vlMolecule::Molecule Class Reference

The Molecule class is used to manage and render 3D molecular structures. More...

#include <Molecule.hpp>

Inheritance diagram for vlMolecule::Molecule:

List of all members.

Public Member Functions

virtual const char * className ()

Returns the name of the class.

Molecule ()

~Molecule ()

Molecule (const Molecule &other)

Molecule & operator= (const Molecule &other)

void reset ()

void setMoleculeName (const std::string &name)

const std::string moleculeName () const

unsigned int id () const

void setId (unsigned int id)

vl::KeyValues * tags ()

const vl::KeyValues * tags () const

const std::vector< vl::ref
< Atom > > & atoms () const

std::vector< vl::ref< Atom > > & atoms ()

int atomCount () const

Atom * atom (int index) const

void addAtom (Atom *atom)

void eraseAtom (Atom *atom)

void eraseAtom (int index)

void eraseAllAtoms ()

const std::vector< vl::ref
< Bond > > & bonds () const

std::vector< vl::ref< Bond > > & bonds ()

int bondCount () const

Bond * bond (int index) const

Bond * bond (Atom *a1, Atom *a2)

void addBond (Bond *bond)

Bond * addBond (Atom *a1, Atom *a2)

void eraseBond (Bond *bond)

void eraseBond (int bond)

void eraseBond (Atom *a1, Atom *a2)

void eraseBond (int a1, int a2)

void eraseAllBonds ()

void computeAtomAdjacency ()

void incidentBonds (std::vector< Bond * > &inc_bonds, Atom *atom)

const std::vector< vl::ref
< Atom > > & cycle (int i) const

Returns the i-th cycle.

std::vector< vl::ref< Atom > > & cycle (int i)

Returns the i-th cycle.

const std::vector< std::vector
< vl::ref< Atom > > > & cycles () const

Returns the list of cycles.

std::vector< std::vector
< vl::ref< Atom > > > & cycles ()

Returns the list of cycles.

void prepareForRendering ()

Generates the geometry representing the current molecule, atom and bond settings.

const vl::ActorTree * actorTree () const

The vl::ActorTree node containing the Actor[s] representing the molecule.

vl::ActorTree * actorTree ()

The vl::ActorTree node containing the Actor[s] representing the molecule.

void setCPKAtomColors ()

Sets all the atoms' color to their CPK color.

void setAtomColors (const vl::fvec4 &color)

Sets all the atoms' color to the specified color.

void setCalculatedAtomRadii (float percentage=1.0f)

Sets all the atoms' radii to their calculated atom radii.

void setEmpiricalAtomRadii (float percentage=1.0f)

Sets all the atoms' radii to their empirical atom radii.

void setCovalentAtomRadii (float percentage=1.0f)

Sets all the atoms' radii to their covalent atom radii.

void setVanDerWaalsAtomRadii (float percentage=1.0f)

Sets all the atoms' radii to their van der Waals atom radii.

void setAtomRadii (float radius)

Sets all the atoms' radii to the specified one.

void setBondRadii (float radius)

Sets all the bonds' radii to the specified one.

void setAtomTypeVisible (EAtomType type, bool visible)

void setMoleculeStyle (EMoleculeStyle style)

The rendering style of the molecule.

EMoleculeStyle moleculeStyle () const

The rendering style of the molecule.

void setAtomDetail (int detail)

Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2).

int atomDetail () const

Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2).

void setBondDetail (int detail)

Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20).

int bondDetail () const

Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20).

float ringOffset () const

void setRingOffset (float offset)

void setAromaticBondsColor (const vl::fvec4 &color)

void setAromaticRingColor (const vl::fvec4 &color)

const vl::fvec4 & aromaticRingColor () const

float lineWidth () const

bool smoothLines () const

void setLineWidth (float w)

void setSmoothLines (bool smooth)

vl::Transform * transformTree ()

The transform tree used by the generated bonds, atoms and labels.

const vl::Transform * transformTree () const

The transform tree used by the generated bonds, atoms and labels.

vl::Text * atomLabelTemplate ()

The text settings to be used to render the atom labels.

const vl::Text * atomLabelTemplate () const

The text settings to be used to render the atom labels.

void setShowAtomNames (bool show)

Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().

bool showAtomNames () const

Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().

const vl::Effect * atomLabelEffect () const

The vl::Effect used to render the atom labels.

vl::Effect * atomLabelEffect ()

The vl::Effect used to render the atom labels.

