BALL::Fragment Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/fragment.h>

Inheritance diagram for BALL::Fragment:

List of all members.

Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES }
	The number of predefined properties for AtomContainer. More...
Public Member Functions
bool	operator== (const Fragment &fragment) const
bool	operator!= (const Fragment &fragment) const
Constructors and Destructors
	Fragment ()
	Fragment (const Fragment &fragment, bool deep=true)
	Fragment (const String &name)
virtual	~Fragment ()
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
Assignment
Fragment &	operator= (const Fragment &fragment)
Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const

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Detailed Description

Fragment class. Fragments are used to represent parts of molecules (for example functional groups, monomers in larger polymers).

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Member Enumeration Documentation

enum BALL::Fragment::Property

The number of predefined properties for AtomContainer.

Enumerator:

NUMBER_OF_PROPERTIES

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::Nucleotide, and BALL::Residue.

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Constructor & Destructor Documentation

BALL::Fragment::Fragment

(

)

Default constructor

BALL::Fragment::Fragment	(	const Fragment &	fragment,
		bool	deep = true
	)

Copy constructor

BALL::Fragment::Fragment

(

const String &

name

)

Constructor

virtual BALL::Fragment::~Fragment

(

)

[virtual]

Destructor

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Member Function Documentation

virtual void BALL::Fragment::dump	(	std::ostream &	s = std::cout,
		Size	depth = 0
	)			const [virtual]

Internal state dump. Dump the current internal state to the output ostream s with dumping depth depth .

Parameters:

	s	- output stream where to output the internal state
	depth	- the dumping depth

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::Nucleotide, and BALL::Residue.

bool BALL::Fragment::operator!=

(

const Fragment &

fragment

)

const

Inequality operator

See also:

operator ==

Fragment& BALL::Fragment::operator=

(

const Fragment &

fragment

)

Assignment operator.

Parameters:

fragment

the Fragment to be copied (cloned)

Returns:

Fragment& - this instance

bool BALL::Fragment::operator==

(

const Fragment &

fragment

)

const

Equality operator. Two fragments are equal if they have the same handle.

See also:

Object::operator ==.

void BALL::Fragment::persistentRead

(

PersistenceManager &

pm

)

throw (Exception::GeneralException) [virtual]

Reads a Fragment object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::Nucleotide, and BALL::Residue.

void BALL::Fragment::persistentWrite	(	PersistenceManager &	pm,
		const char *	name = 0
	)			const throw (Exception::GeneralException) [virtual]

Writes a Fragment object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::Nucleotide, and BALL::Residue.