BALL::HINFile Class Reference

#include <BALL/FORMAT/HINFile.h>

Inheritance diagram for BALL::HINFile:

List of all members.

Public Member Functions
Constructors and Destructors
	HINFile ()
	HINFile (const String &filename, File::OpenMode open_mode=std::ios::in)
virtual	~HINFile ()
Assignment.
const HINFile &	operator= (const HINFile &rhs)
Reading and Writing of Kernel Datastructures
virtual bool	write (const Molecule &molecule)
virtual bool	write (const System &system)
virtual Molecule *	read ()
virtual bool	read (System &system)
Accessors
bool	hasPeriodicBoundary () const
SimpleBox3	getPeriodicBoundary () const
float	getTemperature () const
Protected Member Functions
virtual void	initRead_ ()
	Initialize temperature and box dimensions prior to reading a system.
void	writeAtom_ (const Atom &atom, Size number, Size atom_offset)
Protected Attributes
SimpleBox3	box_
float	temperature_

---

Detailed Description

HyperChem file class. This class enables BALL to read and write HyperChem HIN files.

Note: HIN defines a Molecule as a connected component in the molecule graph If you read e.g. a protein from a PDBFile, such that no bonds are set each atom will be placed into its own molecule. To prevent this from happening use the FragmentDB to build missing bonds.

Definition at line 29 of file HINFile.h.

---

Constructor & Destructor Documentation

BALL::HINFile::HINFile

(

)

Default constructor

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

Detailed constructor

Exceptions:

Exception::FileNotFound

if the file could not be opened

virtual BALL::HINFile::~HINFile

(

)

[virtual]

Destructor

---

Member Function Documentation

SimpleBox3 BALL::HINFile::getPeriodicBoundary

(

)

const

Return the periodic boundary of the file. An empty box is returned if no periodic boundary is defined.

Returns:

the boundary box

float BALL::HINFile::getTemperature

(

)

const

Return the temperature stored in the file. HIN files may contain a sys entry containing the temperature of the last simulation step. If it is set, it is returned. Otherwise 0 is returned.

Returns:

the final simulation temperature

bool BALL::HINFile::hasPeriodicBoundary

(

)

const

Check for a periodic boundary in the file.

virtual void BALL::HINFile::initRead_

(

)

[protected, virtual]

Initialize temperature and box dimensions prior to reading a system.

Reimplemented from BALL::GenericMolFile.

const HINFile& BALL::HINFile::operator=

(

const HINFile &

rhs

)

Assignment operator.

Exceptions:

Exception::FileNotFound

if the file could not be opened

virtual Molecule* BALL::HINFile::read

(

)

[virtual]

Read a molecule from the HIN file

Exceptions:

Exception::ParseError

if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::HINFile::read

(

System &

system

)

[virtual]

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::HINFile::write

(

const Molecule &

molecule

)

[virtual]

Write a molecule to a HIN file. Note that this changes the properties of atoms in the system.

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::HINFile::write

(

const System &

system

)

[virtual]

Write a system to a HIN file. Note that this changes the properties of atoms in the system.

Exceptions:

File::CannotWrite

if writing to the file failed

Reimplemented from BALL::GenericMolFile.

void BALL::HINFile::writeAtom_	(	const Atom &	atom,
		Size	number,
		Size	atom_offset
	)		[protected]

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Member Data Documentation

SimpleBox3 BALL::HINFile::box_ [protected]

Definition at line 114 of file HINFile.h.

float BALL::HINFile::temperature_ [protected]

Definition at line 119 of file HINFile.h.