BALL::Protein Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/protein.h>

Inheritance diagram for BALL::Protein:

[legend]

List of all members.

Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES }
Public Member Functions
bool	operator== (const Protein &protein) const
bool	operator!= (const Protein &protein) const
Constructors and Destructors
	Protein ()
	Default constructor.
	Protein (const Protein &protein, bool deep=true)
	Copy constructor.
	Protein (const String &name, const String &id=BALL_PROTEIN_DEFAULT_ID)
	Detailled constructor.
virtual	~Protein ()
	Destructor.
virtual void	clear ()
	Clears the contents of the protein.
virtual void	destroy ()
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const
void	persistentRead (PersistenceManager &pm)
Assignment Methods
void	set (const Protein &protein, bool deep=true)
Protein &	operator= (const Protein &protein)
void	get (Protein &protein, bool deep=true) const
void	swap (Protein &protein)
Accessors
Chain *	getChain (Position position)
const Chain *	getChain (Position position) const
SecondaryStructure *	getSecondaryStructure (Position position)
const SecondaryStructure *	getSecondaryStructure (Position position) const
Residue *	getResidue (Position position)
const Residue *	getResidue (Position position) const
Residue *	getResidueByID (String residue_ID)
const Residue *	getResidueByID (String residue_ID) const
Residue *	getNTerminal ()
const Residue *	getNTerminal () const
Residue *	getCTerminal ()
const Residue *	getCTerminal () const
PDBAtom *	getPDBAtom (Position position)
const PDBAtom *	getPDBAtom (Position position) const
void	setID (const String &id)
const String &	getID () const
Size	countChains () const
Size	countSecondaryStructures () const
Size	countResidues () const
Size	countPDBAtoms () const
Debugging and Diagnostics
virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
Private Attributes
String	id_

---

Detailed Description

Protein Class. This class is used to represent proteins. A protein may contain several Chain , SecondaryStructure , and Residue .

Definition at line 28 of file protein.h.

---

Member Enumeration Documentation

enum BALL::Protein::Property

Properties

Enumerator:

NUMBER_OF_PROPERTIES

Reimplemented from BALL::Molecule.

Definition at line 41 of file protein.h.

---

Constructor & Destructor Documentation

BALL::Protein::Protein

(

)

Default constructor.

BALL::Protein::Protein	(	const Protein &	protein,
		bool	deep = true
	)

Copy constructor.

BALL::Protein::Protein	(	const String &	name,
		const String &	id = BALL_PROTEIN_DEFAULT_ID
	)

Detailled constructor.

virtual BALL::Protein::~Protein

(

)

[virtual]

Destructor.

---

Member Function Documentation

virtual void BALL::Protein::clear

(

)

[virtual]

Clears the contents of the protein.

Reimplemented from BALL::AtomContainer.

Size BALL::Protein::countChains

(

)

const

Count the child chains.

Returns:

Size the number of chains

Size BALL::Protein::countPDBAtoms

(

)

const

Count the child PDB-Atoms.

Returns:

Size the number of PDB-Atoms

Size BALL::Protein::countResidues

(

)

const

Count the child Residues.

Returns:

Size the number of Residues

Size BALL::Protein::countSecondaryStructures

(

)

const

Count the child SecondaryStructures.

Returns:

Size the number of SecondaryStructures

virtual void BALL::Protein::destroy

(

)

[virtual]

Clear the contents of this instance of AtomContainer and removes it from parent composite structures. This methods clears the base fragment's name, destroys all its children (as in Composite::destroy ), and removes it from its parent composite structures.

Reimplemented from BALL::AtomContainer.

virtual void BALL::Protein::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::Molecule.

void BALL::Protein::get	(	Protein &	protein,
		bool	deep = true
	)			const

Copy this instance to protein . The assignment is either deep or shallow (default).

Parameters:

protein

the Protein to be assigned to

const Chain* BALL::Protein::getChain

(

Position

position

)

const

Get a pointer to a child chain at a given position. The pointer is 0 if this instance does not have a chain at the given position.

Parameters:

position

the position of the child chain

Returns:

Chain* - constant pointer to the child

Chain* BALL::Protein::getChain

(

Position

position

)

Get a pointer to a child chain at a given position. The pointer is 0 if this instance does not have a chain at the given position.

Parameters:

position

the position of the child chain

Returns:

Chain* - mutable pointer to the child

const Residue* BALL::Protein::getCTerminal

(

)

const

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* - constant pointer to the C-terminal Residue

Residue* BALL::Protein::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 String& BALL::Protein::getID

(

)

const

Retrieve the ID of the NucleicAcid.

Returns:

String the ID

const Residue* BALL::Protein::getNTerminal

(

)

const

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* - constant pointer to the N-terminal Residue

Residue* BALL::Protein::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::Protein::getPDBAtom

(

Position

position

)

const

Get a pointer to a child PDB-Atom at a given position. The pointer is 0 if this instance does not have a PDB-Atom at the given position.

Parameters:

position

the position of the child PDB-Atom

Returns:

Residue* - constant pointer to the child

PDBAtom* BALL::Protein::getPDBAtom

(

Position

position

)

Get a pointer to a child PDB-Atom at a given position. The pointer is 0 if this instance does not have a PDB-Atom at the given position.

Parameters:

position

the position of the child PDB-Atom

Returns:

Residue* - mutable pointer to the child

const Residue* BALL::Protein::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 the given position.

Parameters:

position

the position of the child Residue

Returns:

Residue* - constant pointer to the child

Residue* BALL::Protein::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 the given position.

Parameters:

position

the position of the child Residue

Returns:

Residue* - mutable pointer to the child

const Residue* BALL::Protein::getResidueByID

(

String

residue_ID

)

const

Get a pointer to a child Residue with the given ID. The pointer is 0 if this instance does not have a Residue with the given ID.

Parameters:

residue_ID

the ID of the residue

Returns:

Residue* - constant pointer to the child

Residue* BALL::Protein::getResidueByID

(

String

residue_ID

)

Get a pointer to a child Residue with the given ID. The pointer is 0 if this instance does not have a Residue with the given ID.

Parameters:

residue_ID

the ID of the residue

Returns:

Residue* - pointer to the child

const SecondaryStructure* BALL::Protein::getSecondaryStructure

(

Position

position

)

const

Get a pointer to a child SecondaryStructure at a given position. The pointer is 0 if this instance does not have a SecondaryStructure at the given position.

Parameters:

position

the position of the child SecondaryStructure

Returns:

SecondaryStructure* - constant pointer to the child

SecondaryStructure* BALL::Protein::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 the given position.

Parameters:

position

the position of the child SecondaryStructure

Returns:

SecondaryStructure* - mutable pointer to the child

virtual bool BALL::Protein::isValid

(

)

const [virtual]

Internal state and consistency self-validation.

Returns:

bool -true if the internal state of this instance is correct (self-validated) and consistent, false otherwise

Reimplemented from BALL::AtomContainer.

bool BALL::Protein::operator!=

(

const Protein &

protein

)

const

Inequality operator

See also:

operator ==

Protein& BALL::Protein::operator=

(

const Protein &

protein

)

Assignment operator.

Parameters:

protein

the Protein to be copied (cloned)

Returns:

Protein& - this instance

bool BALL::Protein::operator==

(

const Protein &

protein

)

const

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

See also:

Object::operator ==.

void BALL::Protein::persistentRead

(

PersistenceManager &

pm

)

[virtual]

Reads a Protein object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Molecule.

void BALL::Protein::persistentWrite	(	PersistenceManager &	pm,
		const char *	name = 0
	)			const [virtual]

Writes a Protein object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Molecule.

void BALL::Protein::set	(	const Protein &	protein,
		bool	deep = true
	)

Assignment with cloning facility. The assignment is either deep or shallow (default).

Parameters:

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

void BALL::Protein::setID

(

const String &

id

)

Set the ID of the NucleicAcid.

Parameters:

id

the new ID

void BALL::Protein::swap

(

Protein &

protein

)

Swapping of two proteins.

Parameters:

protein

to swap with this instance

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Member Data Documentation

String BALL::Protein::id_ [private]

Definition at line 303 of file protein.h.