Protected Member Functions

void prepareAtomInsert (int bonus=100)

void prepareBondInsert (int bonus=100)

void wireframeStyle ()

void atomsStyle ()

void ballAndStickStyle ()

void sticksStyle ()

void generateRings ()

void generateAtomLabels ()

void generateAtomLabel (const Atom *atom, vl::Transform *tr)

Protected Attributes

vl::fvec4 mAromaticRingColor

vl::ref< vl::ActorTree > mActorTree

vl::ref< vl::Transform > mTransformTree

std::vector< vl::ref< Atom > > mAtoms

std::vector< vl::ref< Bond > > mBonds

std::vector< std::vector
< vl::ref< Atom > > > mCycles

std::string mMoleculeName

vl::ref< vl::KeyValues > mTags

vl::ref< vl::Text > mAtomLabelTemplate

vl::ref< vl::Effect > mAtomLabelEffect

unsigned int mId

EMoleculeStyle mMoleculeStyle

int mAtomDetail

int mBondDetail

float mRingOffset

float mLineWidth

bool mSmoothLines

bool mShowAtomNames

Detailed Description

The Molecule class is used to manage and render 3D molecular structures.

See also:

Constructor & Destructor Documentation

Molecule::Molecule ( )

vlMolecule::Molecule::~Molecule ( ) [inline]

vlMolecule::Molecule::Molecule ( const Molecule & other ) [inline]

Member Function Documentation

virtual const char* vlMolecule::Molecule::className ( ) [inline, virtual]

Returns the name of the class.

Reimplemented from vl::Object.

Molecule & Molecule::operator= ( const Molecule & other )

void Molecule::reset ( )

void vlMolecule::Molecule::setMoleculeName ( const std::string & name ) [inline]

const std::string vlMolecule::Molecule::moleculeName ( ) const [inline]

unsigned int vlMolecule::Molecule::id ( ) const [inline]

void vlMolecule::Molecule::setId ( unsigned int id ) [inline]

vl::KeyValues* vlMolecule::Molecule::tags ( ) [inline]

const vl::KeyValues* vlMolecule::Molecule::tags ( ) const [inline]

const std::vector< vl::ref<Atom> >& vlMolecule::Molecule::atoms ( ) const [inline]

std::vector< vl::ref<Atom> >& vlMolecule::Molecule::atoms ( ) [inline]

int vlMolecule::Molecule::atomCount ( ) const [inline]

Atom * Molecule::atom ( int index ) const

void Molecule::addAtom ( Atom * atom )

void Molecule::eraseAtom ( Atom * atom )

void Molecule::eraseAtom ( int index )

void Molecule::eraseAllAtoms ( )

const std::vector< vl::ref<Bond> >& vlMolecule::Molecule::bonds ( ) const [inline]

std::vector< vl::ref<Bond> >& vlMolecule::Molecule::bonds ( ) [inline]

int vlMolecule::Molecule::bondCount ( ) const [inline]

Bond * Molecule::bond ( int index ) const

Bond * Molecule::bond	(	Atom *	a1,
		Atom *	a2
	)

void Molecule::addBond ( Bond * bond )

Bond * Molecule::addBond	(	Atom *	a1,
		Atom *	a2
	)

void Molecule::eraseBond ( Bond * bond )

void Molecule::eraseBond ( int bond )

void Molecule::eraseBond	(	Atom *	a1,
		Atom *	a2
	)

void Molecule::eraseBond	(	int	a1,
		int	a2
	)

void Molecule::eraseAllBonds ( )

void Molecule::computeAtomAdjacency ( )

void Molecule::incidentBonds	(	std::vector< Bond * > &	inc_bonds,
		Atom *	atom
	)

const std::vector< vl::ref<Atom> >& vlMolecule::Molecule::cycle ( int i ) const [inline]

Returns the i-th cycle.

std::vector< vl::ref<Atom> >& vlMolecule::Molecule::cycle ( int i ) [inline]

Returns the i-th cycle.

const std::vector< std::vector< vl::ref<Atom> > >& vlMolecule::Molecule::cycles ( ) const [inline]

Returns the list of cycles.

std::vector< std::vector< vl::ref<Atom> > >& vlMolecule::Molecule::cycles ( ) [inline]

Returns the list of cycles.

void Molecule::prepareForRendering ( )

Generates the geometry representing the current molecule, atom and bond settings.

