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

#include <Atom.hpp>

Inheritance diagram for vl::Atom:

Public Member Functions
	Atom ()

	Atom (const Atom &other)

Atom &	operator= (const Atom &other)
	Assignment operator: does not assign the adjacent atoms. More...

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(). More...

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

Public Member Functions inherited from vl::Object
	Object ()
	Constructor. More...

	Object (const Object &other)
	Copy constructor: copies the name, ref count mutex and user data. More...

Object &	operator= (const Object &other)
	Copy operator: copies the object's name, ref count mutex and user data. More...

const std::string &	objectName () const
	The name of the object, by default set to the object's class name. More...

void	setObjectName (const char *name)
	The name of the object, by default set to the object's class name in debug builds. More...

void	setObjectName (const std::string &name)
	The name of the object, by default set to the object's class name in debug builds. More...

void	setRefCountMutex (IMutex *mutex)
	The mutex used to protect the reference counting of an Object across multiple threads. More...

IMutex *	refCountMutex ()
	The mutex used to protect the reference counting of an Object across multiple threads. More...

const IMutex *	refCountMutex () const
	The mutex used to protect the reference counting of an Object across multiple threads. More...

int	referenceCount () const
	Returns the number of references of an object. More...

void	incReference () const
	Increments the reference count of an object. More...

void	decReference ()
	Decrements the reference count of an object and deletes it if both automaticDelete() is `true` the count reaches 0. More...

void	setAutomaticDelete (bool autodel_on)
	If set to true the Object is deleted when its reference count reaches 0. More...

bool	automaticDelete () const
	If set to true the Object is deleted when its reference count reaches 0. More...

template<class T >
T *	as ()
	Casts an Object to the specified class. More...

template<class T >
const T *	as () const
	Casts an Object to the specified class. More...

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

Protected Attributes inherited from vl::Object
std::string	mObjectName

IMutex *	mRefCountMutex

int	mReferenceCount

bool	mAutomaticDelete

Additional Inherited Members
Protected Member Functions inherited from vl::Object
virtual	~Object ()

Detailed Description

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

See also

Definition at line 51 of file Atom.hpp.

Constructor & Destructor Documentation

◆ Atom() [1/2]

vl::Atom::Atom ( )

inline

Definition at line 56 of file Atom.hpp.

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

◆ Atom() [2/2]

vl::Atom::Atom ( const Atom & other )

inline

Definition at line 70 of file Atom.hpp.

Member Function Documentation

◆ adjacentAtoms() [1/2]

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().

◆ adjacentAtoms() [2/2]

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

inline

Definition at line 98 of file Atom.hpp.

References mAdjacentAtoms.

◆ atomName()

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

inline

Definition at line 116 of file Atom.hpp.

References mAtomName.

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

◆ atomType()

EAtomType vl::Atom::atomType ( ) const

inline

Definition at line 100 of file Atom.hpp.

References mAtomType.

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

◆ color()

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().

◆ coordinates()

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().

◆ id()

unsigned int vl::Atom::id ( ) const

inline

Definition at line 103 of file Atom.hpp.

References mId.

Referenced by setId().

◆ isAtomAdjacent()

bool vl::Atom::isAtomAdjacent ( Atom * atom ) const

inline

Definition at line 89 of file Atom.hpp.

References adjacentAtoms().

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

◆ operator=()

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.

◆ radius()

float vl::Atom::radius ( ) const

inline

Definition at line 109 of file Atom.hpp.

References mRadius.

Referenced by setRadius().

◆ setAtomName()

void vl::Atom::setAtomName ( const std::string & name )

inline

Definition at line 115 of file Atom.hpp.

References mAtomName.

◆ setAtomType()

void vl::Atom::setAtomType ( EAtomType type )

inline

Definition at line 101 of file Atom.hpp.

References mAtomType.

◆ setColor()

void vl::Atom::setColor ( const fvec4 & color )

inline

Definition at line 119 of file Atom.hpp.

References color(), and mColor.

◆ setCoordinates()

void vl::Atom::setCoordinates ( const fvec3 & coordinates )

inline

Definition at line 107 of file Atom.hpp.

References coordinates(), and mCoordinates.

◆ setId()

void vl::Atom::setId ( unsigned int id )

inline

Definition at line 104 of file Atom.hpp.

References id(), and mId.

◆ setRadius()

void vl::Atom::setRadius ( float radius )

inline

Definition at line 110 of file Atom.hpp.

References mRadius, and radius().

◆ setShowAtomName()

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.

◆ setVisible()

void vl::Atom::setVisible ( bool visible )

inline

Definition at line 122 of file Atom.hpp.

References mVisible, and visible().

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

◆ setVisited()

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().

◆ showAtomName()

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().

◆ visible()

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().

◆ visited()

bool vl::Atom::visited ( ) const

inline

Definition at line 113 of file Atom.hpp.

References mVisited.

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

Member Data Documentation

◆ mAdjacentAtoms

std::vector< Atom* > vl::Atom::mAdjacentAtoms

protected

Definition at line 134 of file Atom.hpp.

Referenced by adjacentAtoms().

◆ mAtomName

std::string vl::Atom::mAtomName

protected

Definition at line 135 of file Atom.hpp.

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

◆ mAtomType

EAtomType vl::Atom::mAtomType

protected

Definition at line 132 of file Atom.hpp.

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

◆ mColor

fvec4 vl::Atom::mColor

protected

Definition at line 130 of file Atom.hpp.

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

◆ mCoordinates

fvec3 vl::Atom::mCoordinates

protected

Definition at line 131 of file Atom.hpp.

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

◆ mId

unsigned int vl::Atom::mId

protected

Definition at line 136 of file Atom.hpp.

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

◆ mRadius

float vl::Atom::mRadius

protected

Definition at line 133 of file Atom.hpp.

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

◆ mShowAtomName

bool vl::Atom::mShowAtomName

protected

Definition at line 142 of file Atom.hpp.

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

◆ mVisible

bool vl::Atom::mVisible

protected

Definition at line 140 of file Atom.hpp.

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

◆ mVisited

bool vl::Atom::mVisited

protected

Definition at line 138 of file Atom.hpp.

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

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

C:/git/VL/src/vlMolecule/Atom.hpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Atom() [1/2]

◆ Atom() [2/2]

Member Function Documentation

◆ adjacentAtoms() [1/2]

◆ adjacentAtoms() [2/2]

◆ atomName()

◆ atomType()

◆ color()

◆ coordinates()

◆ id()

◆ isAtomAdjacent()

◆ operator=()

◆ radius()

◆ setAtomName()

◆ setAtomType()

◆ setColor()

◆ setCoordinates()

◆ setId()

◆ setRadius()

◆ setShowAtomName()

◆ setVisible()

◆ setVisited()

◆ showAtomName()

◆ visible()

◆ visited()

Member Data Documentation

◆ mAdjacentAtoms

◆ mAtomName

◆ mAtomType

◆ mColor

◆ mCoordinates

◆ mId

◆ mRadius

◆ mShowAtomName

◆ mVisible

◆ mVisited