Avogadro::Residue Class Reference

A biological residue that contains atoms and bonds. More...

#include <avogadro/residue.h>

Inheritance diagram for Avogadro::Residue:

List of all members.

Public Member Functions
	Residue (QObject *parent=0)
	~Residue ()
void	addAtom (unsigned long id)
void	removeAtom (unsigned long id)
void	setNumber (const QString &number)
QString	number ()
void	setChainNumber (unsigned int number)
unsigned int	chainNumber ()
void	setChainID (char id)
char	chainID ()
bool	setAtomId (unsigned long id, QString atomId)
bool	setAtomIds (const QList< QString > &atomIds)
QString	atomId (unsigned long id)
const QList< QString > &	atomIds () const
Protected Attributes
QString	m_number
QList< QString >	m_atomId
unsigned int	m_chainNumber
char	m_chainID

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Detailed Description

A biological residue that contains atoms and bonds.

Author:

Marcus D. Hanwell

The Residue class is a Fragment subclass that provides the unique additional information required for residues.

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Constructor & Destructor Documentation

Avogadro::Residue::Residue

(

QObject *

parent = 0

)

Constructor.

Avogadro::Residue::~Residue

(

)

Destructor.

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Member Function Documentation

void Avogadro::Residue::addAtom

(

unsigned long

id

)

Add an Atom to the Fragment.

Reimplemented from Avogadro::Fragment.

References Avogadro::Molecule::atomById(), QObject::connect(), QList::contains(), Avogadro::Fragment::m_atoms, QList::push_back(), Avogadro::Atom::setResidue(), and Avogadro::Primitive::updated().

Referenced by Avogadro::Molecule::operator+=(), Avogadro::Molecule::operator=(), and Avogadro::Molecule::setOBMol().

QString Avogadro::Residue::atomId

(

unsigned long

id

)

Returns the atom text id, as in the Residue.

Parameters:

id	The unique id of the Atom.

Returns:

The text id of the supplied atom in the Residue.

References QList::at(), Avogadro::Primitive::index(), QList::indexOf(), m_atomId, Avogadro::Fragment::m_atoms, and QList::size().

Referenced by Avogadro::Molecule::OBMol().

const QList< QString > & Avogadro::Residue::atomIds

(

)

const

Returns:

QList of all atom text ids in the Residue.

References m_atomId.

Referenced by Avogadro::Molecule::operator+=(), Avogadro::Molecule::operator=(), and setAtomIds().

char Avogadro::Residue::chainID

(

)

Returns:

The chain ID (' ', 'A', 'B', ...) that the residue belongs to.

References m_chainID.

Referenced by Avogadro::Molecule::OBMol(), Avogadro::Molecule::operator+=(), and Avogadro::Molecule::operator=().

unsigned int Avogadro::Residue::chainNumber

(

)

Returns:

The chain number that the residue belongs to.

References m_chainNumber.

Referenced by Avogadro::Molecule::operator+=(), and Avogadro::Molecule::operator=().

QString Avogadro::Residue::number

(

)

Returns:

The "number" of the residue, e.g. 5A, 69, etc.

Referenced by Avogadro::Molecule::OBMol(), Avogadro::Molecule::operator+=(), Avogadro::Molecule::operator=(), setChainNumber(), and setNumber().

void Avogadro::Residue::removeAtom

(

unsigned long

id

)

Remove the Atom from the Fragment.

Reimplemented from Avogadro::Fragment.

References Avogadro::Molecule::atomById(), QObject::disconnect(), Avogadro::Primitive::index(), QList::indexOf(), Avogadro::Fragment::m_atoms, QList::removeAt(), Avogadro::Atom::setResidue(), and Avogadro::Primitive::updated().

bool Avogadro::Residue::setAtomId	(	unsigned long	id,
		QString	atomId
	)

Set the text id of the Atom.

Parameters:

id	The unique id of the Atom.
atomId	The text id of the Atom in the Residue.

Returns:

False if the atom id could not be set, true otherwise.

References Avogadro::Primitive::index(), QList::indexOf(), m_atomId, Avogadro::Fragment::m_atoms, QList::push_back(), QList::size(), and QString::trimmed().

Referenced by Avogadro::Molecule::setOBMol().

bool Avogadro::Residue::setAtomIds

(

const QList< QString > &

atomIds

)

Set the text id of all the Atom objects.

Parameters:

atomIds

QList containing the text ids of all the atoms.

Returns:

False if the atom ids could not be set, true otherwise.

References atomIds(), QList::clear(), m_atomId, Avogadro::Fragment::m_atoms, and QList::size().

Referenced by Avogadro::Molecule::operator+=(), and Avogadro::Molecule::operator=().

void Avogadro::Residue::setChainID

(

char

id

)

Set the chain ID (' ', 'A', 'B', ...) that this residue belongs to.

References Avogadro::Primitive::id(), and m_chainID.

Referenced by Avogadro::Molecule::operator+=(), Avogadro::Molecule::operator=(), and Avogadro::Molecule::setOBMol().

void Avogadro::Residue::setChainNumber

(

unsigned int

number

)

Set the chain number that this residue belongs to.

References m_chainNumber, and number().

Referenced by Avogadro::Molecule::operator+=(), Avogadro::Molecule::operator=(), and Avogadro::Molecule::setOBMol().

void Avogadro::Residue::setNumber

(

const QString &

number

)

Set the number of the Residue, as in the file, e.g. 5A, 69, etc.

References number().

Referenced by Avogadro::Molecule::operator+=(), Avogadro::Molecule::operator=(), and Avogadro::Molecule::setOBMol().

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Member Data Documentation

QList<QString> Avogadro::Residue::m_atomId [protected]

Residue number as in the file, e.g. 5A, 69, etc.

Referenced by atomId(), atomIds(), setAtomId(), and setAtomIds().

char Avogadro::Residue::m_chainID [protected]

The chain number that the residue belongs to.

Referenced by chainID(), and setChainID().

unsigned int Avogadro::Residue::m_chainNumber [protected]

Atom text ids.

Referenced by chainNumber(), and setChainNumber().

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The documentation for this class was generated from the following files:

• /home/kitware/dashboards/avogadro/libavogadro/src/residue.h
• /home/kitware/dashboards/avogadro/libavogadro/src/residue.cpp