The actors, geometry, and transforms generated by this function can be found in actorTree() and transformTree().

const vl::ActorTree* vlMolecule::Molecule::actorTree ( ) const [inline]

The vl::ActorTree node containing the Actor[s] representing the molecule.

vl::ActorTree* vlMolecule::Molecule::actorTree ( ) [inline]

The vl::ActorTree node containing the Actor[s] representing the molecule.

void Molecule::setCPKAtomColors ( )

Sets all the atoms' color to their CPK color.

void Molecule::setAtomColors ( const vl::fvec4 & color )

Sets all the atoms' color to the specified color.

void Molecule::setCalculatedAtomRadii ( float percentage = 1.0f )

Sets all the atoms' radii to their calculated atom radii.

void Molecule::setEmpiricalAtomRadii ( float percentage = 1.0f )

Sets all the atoms' radii to their empirical atom radii.

void Molecule::setCovalentAtomRadii ( float percentage = 1.0f )

Sets all the atoms' radii to their covalent atom radii.

void Molecule::setVanDerWaalsAtomRadii ( float percentage = 1.0f )

Sets all the atoms' radii to their van der Waals atom radii.

void Molecule::setAtomRadii ( float radius )

Sets all the atoms' radii to the specified one.

void Molecule::setBondRadii ( float radius )

Sets all the bonds' radii to the specified one.

void Molecule::setAtomTypeVisible	(	EAtomType	type,
		bool	visible
	)

void vlMolecule::Molecule::setMoleculeStyle ( EMoleculeStyle style ) [inline]

The rendering style of the molecule.

EMoleculeStyle vlMolecule::Molecule::moleculeStyle ( ) const [inline]

The rendering style of the molecule.

void vlMolecule::Molecule::setAtomDetail ( int detail ) [inline]

Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2).

int vlMolecule::Molecule::atomDetail ( ) const [inline]

Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2).

void vlMolecule::Molecule::setBondDetail ( int detail ) [inline]

Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20).

int vlMolecule::Molecule::bondDetail ( ) const [inline]

Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20).

float vlMolecule::Molecule::ringOffset ( ) const [inline]

void vlMolecule::Molecule::setRingOffset ( float offset ) [inline]

void Molecule::setAromaticBondsColor ( const vl::fvec4 & color )

void vlMolecule::Molecule::setAromaticRingColor ( const vl::fvec4 & color ) [inline]

const vl::fvec4& vlMolecule::Molecule::aromaticRingColor ( ) const [inline]

float vlMolecule::Molecule::lineWidth ( ) const [inline]

bool vlMolecule::Molecule::smoothLines ( ) const [inline]

void vlMolecule::Molecule::setLineWidth ( float w ) [inline]

void vlMolecule::Molecule::setSmoothLines ( bool smooth ) [inline]

vl::Transform* vlMolecule::Molecule::transformTree ( ) [inline]

The transform tree used by the generated bonds, atoms and labels.

const vl::Transform* vlMolecule::Molecule::transformTree ( ) const [inline]

The transform tree used by the generated bonds, atoms and labels.

vl::Text* vlMolecule::Molecule::atomLabelTemplate ( ) [inline]

The text settings to be used to render the atom labels.

const vl::Text* vlMolecule::Molecule::atomLabelTemplate ( ) const [inline]

The text settings to be used to render the atom labels.

void vlMolecule::Molecule::setShowAtomNames ( bool show ) [inline]

Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().

bool vlMolecule::Molecule::showAtomNames ( ) const [inline]

Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().

const vl::Effect* vlMolecule::Molecule::atomLabelEffect ( ) const [inline]

The vl::Effect used to render the atom labels.

