BALL::XYZFile Class Reference
[Molecular structure file formats]

#include <BALL/FORMAT/XYZFile.h>

Inheritance diagram for BALL::XYZFile:

[legend]

List of all members.

Public Member Functions
Constructors and Destructors
	XYZFile ()
	XYZFile (const String &filename, File::OpenMode open_mode=std::ios::in)
virtual	~XYZFile ()
Reading and Writing of Kernel Datastructures
String	comment_
virtual bool	write (const AtomContainer &ac)
virtual bool	write (const System &system)
virtual bool	write (const Molecule &mol)
virtual bool	read (System &system)
virtual Molecule *	read ()
BALL_DEPRECATED const String &	getComent () const
const String &	getComment () const
const XYZFile &	operator= (const XYZFile &file)

---

Detailed Description

XYZ file class. This class enables BALL to read and write XMol XYZ files. The XYZ format is a very simple molecular file format. In general it contains only the atom type (i.e., the element) and the cartesian coordinates of the structure. Newer versions of this file format also contain bonds (without bond order) and atom names.

The first line of each XYZ file contains a single integer number: the number of atoms in the file. The second line is just a comment line. When reading a XYZ file, BALL stores this comment as the name attribute of the system read. Similarly, on writing the system, it's name is written to this comment line. All remaining lines contain the element symbol and the three coordinates in free format.

Definition at line 34 of file XYZFile.h.

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Constructor & Destructor Documentation

BALL::XYZFile::XYZFile

(

)

Default constructor

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

Detailed constructor. Create a XYZ file and open it with mode open_mode (reading is default)

Parameters:

	filename	the filename
	open_mode	the openmode - default is File::IN

Exceptions:

Exception::FileNotFound

if the file could not be opened

virtual BALL::XYZFile::~XYZFile

(

)

[virtual]

Destructor

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Member Function Documentation

BALL_DEPRECATED const String& BALL::XYZFile::getComent

(

)

const [inline]

Deprecated:

Instead of this method use XYZFile::getComment()

Definition at line 90 of file XYZFile.h.

const String& BALL::XYZFile::getComment

(

)

const [inline]

Definition at line 93 of file XYZFile.h.

const XYZFile& BALL::XYZFile::operator=

(

const XYZFile &

file

)

[private]

virtual Molecule* BALL::XYZFile::read

(

)

[virtual]

Read a molecule from the XYZ file

Exceptions:

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::XYZFile::read

(

System &

system

)

[virtual]

Read a system from the XYZ file

Exceptions:

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::XYZFile::write

(

const Molecule &

mol

)

[virtual]

Write a molecule to the XYZ file

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::XYZFile::write

(

const System &

system

)

[virtual]

Write a system to the XYZ file

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::XYZFile::write

(

const AtomContainer &

ac

)

[virtual]

Write an AtomContainer to the XYZ file

Exceptions:

File::CannotWrite

if writing to the file failed

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Member Data Documentation

String BALL::XYZFile::comment_ [private]

Definition at line 98 of file XYZFile.h.