vl::Atom Class Reference

The Atom class represents an atom to be used with the Molecule class. More...

#include <Atom.hpp>

Inheritance diagram for vl::Atom:

List of all members.

Public Member Functions
	Atom ()
	Atom (const Atom &other)
Atom &	operator= (const Atom &other)
	Assignment operator: does not assign the adjacent atoms.
bool	isAtomAdjacent (Atom *atom) const
const std::vector< Atom * > &	adjacentAtoms () const
std::vector< Atom * > &	adjacentAtoms ()
EAtomType	atomType () const
void	setAtomType (EAtomType type)
unsigned int	id () const
void	setId (unsigned int id)
const fvec3 &	coordinates () const
void	setCoordinates (const fvec3 &coordinates)
float	radius () const
void	setRadius (float radius)
void	setVisited (bool visited)
bool	visited () const
void	setAtomName (const std::string &name)
const std::string &	atomName () const
const fvec4 &	color () const
void	setColor (const fvec4 &color)
bool	visible () const
void	setVisible (bool visible)
void	setShowAtomName (bool show)
	Defines whether the atom name should be rendered or not. See also Molecule::setShowAtomNames().
bool	showAtomName () const
	Defines whether the atom name should be rendered or not. See also Molecule::setShowAtomNames().
Protected Attributes
fvec4	mColor
fvec3	mCoordinates
EAtomType	mAtomType
float	mRadius
std::vector< Atom * >	mAdjacentAtoms
std::string	mAtomName
unsigned int	mId
bool	mVisited
bool	mVisible
bool	mShowAtomName

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Detailed Description

The Atom class represents an atom to be used with the Molecule class.

See also:

• Molecule Visualization Tutorial
• Molecule
• Bond

Definition at line 51 of file Atom.hpp.

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Constructor & Destructor Documentation

vl::Atom::Atom

(

)

[inline]

Definition at line 56 of file Atom.hpp.

References vl::AT_Unknown, mAtomType, mColor, mCoordinates, mId, mRadius, mShowAtomName, mVisible, mVisited, and VL_DEBUG_SET_OBJECT_NAME.

vl::Atom::Atom

(

const Atom &

other )

[inline]

Definition at line 70 of file Atom.hpp.

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Member Function Documentation

Atom& vl::Atom::operator=

(

const Atom &

other )

[inline]

Assignment operator: does not assign the adjacent atoms.

Definition at line 73 of file Atom.hpp.

References mAtomName, mAtomType, mColor, mCoordinates, mId, mRadius, mShowAtomName, and mVisible.

bool vl::Atom::isAtomAdjacent

(

Atom *

atom )

const [inline]

Definition at line 89 of file Atom.hpp.

References adjacentAtoms().

Referenced by vl::RingExtractor::sortCycles().

const std::vector< Atom* >& vl::Atom::adjacentAtoms

(

)

const [inline]

Definition at line 97 of file Atom.hpp.

References mAdjacentAtoms.

Referenced by vl::Molecule::computeAtomAdjacency(), vl::RingExtractor::depthFirstVisit(), and isAtomAdjacent().

std::vector< Atom* >& vl::Atom::adjacentAtoms

(

)

[inline]

Definition at line 98 of file Atom.hpp.

References mAdjacentAtoms.

EAtomType vl::Atom::atomType

(

)

const [inline]

Definition at line 100 of file Atom.hpp.

References mAtomType.

Referenced by vl::Molecule::setAtomTypeVisible().

void vl::Atom::setAtomType

(

EAtomType

type )

[inline]

Definition at line 101 of file Atom.hpp.

References mAtomType.

unsigned int vl::Atom::id

(

)

const [inline]

Definition at line 103 of file Atom.hpp.

References mId.

Referenced by setId().

void vl::Atom::setId

(

unsigned int

id )

[inline]

Definition at line 104 of file Atom.hpp.

References id(), and mId.

const fvec3& vl::Atom::coordinates

(

)

const [inline]

Definition at line 106 of file Atom.hpp.

References mCoordinates.

Referenced by vl::Molecule::ballAndStickStyle(), vl::RingExtractor::keepPlanarCycles(), setCoordinates(), vl::Molecule::sticksStyle(), and vl::Molecule::wireframeStyle().

void vl::Atom::setCoordinates

(

const fvec3 &

coordinates )

[inline]

Definition at line 107 of file Atom.hpp.

References coordinates(), and mCoordinates.

float vl::Atom::radius

(

)

const [inline]

Definition at line 109 of file Atom.hpp.

References mRadius.

Referenced by setRadius().

void vl::Atom::setRadius

(

float

radius )

[inline]

Definition at line 110 of file Atom.hpp.

References mRadius, and radius().

void vl::Atom::setVisited

(

bool

visited )

[inline]

Definition at line 112 of file Atom.hpp.

References mVisited, and visited().

Referenced by vl::RingExtractor::bootstrap(), and vl::RingExtractor::depthFirstVisit().

bool vl::Atom::visited

(

)

const [inline]

Definition at line 113 of file Atom.hpp.

References mVisited.

Referenced by vl::RingExtractor::depthFirstVisit(), and setVisited().

void vl::Atom::setAtomName

(

const std::string &

name )

[inline]

Definition at line 115 of file Atom.hpp.

References mAtomName.

const std::string& vl::Atom::atomName

(

)

const [inline]

Definition at line 116 of file Atom.hpp.

References mAtomName.

Referenced by vl::Molecule::generateAtomLabel().

const fvec4& vl::Atom::color

(

)

const [inline]

Definition at line 118 of file Atom.hpp.

References mColor.

Referenced by vl::Molecule::ballAndStickStyle(), setColor(), vl::Molecule::sticksStyle(), and vl::Molecule::wireframeStyle().

void vl::Atom::setColor

(

const fvec4 &

color )

[inline]

Definition at line 119 of file Atom.hpp.

References color(), and mColor.

bool vl::Atom::visible

(

)

const [inline]

Definition at line 121 of file Atom.hpp.

References mVisible.

Referenced by vl::Molecule::generateAtomLabel(), setVisible(), and vl::Molecule::wireframeStyle().

void vl::Atom::setVisible

(

bool

visible )

[inline]

Definition at line 122 of file Atom.hpp.

References mVisible, and visible().

Referenced by vl::Molecule::setAtomTypeVisible().

void vl::Atom::setShowAtomName

(

bool

show )

[inline]

Defines whether the atom name should be rendered or not. See also Molecule::setShowAtomNames().

Definition at line 125 of file Atom.hpp.

References mShowAtomName.

bool vl::Atom::showAtomName

(

)

const [inline]

Defines whether the atom name should be rendered or not. See also Molecule::setShowAtomNames().

Definition at line 127 of file Atom.hpp.

References mShowAtomName.

Referenced by vl::Molecule::generateAtomLabel().

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Member Data Documentation

fvec4 vl::Atom::mColor [protected]

Definition at line 130 of file Atom.hpp.

Referenced by Atom(), color(), operator=(), and setColor().

fvec3 vl::Atom::mCoordinates [protected]

Definition at line 131 of file Atom.hpp.

Referenced by Atom(), coordinates(), operator=(), and setCoordinates().

EAtomType vl::Atom::mAtomType [protected]

Definition at line 132 of file Atom.hpp.

Referenced by Atom(), atomType(), operator=(), and setAtomType().

float vl::Atom::mRadius [protected]

Definition at line 133 of file Atom.hpp.

Referenced by Atom(), operator=(), radius(), and setRadius().

std::vector< Atom* > vl::Atom::mAdjacentAtoms [protected]

Definition at line 134 of file Atom.hpp.

Referenced by adjacentAtoms().

std::string vl::Atom::mAtomName [protected]

Definition at line 135 of file Atom.hpp.

Referenced by atomName(), operator=(), and setAtomName().

unsigned int vl::Atom::mId [protected]

Definition at line 136 of file Atom.hpp.

Referenced by Atom(), id(), operator=(), and setId().

bool vl::Atom::mVisited [protected]

Definition at line 138 of file Atom.hpp.

Referenced by Atom(), setVisited(), and visited().

bool vl::Atom::mVisible [protected]

Definition at line 140 of file Atom.hpp.

Referenced by Atom(), operator=(), setVisible(), and visible().

bool vl::Atom::mShowAtomName [protected]

Definition at line 142 of file Atom.hpp.

Referenced by Atom(), operator=(), setShowAtomName(), and showAtomName().

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

• /home/master/UCL/VisualizationLibrary/src/vlMolecule/Atom.hpp