vl::Effect* vlMolecule::Molecule::atomLabelEffect ( ) [inline]

The vl::Effect used to render the atom labels.

void vlMolecule::Molecule::prepareAtomInsert ( int bonus = 100 ) [inline, protected]

void vlMolecule::Molecule::prepareBondInsert ( int bonus = 100 ) [inline, protected]

void Molecule::wireframeStyle ( ) [protected]

void Molecule::atomsStyle ( ) [protected]

void Molecule::ballAndStickStyle ( ) [protected]

void Molecule::sticksStyle ( ) [protected]

void Molecule::generateRings ( ) [protected]

void Molecule::generateAtomLabels ( ) [protected]

void Molecule::generateAtomLabel	(	const Atom *	atom,
		vl::Transform *	tr
	)			`[protected]`

Member Data Documentation

vl::fvec4 vlMolecule::Molecule::mAromaticRingColor [protected]

vl::ref<vl::ActorTree> vlMolecule::Molecule::mActorTree [protected]

vl::ref<vl::Transform> vlMolecule::Molecule::mTransformTree [protected]

std::vector< vl::ref<Atom> > vlMolecule::Molecule::mAtoms [protected]

std::vector< vl::ref<Bond> > vlMolecule::Molecule::mBonds [protected]

std::vector< std::vector< vl::ref<Atom> > > vlMolecule::Molecule::mCycles [protected]

std::string vlMolecule::Molecule::mMoleculeName [protected]

vl::ref<vl::KeyValues> vlMolecule::Molecule::mTags [protected]

vl::ref<vl::Text> vlMolecule::Molecule::mAtomLabelTemplate [protected]

vl::ref<vl::Effect> vlMolecule::Molecule::mAtomLabelEffect [protected]

unsigned int vlMolecule::Molecule::mId [protected]

EMoleculeStyle vlMolecule::Molecule::mMoleculeStyle [protected]

int vlMolecule::Molecule::mAtomDetail [protected]

int vlMolecule::Molecule::mBondDetail [protected]

float vlMolecule::Molecule::mRingOffset [protected]

float vlMolecule::Molecule::mLineWidth [protected]

bool vlMolecule::Molecule::mSmoothLines [protected]

bool vlMolecule::Molecule::mShowAtomNames [protected]

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

E:/VisualizationLibrary/Visualization_Library_SDK/src/vlMolecule/Molecule.hpp
E:/VisualizationLibrary/Visualization_Library_SDK/src/vlMolecule/Molecule.cpp
E:/VisualizationLibrary/Visualization_Library_SDK/src/vlMolecule/Molecule_rendering.cpp


