 = 60, L3 = 63, T3 = 103, T6 = 106, Q4 = 104, Q8 = 108, TH4 = 204, TH10 = 210, P6 = 206, P15 = 215, H8 = 208, H20 = 220 }

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 }

Public Member Functions
Constructors and Destructor
	HMOFile ()
	Default constructor. More...

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

virtual	~HMOFile ()
	Destructor. More...

Assignment
virtual void	clear ()
	Clear method. More...

Predicates
bool	operator== (const HMOFile &file)
	Equality operator. More...

Accessors
bool	hasCharges () const
	Test for the presence of charges. More...

std::vector< HMOCharge > &	getCharges ()
	Accessor for the vector of charges. More...

std::vector< HMOCharge > const &	getCharges () const
	Accessor for the vector of charges, const version. More...

bool	hasComments () const
	Test for the presence of comments. More...

std::vector< String > &	getComments ()
	Accessor for the vector of comments. More...

std::vector< String > const &	getComments () const
	Accessor for the vector of comments, const version. More...

Public methods for file handling
virtual bool	open (const String &name, File::OpenMode open_mode=std::ios::in)

virtual bool	read (Surface &surface)

virtual bool	write (Surface const &surface)

virtual bool	write (Surface const &surface, AtomContainer const &ac)

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

Protected Member Functions
void	readNodeData_ (Surface &surface)

void	readElementData_ (Surface &surface)

void	readChargeData_ ()

bool	readUntil_ (String const &pattern)

void	writeNodes_ (Surface const &surface)

void	writeElements_ (Surface const &surface)

void	writeCharges_ (AtomContainer const &ac)

Protected Attributes
std::vector< HMOCharge >	charges_

std::vector< String >	comments_

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
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 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...

Static Protected Attributes inherited from BALL::File
static HashSet< String >	created_temp_filenames_

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

HMO mesh file format.

This class enables BALL to read and write the HMO format for polygonal meshes of surfaces. For the moment, we do not implement all variants allowed by HMO, but rather focus on triangular surface meshes. In addition, we read and write an extension to HMO (CHARGE_DATA), which contains information about positions and magnitudes of partially charged atoms in the system.

Definition at line 32 of file HMOFile.h.

Member Enumeration Documentation

enum BALL::HMOFile::ElementType

Enumerator
L2
L3
T3
T6
Q4
Q8
TH4
TH10
P6
P15
H8
H20

Definition at line 51 of file HMOFile.h.

Constructor & Destructor Documentation

BALL::HMOFile::HMOFile ( )

Default constructor.

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

Detailed constructor

Exceptions

Exception::FileNotFound if the file could not be opened

virtual BALL::HMOFile::~HMOFile ( )

virtual

Destructor.

Member Function Documentation

virtual void BALL::HMOFile::clear ( )

virtual

Clear method.

Reimplemented from BALL::File.

std::vector<HMOCharge>& BALL::HMOFile::getCharges ( )

inline

Accessor for the vector of charges.

Definition at line 114 of file HMOFile.h.

std::vector<HMOCharge> const& BALL::HMOFile::getCharges ( ) const

inline

Accessor for the vector of charges, const version.

Definition at line 120 of file HMOFile.h.

std::vector<String>& BALL::HMOFile::getComments ( )

inline

Accessor for the vector of comments.

Definition at line 132 of file HMOFile.h.

std::vector<String> const& BALL::HMOFile::getComments ( ) const

inline

Accessor for the vector of comments, const version.

Definition at line 138 of file HMOFile.h.

bool BALL::HMOFile::hasCharges ( ) const

inline

Test for the presence of charges.

Definition at line 108 of file HMOFile.h.

bool BALL::HMOFile::hasComments ( ) const

inline

Test for the presence of comments.

Definition at line 126 of file HMOFile.h.

virtual bool BALL::HMOFile::open	(	const String &	name,
		File::OpenMode	open_mode = `std::ios::in`
	)

virtual

Open an HMOFile

Exceptions

Exception::FileNotFound if the file could not be opened

bool BALL::HMOFile::operator== ( const HMOFile & file )

Equality operator.

virtual bool BALL::HMOFile::read ( Surface & surface )

virtual

Read the file into a Surface

Exceptions

Exception::ParseError if the file was invalid

void BALL::HMOFile::readChargeData_ ( )

protected

void BALL::HMOFile::readElementData_ ( Surface & surface )

protected

void BALL::HMOFile::readNodeData_ ( Surface & surface )

protected

bool BALL::HMOFile::readUntil_ ( String const & pattern )

protected

virtual bool BALL::HMOFile::write ( Surface const & surface )

virtual

Write a given surface to an HMO file

If the vector of comments is not empty, it is prepended to the written file. Otherwise, a generic comment is used.

Return true if the file could be written succesfully, false otherwise

virtual bool BALL::HMOFile::write	(	Surface const &	surface,
		AtomContainer const &	ac
	)

virtual

Write a given surface and the charges contained in a given AtomContainer to an HMO file

If the vector of comments is not empty, it is prepended to the written file. Otherwise, a generic comment is used.

Return true if the file could be written successfully, false otherwise

void BALL::HMOFile::writeCharges_ ( AtomContainer const & ac )

protected

void BALL::HMOFile::writeElements_ ( Surface const & surface )

protected

void BALL::HMOFile::writeNodes_ ( Surface const & surface )

protected

Member Data Documentation

std::vector<HMOCharge> BALL::HMOFile::charges_

protected

Definition at line 181 of file HMOFile.h.

std::vector<String> BALL::HMOFile::comments_

protected

Definition at line 184 of file HMOFile.h.

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation