Chain Class Reference
[Molecular Datastructures]

#include <chain.h>

Inheritance diagram for Chain:


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 throw ()
	Equality operator.
bool	operator!= (const Chain &chain) const throw ()
	Inequality operator.
Constructors and Destructors
	Chain () throw ()
	Default constrcutor.
	Chain (const Chain &chain, bool deep=true) throw ()
	Copy constructor.
	Chain (const String &name) throw ()
	Detailled constructor.
virtual	~Chain () throw ()
	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) throw ()
	Assignment with cloning facility.
Chain &	operator= (const Chain &chain) throw ()
	Assignment operator.
void	get (Chain &chain, bool deep=true) const throw ()
	Copying with cloning facility.
void	swap (Chain &chain) throw ()
	Swapping of chains.
Accessors
Protein *	getProtein () throw ()
	Get a pointer to the parent protein.
const Protein *	getProtein () const throw ()
	Get a constant pointer to the parent protein.
SecondaryStructure *	getSecondaryStructure (Position position) throw ()
	Get a pointer to a child SecondaryStructure at a given position.
const SecondaryStructure *	getSecondaryStructure (Position position) const throw ()
	Get a constant pointer to a child SecondaryStructure at a given position.
Residue *	getResidue (Position position) throw ()
	Get a pointer to a child Residue at a given position.
const Residue *	getResidue (Position position) const throw ()
	Get a pointer to a child Residue at a given position.
Residue *	getNTerminal () throw ()
	Get a pointer to the N-terminal Residue.
const Residue *	getNTerminal () const throw ()
	Get a constant pointer to the N-terminal Residue.
Residue *	getCTerminal () throw ()
	Get a pointer to the C-terminal Residue.
const Residue *	getCTerminal () const throw ()
	Get a constant pointer to the C-terminal Residue.
PDBAtom *	getPDBAtom (Position position) throw ()
	Get a pointer to a child PDBAtom at a given position.
const PDBAtom *	getPDBAtom (Position position) const throw ()
	Get a pointer to a child PDBAtom at a given position.
Size	countSecondaryStructures () const throw ()
	Count the SecondaryStructures.
Size	countResidues () const throw ()
	Count the Residues.
Size	countPDBAtoms () const throw ()
	Count the PDBAtoms.
void	prepend (SecondaryStructure &secondary_structure) throw ()
	Prepend a SecondaryStructure at position 0.
void	append (SecondaryStructure &secondary_structure) throw ()
	Append a SecondaryStructure after the last position.
void	insert (SecondaryStructure &secondary_structure) throw ()
	Insert a SecondaryStructure after the last position.
void	insertBefore (SecondaryStructure &secondary_structure, Composite &before) throw ()
	Insert a SecondaryStructure before a given Composite object.
void	insertAfter (SecondaryStructure &secondary_structure, Composite &after) throw ()
	Insert a SecondaryStructure after a given Composite object.
bool	remove (SecondaryStructure &secondary_structure) throw ()
	Remove a SecondaryStructure.
void	prepend (Residue &residue) throw ()
	Prepend a Residue at position 0.
void	append (Residue &residue) throw ()
	Append a Residue after the last position.
void	insert (Residue &residue) throw ()
	Insert a Residue after the last position.
void	insertBefore (Residue &residue, Composite &before) throw ()
	Insert a Residue before a given Composite object.
void	insertAfter (Residue &residue, Composite &after) throw ()
	Insert a Residue after a given Composite object.
bool	remove (Residue &residue) throw ()
	Remove a Residue.
void	spliceBefore (Chain &chain) throw ()
	Cut all children of `chain` and prepend them before the children of this chain.
void	spliceAfter (Chain &chain) throw ()
	Cut all children of `chain` and append them after the children of this chain.
void	splice (Chain &chain) throw ()
	Move the children of `chain` into this chain.
Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const throw ()
	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 Chain::append ( Residue & residue ) throw ()

Append a Residue after the last position.

Parameters:

residue the Residue to append

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

Append a SecondaryStructure after the last position.

Parameters:

secondary_structure the SecondaryStructure to append

Size Chain::countPDBAtoms ( ) const throw ()

Count the PDBAtoms.

Returns:
Size the number of PDBAtoms

Size Chain::countResidues ( ) const throw ()

Count the Residues.

Returns:
Size the number of residues

Size Chain::countSecondaryStructures ( ) const throw ()

Count the SecondaryStructures.

Returns:
Size the number of secondary structures

virtual void Chain::dump ( std::ostream & s = std::cout,

Size depth = 0

) const throw () [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 AtomContainer.

void Chain::get ( Chain & chain,

bool deep = true

) const throw ()

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* Chain::getCTerminal ( ) const throw ()

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* Chain::getCTerminal ( ) throw ()

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* Chain::getNTerminal ( ) const throw ()

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* Chain::getNTerminal ( ) throw ()

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* Chain::getPDBAtom ( Position position ) const throw ()

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* Chain::getPDBAtom ( Position position ) throw ()

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* Chain::getProtein ( ) const throw ()

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* Chain::getProtein ( ) throw ()

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* Chain::getResidue ( Position position ) const throw ()

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* Chain::getResidue ( Position position ) throw ()

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* Chain::getSecondaryStructure ( Position position ) const throw ()

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* Chain::getSecondaryStructure ( Position position ) throw ()

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 Chain::insert ( Residue & residue ) throw ()

Insert a Residue after the last position.

Parameters:

residue the Residue to insert

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

Insert a SecondaryStructure after the last position.

Parameters:

secondary_structure the SecondaryStructure to insert

void Chain::insertAfter ( Residue & residue,

Composite & after

) throw ()

Insert a Residue after a given Composite object.

Parameters:

residue the Residue to insert

after the Composite object to insert after

void Chain::insertAfter ( SecondaryStructure & secondary_structure,

Composite & after

) throw ()

Insert a SecondaryStructure after a given Composite object.

Parameters:

secondary_structure the SecondaryStructure to insert

after the Composite object to insert after

void Chain::insertBefore ( Residue & residue,

Composite & before

) throw ()

Insert a Residue before a given Composite object.

Parameters:

residue the Residue to insert

before the Composite object to insert before

void Chain::insertBefore ( SecondaryStructure & secondary_structure,

Composite & before

) throw ()

Insert a SecondaryStructure before a given Composite object.

Parameters:

secondary_structure the SecondaryStructure to insert

before the Composite object to insert before

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

Inequality operator.

See also:
operator ==

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

Assignment operator.
The assignment is deep.
Parameters:

chain the chain to be copied (cloned)

Returns:
chain& - this instance.

See also:
chain::set

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

Equality operator.
Two chains are equal if they have the same handle.
See also:
Object::operator ==

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

Reads a Chain object from a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from AtomContainer.

void 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 AtomContainer.

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

Prepend a Residue at position 0.

Parameters:

residue the Residue to prepend

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

Prepend a SecondaryStructure at position 0.

Parameters:

secondary_structure the SecondaryStructure to prepend

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

Remove a Residue.

Parameters:

residue the Residue to remove

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

Remove a SecondaryStructure.

Parameters:

secondary_structure the SecondaryStructure to remove

void Chain::set ( const Chain & chain,

bool deep = true

) throw ()

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 Chain::splice ( Chain & chain ) throw ()

Move the children of chain into this chain.
The children of chain are inserted using spliceBefore .

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

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

Parameters:

chain the chain to access

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

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

Parameters:

chain the chain to access

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

Swapping of chains.

Parameters:

chain the chain this instance is being swapped with

Chain Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Detailed Description

Member Function Documentation

Chain Class Reference
[Molecular Datastructures]