Public Member Functions
virtual const char *	className ()
	Returns the name of the class.
	Molecule ()
	~Molecule ()
	Molecule (const Molecule &other)
Molecule &	operator= (const Molecule &other)
void	reset ()
void	setMoleculeName (const std::string &name)
const std::string	moleculeName () const
unsigned int	id () const
void	setId (unsigned int id)
vl::KeyValues *	tags ()
const vl::KeyValues *	tags () const
const std::vector< vl::ref < Atom > > &	atoms () const
std::vector< vl::ref< Atom > > &	atoms ()
int	atomCount () const
Atom *	atom (int index) const
void	addAtom (Atom *atom)
void	eraseAtom (Atom *atom)
void	eraseAtom (int index)
void	eraseAllAtoms ()
const std::vector< vl::ref < Bond > > &	bonds () const
std::vector< vl::ref< Bond > > &	bonds ()
int	bondCount () const
Bond *	bond (int index) const
Bond *	bond (Atom a1, Atom a2)
void	addBond (Bond *bond)
Bond *	addBond (Atom a1, Atom a2)
void	eraseBond (Bond *bond)
void	eraseBond (int bond)
void	eraseBond (Atom a1, Atom a2)
void	eraseBond (int a1, int a2)
void	eraseAllBonds ()
void	computeAtomAdjacency ()
void	incidentBonds (std::vector< Bond * > &inc_bonds, Atom *atom)
const std::vector< vl::ref < Atom > > &	cycle (int i) const
	Returns the i-th cycle.
std::vector< vl::ref< Atom > > &	cycle (int i)
	Returns the i-th cycle.
const std::vector< std::vector < vl::ref< Atom > > > &	cycles () const
	Returns the list of cycles.
std::vector< std::vector < vl::ref< Atom > > > &	cycles ()
	Returns the list of cycles.
void	prepareForRendering ()
	Generates the geometry representing the current molecule, atom and bond settings.
const vl::ActorTree *	actorTree () const
	The vl::ActorTree node containing the Actor[s] representing the molecule.
vl::ActorTree *	actorTree ()
	The vl::ActorTree node containing the Actor[s] representing the molecule.
void	setCPKAtomColors ()
	Sets all the atoms' color to their CPK color.
void	setAtomColors (const vl::fvec4 &color)
	Sets all the atoms' color to the specified color.
void	setCalculatedAtomRadii (float percentage=1.0f)
	Sets all the atoms' radii to their calculated atom radii.
void	setEmpiricalAtomRadii (float percentage=1.0f)
	Sets all the atoms' radii to their empirical atom radii.
void	setCovalentAtomRadii (float percentage=1.0f)
	Sets all the atoms' radii to their covalent atom radii.
void	setVanDerWaalsAtomRadii (float percentage=1.0f)
	Sets all the atoms' radii to their van der Waals atom radii.
void	setAtomRadii (float radius)
	Sets all the atoms' radii to the specified one.
void	setBondRadii (float radius)
	Sets all the bonds' radii to the specified one.
void	setAtomTypeVisible (EAtomType type, bool visible)
void	setMoleculeStyle (EMoleculeStyle style)
	The rendering style of the molecule.
EMoleculeStyle	moleculeStyle () const
	The rendering style of the molecule.
void	setAtomDetail (int detail)
	Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2).
int	atomDetail () const
	Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2).
void	setBondDetail (int detail)
	Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20).
int	bondDetail () const
	Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20).
float	ringOffset () const
void	setRingOffset (float offset)
void	setAromaticBondsColor (const vl::fvec4 &color)
void	setAromaticRingColor (const vl::fvec4 &color)
const vl::fvec4 &	aromaticRingColor () const
float	lineWidth () const
bool	smoothLines () const
void	setLineWidth (float w)
void	setSmoothLines (bool smooth)
vl::Transform *	transformTree ()
	The transform tree used by the generated bonds, atoms and labels.
const vl::Transform *	transformTree () const
	The transform tree used by the generated bonds, atoms and labels.
vl::Text *	atomLabelTemplate ()
	The text settings to be used to render the atom labels.
const vl::Text *	atomLabelTemplate () const
	The text settings to be used to render the atom labels.
void	setShowAtomNames (bool show)
	Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().
bool	showAtomNames () const
	Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().
const vl::Effect *	atomLabelEffect () const
	The vl::Effect used to render the atom labels.
vl::Effect *	atomLabelEffect ()
	The vl::Effect used to render the atom labels.
Protected Member Functions
void	prepareAtomInsert (int bonus=100)
void	prepareBondInsert (int bonus=100)
void	wireframeStyle ()
void	atomsStyle ()
void	ballAndStickStyle ()
void	sticksStyle ()
void	generateRings ()
void	generateAtomLabels ()
void	generateAtomLabel (const Atom atom, vl::Transform tr)
Protected Attributes
vl::fvec4	mAromaticRingColor
vl::ref< vl::ActorTree >	mActorTree
vl::ref< vl::Transform >	mTransformTree
std::vector< vl::ref< Atom > >	mAtoms
std::vector< vl::ref< Bond > >	mBonds
std::vector< std::vector < vl::ref< Atom > > >	mCycles
std::string	mMoleculeName
vl::ref< vl::KeyValues >	mTags
vl::ref< vl::Text >	mAtomLabelTemplate
vl::ref< vl::Effect >	mAtomLabelEffect
unsigned int	mId
EMoleculeStyle	mMoleculeStyle
int	mAtomDetail
int	mBondDetail
float	mRingOffset
float	mLineWidth
bool	mSmoothLines
bool	mShowAtomNames

Visualization Library

vlMolecule::Molecule Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation