Avogadro::Primitive Class Reference

Base class for all primitives (Molecule, Atom, Bond, Residue, ...). More...

#include <avogadro/primitive.h>

Inheritance diagram for Avogadro::Primitive:

List of all members.

Public Types
enum	Type {   OtherType = 0, MoleculeType, AtomType, BondType,   ResidueType, ChainType, FragmentType, SurfaceType,   MeshType, CubeType, PlaneType, GridType,   PointType, LineType, VectorType, NonbondedType,   TextType, LastType, FirstType = OtherType }
Signals
void	updated ()
Public Member Functions
	Primitive (QObject *parent=0)
	Primitive (Type type, QObject *parent=0)
virtual	~Primitive ()
void	update ()
Type	type () const
unsigned long	id () const
unsigned long	index () const
Protected Member Functions
void	setId (unsigned long m_id)
void	setIndex (unsigned long m_index)
	Primitive (PrimitivePrivate &dd, QObject *parent=0)
	Primitive (PrimitivePrivate &dd, Type type, QObject *parent=0)
Protected Attributes
PrimitivePrivate *const	d_ptr
enum Primitive::Type	m_type
unsigned long	m_id
unsigned long	m_index
Properties
Type	type

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Detailed Description

Base class for all primitives (Molecule, Atom, Bond, Residue, ...).

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Member Enumeration Documentation

enum Avogadro::Primitive::Type

This enum allows us to iterate through the various types of primitives.

Holds the primitive type

Enumerator:

OtherType	Untyped Primitive.
MoleculeType	Molecule Primitive.
AtomType	Atom Primitive.
BondType	Bond Primitive.
ResidueType	Residue Primitive.
ChainType	Chain Primitive (i.e., a set of residues)
FragmentType	Fragment Primitve.
SurfaceType	Surface Primitive.
MeshType	Surface Mesh Primitive.
CubeType	Cube Primitive.
PlaneType	Plane Primitive.
GridType	Grid Primitive.
PointType	Points (i.e., non-atoms)
LineType	Lines.
VectorType	Vectors (i.e., arrows, dipole moments)
NonbondedType	Non-bonded interactions (i.e., non-bond connections)
TextType	Text annoations.
LastType	End Placeholder.
FirstType	First Placeholder.

Reimplemented in Avogadro::Cube.

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Constructor & Destructor Documentation

Avogadro::Primitive::Primitive

(

QObject *

parent = 0

)

Default constructor.

Parameters:

parent

the object parent

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

Constructor

Parameters:

type	the primitive type
parent	the object parent

Avogadro::Primitive::~Primitive

(

)

[virtual]

Destructor

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Member Function Documentation

unsigned long Avogadro::Primitive::id

(

)

const [inline]

Returns:

The unique id of the primitive.

Referenced by Avogadro::Molecule::addAtom(), Avogadro::Molecule::addBond(), Avogadro::Atom::addBond(), Avogadro::Molecule::addCube(), Avogadro::Molecule::addMesh(), Avogadro::GLWidget::addNamedSelection(), Avogadro::Molecule::addResidue(), Avogadro::Molecule::addRing(), Avogadro::ZMatrix::addRow(), Avogadro::IDList::append(), Avogadro::Molecule::bond(), Avogadro::Protein::chainResidues(), Avogadro::Molecule::computeGeomInfo(), Avogadro::IDList::contains(), Avogadro::Molecule::copyAtomsAndBonds(), Avogadro::Molecule::operator+=(), Avogadro::IDList::removeAll(), Avogadro::Molecule::removeAtom(), Avogadro::Molecule::removeBond(), Avogadro::Atom::removeBond(), Avogadro::Molecule::removeCube(), Avogadro::Molecule::removeHydrogens(), Avogadro::Molecule::removeMesh(), Avogadro::Molecule::removeResidue(), Avogadro::Molecule::removeRing(), Avogadro::Molecule::setAtomPos(), Avogadro::Bond::setBegin(), Avogadro::Residue::setChainID(), Avogadro::Bond::setEnd(), Avogadro::Animation::setFrame(), setId(), Avogadro::Molecule::setOBMol(), Avogadro::Atom::setResidue(), and Avogadro::Molecule::translate().

unsigned long Avogadro::Primitive::index

(

)

const [inline]

Returns:

The index of the primitive.

Note:

Replaces GetIdx().

Referenced by Avogadro::Molecule::addConformer(), Avogadro::Molecule::addHydrogens(), Avogadro::Residue::atomId(), Avogadro::Molecule::energy(), Avogadro::Protein::isHelix(), Avogadro::Protein::isSheet(), Avogadro::NeighborList::nbrs(), Avogadro::Molecule::OBMol(), Avogadro::Molecule::operator+=(), Avogadro::Residue::removeAtom(), Avogadro::Fragment::removeAtom(), Avogadro::Molecule::removeAtom(), Avogadro::Fragment::removeBond(), Avogadro::Molecule::removeBond(), Avogadro::Atom::removeBond(), Avogadro::Molecule::removeCube(), Avogadro::Molecule::removeMesh(), Avogadro::Molecule::removeResidue(), Avogadro::Molecule::removeRing(), Avogadro::Residue::setAtomId(), Avogadro::Molecule::setConformer(), Avogadro::Molecule::setEnergy(), Avogadro::Atom::setGroupIndex(), setIndex(), Avogadro::Molecule::setOBMol(), Avogadro::Cube::setValue(), and Avogadro::Cube::value().

void Avogadro::Primitive::setId

(

unsigned long

m_id

)

[protected]

Set the id of the primitive, used to uniquely indentify the primitive.

Note:

That this should only be set by the container class.

References id().

Referenced by Avogadro::Molecule::addAtom(), Avogadro::Molecule::addBond(), Avogadro::Molecule::addCube(), Avogadro::Molecule::addMesh(), Avogadro::Molecule::addResidue(), Avogadro::Molecule::addRing(), and Avogadro::Molecule::operator=().

void Avogadro::Primitive::setIndex

(

unsigned long

m_index

)

[protected]

Set the index of the primitive, starting at zero.

Note:

That this should only be set by the container class.

References index().

Referenced by Avogadro::Molecule::addAtom(), Avogadro::Molecule::addBond(), Avogadro::Molecule::addCube(), Avogadro::Molecule::addMesh(), Avogadro::Molecule::addResidue(), Avogadro::Molecule::addRing(), Avogadro::Molecule::operator=(), and Avogadro::Molecule::removeAtom().

Type Avogadro::Primitive::type

(

)

const

Returns:

The primitive type (one of Primitive::Type)

void Avogadro::Primitive::update

(

)

Function used to push changes to a primitive to the rest of the system. At this time there is no way (other than this) to generate a signal when properties of a primitive change.

In the case of the Atom primitive, this should be called when changes to coordinates have been made.

Reimplemented in Avogadro::Molecule.

References updated().

Referenced by Avogadro::Atom::setAtomicNumber(), and Avogadro::GLWidget::setSelected().

void Avogadro::Primitive::updated

(

)

[signal]

Emitted when the primitive has been updated.

Referenced by Avogadro::Residue::addAtom(), Avogadro::Molecule::addAtom(), Avogadro::Molecule::addBond(), Avogadro::Molecule::addCube(), Avogadro::Molecule::addMesh(), Avogadro::Molecule::addResidue(), Avogadro::Molecule::addRing(), Avogadro::Molecule::Molecule(), Avogadro::Residue::removeAtom(), Avogadro::Molecule::removeAtom(), Avogadro::Molecule::removeBond(), Avogadro::Molecule::removeCube(), Avogadro::Molecule::removeMesh(), Avogadro::Molecule::removeResidue(), Avogadro::Molecule::removeRing(), Avogadro::Molecule::update(), update(), and Avogadro::Molecule::updateMolecule().

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

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