Avogadro::Fragment Class Reference

A fragment containing atoms and bonds. More...

#include <avogadro/fragment.h>

Inheritance diagram for Avogadro::Fragment:

List of all members.

Public Member Functions
	Fragment (QObject *parent=0)
	Fragment (Type type, QObject *parent=0)
	~Fragment ()
QString	name () const
void	setName (QString name)
void	addAtom (unsigned long id)
void	removeAtom (unsigned long id)
QList< unsigned long >	atoms () const
void	addBond (unsigned long id)
void	removeBond (unsigned long id)
QList< unsigned long >	bonds () const
Protected Attributes
Molecule *	m_molecule
QString	m_name
QList< unsigned long >	m_atoms
QList< unsigned long >	m_bonds

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Detailed Description

A fragment containing atoms and bonds.

Author:

Marcus D. Hanwell

The Fragment class is a Primitive subclass that provides a generic way of addressing fragments. This is intended to be suitable for rings, residues, molecule fragments etc. That is anything that needs to address a subset of atoms/bonds in a Molecule.

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Constructor & Destructor Documentation

Avogadro::Fragment::Fragment

(

QObject *

parent = 0

)

Constructor

Parameters:

parent

the object parent.

References QObject::parent().

Avogadro::Fragment::Fragment	(	Type	type,
		QObject *	parent = 0
	)		[explicit]

Consttructor. This class is further inherited by Residue.

References QObject::parent().

Avogadro::Fragment::~Fragment

(

)

Destructor.

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Member Function Documentation

void Avogadro::Fragment::addAtom

(

unsigned long

id

)

Add an Atom to the Fragment.

Reimplemented in Avogadro::Residue.

References QList::contains(), m_atoms, and QList::push_back().

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

void Avogadro::Fragment::addBond

(

unsigned long

id

)

Add a Bond to the Fragment.

References QList::contains(), m_bonds, and QList::push_back().

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

QList< unsigned long > Avogadro::Fragment::atoms

(

)

const

Returns:

QList of the unique ids of the atoms in this Fragment.

References m_atoms.

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

QList< unsigned long > Avogadro::Fragment::bonds

(

)

const

Returns:

QList of the unique ids of the bonds in this Fragment.

References m_bonds.

QString Avogadro::Fragment::name

(

)

const [inline]

Returns:

the name of the fragment.

Note:

Replaces GetName().

Reimplemented from QObject.

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

void Avogadro::Fragment::removeAtom

(

unsigned long

id

)

Remove the Atom from the Fragment.

Reimplemented in Avogadro::Residue.

References Avogadro::Primitive::index(), QList::indexOf(), m_atoms, and QList::removeAt().

void Avogadro::Fragment::removeBond

(

unsigned long

id

)

Remove the Bond from the Fragment.

References Avogadro::Primitive::index(), QList::indexOf(), m_bonds, and QList::removeAt().

void Avogadro::Fragment::setName

(

QString

name

)

[inline]

Set the name of the fragment.

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

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Member Data Documentation

QList<unsigned long> Avogadro::Fragment::m_atoms [protected]

The name of the Fragment.

Referenced by Avogadro::Residue::addAtom(), addAtom(), Avogadro::Residue::atomId(), atoms(), Avogadro::Residue::removeAtom(), removeAtom(), Avogadro::Residue::setAtomId(), and Avogadro::Residue::setAtomIds().

QList<unsigned long> Avogadro::Fragment::m_bonds [protected]

QList of the atom ids.

Referenced by addBond(), bonds(), and removeBond().

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

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