BALL::Chain Class Reference
[Molecular Datastructures]

#include <chain.h>

Inheritance diagram for BALL::Chain:

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Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES }
	The number of predefined properties for AtomContainer.
Public Member Functions
bool	operator== (const Chain &chain) const
	Equality operator.
bool	operator!= (const Chain &chain) const
	Inequality operator.
Constructors and Destructors
	Chain ()
	Default constrcutor.
	Chain (const Chain &chain, bool deep=true)
	Copy constructor.
	Chain (const String &name)
	Detailled constructor.
virtual	~Chain ()
	Destructor.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Writes a Chain object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a Chain object from a persistent stream.
Assignment
void	set (const Chain &chain, bool deep=true)
	Assignment with cloning facility.
Chain &	operator= (const Chain &chain)
	Assignment operator.
void	get (Chain &chain, bool deep=true) const
	Copying with cloning facility.
void	swap (Chain &chain)
	Swapping of chains.
Accessors
Protein *	getProtein ()
	Get a pointer to the parent protein.
const Protein *	getProtein () const
	Get a constant pointer to the parent protein.
SecondaryStructure *	getSecondaryStructure (Position position)
	Get a pointer to a child SecondaryStructure at a given position.
const SecondaryStructure *	getSecondaryStructure (Position position) const
	Get a constant pointer to a child SecondaryStructure at a given position.
Residue *	getResidue (Position position)
	Get a pointer to a child Residue at a given position.
const Residue *	getResidue (Position position) const
	Get a pointer to a child Residue at a given position.
Residue *	getNTerminal ()
	Get a pointer to the N-terminal Residue.
const Residue *	getNTerminal () const
	Get a constant pointer to the N-terminal Residue.
Residue *	getCTerminal ()
	Get a pointer to the C-terminal Residue.
const Residue *	getCTerminal () const
	Get a constant pointer to the C-terminal Residue.
PDBAtom *	getPDBAtom (Position position)
	Get a pointer to a child PDBAtom at a given position.
const PDBAtom *	getPDBAtom (Position position) const
	Get a pointer to a child PDBAtom at a given position.
Size	countSecondaryStructures () const
	Count the SecondaryStructures.
Size	countResidues () const
	Count the Residues.
Size	countPDBAtoms () const
	Count the PDBAtoms.
void	prepend (SecondaryStructure &secondary_structure)
	Prepend a SecondaryStructure at position 0.
void	append (SecondaryStructure &secondary_structure)
	Append a SecondaryStructure after the last position.
void	insert (SecondaryStructure &secondary_structure)
	Insert a SecondaryStructure after the last position.
void	insertBefore (SecondaryStructure &secondary_structure, Composite &before)
	Insert a SecondaryStructure before a given Composite object.
void	insertAfter (SecondaryStructure &secondary_structure, Composite &after)
	Insert a SecondaryStructure after a given Composite object.
bool	remove (SecondaryStructure &secondary_structure)
	Remove a SecondaryStructure.
void	prepend (Residue &residue)
	Prepend a Residue at position 0.
void	append (Residue &residue)
	Append a Residue after the last position.
void	insert (Residue &residue)
	Insert a Residue after the last position.
void	insertBefore (Residue &residue, Composite &before)
	Insert a Residue before a given Composite object.
void	insertAfter (Residue &residue, Composite &after)
	Insert a Residue after a given Composite object.
bool	remove (Residue &residue)
	Remove a Residue.
void	spliceBefore (Chain &chain)
	Cut all children of `chain` and prepend them before the children of this chain.
void	spliceAfter (Chain &chain)
	Cut all children of `chain` and append them after the children of this chain.
void	splice (Chain &chain)
	Move the children of `chain` into this chain.
Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
	Internal state dump.

Detailed Description

Protein chain class.

This class represents a polypeptide chain within a Protein . Chains can contain SecondaryStructure s or Residue s.

Member Function Documentation

void BALL::Chain::append ( Residue & residue )

Append a Residue after the last position.

Parameters:

residue

the Residue to append

void BALL::Chain::append ( SecondaryStructure & secondary_structure )

Append a SecondaryStructure after the last position.

Parameters:

secondary_structure

the SecondaryStructure to append

Size BALL::Chain::countPDBAtoms ( ) const

Count the PDBAtoms.

Returns:: Size the number of PDBAtoms

Size BALL::Chain::countResidues ( ) const

Count the Residues.

Returns:: Size the number of residues

Size BALL::Chain::countSecondaryStructures ( ) const

Count the SecondaryStructures.

Returns:: Size the number of secondary structures

virtual void BALL::Chain::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.

void BALL::Chain::get	(	Chain &	chain,
		bool	deep = `true`
	)			const

Copying with cloning facility.

The assignment is either deep or shallow (default).

Parameters:

chain

the chain to be assigned to

See also:: chain::set

const Residue* BALL::Chain::getCTerminal ( ) const

Get a constant pointer to the C-terminal Residue.

The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - constant pointer to the C-terminal Residue

Residue* BALL::Chain::getCTerminal ( )

Get a pointer to the C-terminal Residue.

The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - mutable pointer to the C-terminal Residue

const Residue* BALL::Chain::getNTerminal ( ) const

Get a constant pointer to the N-terminal Residue.

The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - constant pointer to the N-terminal Residue

Residue* BALL::Chain::getNTerminal ( )

Get a pointer to the N-terminal Residue.

The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - mutable pointer to the N-terminal Residue

const PDBAtom* BALL::Chain::getPDBAtom ( Position position ) const

Get a pointer to a child PDBAtom at a given position.

The pointer is 0 if this instance does not have a PDBAtom at this position.

Parameters:

position

the position of the child PDBAtom

Returns:: PDBAtom* - constant pointer to the child PDBAtom at position

PDBAtom* BALL::Chain::getPDBAtom ( Position position )

Get a pointer to a child PDBAtom at a given position.

The pointer is 0 if this instance does not have a PDBAtom at this position.

Parameters:

position

the position of the child PDBAtom

Returns:: PDBAtom* - mutable pointer to the child PDBAtom at position

const Protein* BALL::Chain::getProtein ( ) const

Get a constant pointer to the parent protein.

The pointer is 0 if this instance does not have a parent protein.

Returns:: Protein* - constant pointer to the parent protein

Protein* BALL::Chain::getProtein ( )

Get a pointer to the parent protein.

The pointer is 0 if this instance does not have a parent protein.

Returns:: Protein* - mutable pointer to the parent protein

const Residue* BALL::Chain::getResidue ( Position position ) const

Get a pointer to a child Residue at a given position.

The pointer is 0 if this instance does not have a Residue at this position.

Parameters:

position

the position of the child Residue

Returns:: Residue* - constant pointer to the child Residue at position

Residue* BALL::Chain::getResidue ( Position position )

Get a pointer to a child Residue at a given position.

The pointer is 0 if this instance does not have a Residue at this position.

Parameters:

position

the position of the child Residue

Returns:: Residue* - mutable pointer to the child Residue at position

const SecondaryStructure* BALL::Chain::getSecondaryStructure ( Position position ) const

Get a constant pointer to a child SecondaryStructure at a given position.

The pointer is 0 if this instance does not have a SecondaryStructure at this position.

Parameters:

position

the position of the child SecondaryStructure

Returns:: SecondaryStructure* - constant pointer to the child SecondaryStructure at position

SecondaryStructure* BALL::Chain::getSecondaryStructure ( Position position )

Get a pointer to a child SecondaryStructure at a given position.

The pointer is 0 if this instance does not have a SecondaryStructure at this position.

Parameters:

position

the position of the child SecondaryStructure

Returns:: SecondaryStructure* - mutable pointer to the child SecondaryStructure at position

void BALL::Chain::insert ( Residue & residue )

Insert a Residue after the last position.

Parameters:

residue

the Residue to insert

void BALL::Chain::insert ( SecondaryStructure & secondary_structure )

Insert a SecondaryStructure after the last position.

Parameters:

secondary_structure

the SecondaryStructure to insert

void BALL::Chain::insertAfter	(	Residue &	residue,
		Composite &	after
	)

Insert a Residue after a given Composite object.

Parameters:

	residue	the Residue to insert
	after	the Composite object to insert after

void BALL::Chain::insertAfter	(	SecondaryStructure &	secondary_structure,
		Composite &	after
	)

Insert a SecondaryStructure after a given Composite object.

Parameters:

	secondary_structure	the SecondaryStructure to insert
	after	the Composite object to insert after

void BALL::Chain::insertBefore	(	Residue &	residue,
		Composite &	before
	)

Insert a Residue before a given Composite object.

Parameters:

	residue	the Residue to insert
	before	the Composite object to insert before

void BALL::Chain::insertBefore	(	SecondaryStructure &	secondary_structure,
		Composite &	before
	)

Insert a SecondaryStructure before a given Composite object.

Parameters:

	secondary_structure	the SecondaryStructure to insert
	before	the Composite object to insert before

bool BALL::Chain::operator!= ( const Chain & chain ) const

Inequality operator.

See also:: operator ==

Chain& BALL::Chain::operator= ( const Chain & chain )

Assignment operator.

The assignment is deep.

Parameters:

chain

the chain to be copied (cloned)

Returns:: chain& - this instance.

See also:: chain::set

bool BALL::Chain::operator== ( const Chain & chain ) const

Equality operator.

Two chains are equal if they have the same handle.

See also:: Object::operator ==

void BALL::Chain::persistentRead ( PersistenceManager & pm ) throw (Exception::GeneralException) [virtual]

Reads a Chain object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

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

Writes a Chain object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

void BALL::Chain::prepend ( Residue & residue )

Prepend a Residue at position 0.

Parameters:

residue

the Residue to prepend

void BALL::Chain::prepend ( SecondaryStructure & secondary_structure )

Prepend a SecondaryStructure at position 0.

Parameters:

secondary_structure

the SecondaryStructure to prepend

bool BALL::Chain::remove ( Residue & residue )

Remove a Residue.

Parameters:

residue

the Residue to remove

bool BALL::Chain::remove ( SecondaryStructure & secondary_structure )

Remove a SecondaryStructure.

Parameters:

secondary_structure

the SecondaryStructure to remove

void BALL::Chain::set	(	const Chain &	chain,
		bool	deep = `true`
	)

Assignment with cloning facility.

The assignment is either deep or shallow (default).

Parameters:

	chain	the chain to be copied (cloned)
	deep	make a deep (=`true`) or shallow (=`false`) copy

void BALL::Chain::splice ( Chain & chain )

Move the children of chain into this chain.

The children of chain are inserted using spliceBefore .

void BALL::Chain::spliceAfter ( Chain & chain )

Cut all children of chain and append them after the children of this chain.

Parameters:

chain

the chain to access

void BALL::Chain::spliceBefore ( Chain & chain )

Cut all children of chain and prepend them before the children of this chain.

Parameters:

chain

the chain to access

void BALL::Chain::swap ( Chain & chain )

Swapping of chains.

Parameters:

chain

the chain this instance is being swapped with

BALL::Chain Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Detailed Description

Member Function Documentation

BALL::Chain Class Reference
[Molecular Datastructures]