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

#include <Molecule.hpp>

Inheritance diagram for vl::Molecule:

Public Member Functions
	Molecule ()
	~Molecule ()
	Molecule (const Molecule &other)
Molecule &	operator= (const Molecule &other)
void	reset ()
void	setMoleculeName (const String &name)
const String	moleculeName () const
unsigned int	id () const
void	setId (unsigned int id)
KeyValues *	tags ()
const KeyValues *	tags () const
const std::vector< ref< Atom > > &	atoms () const
std::vector< ref< Atom > > &	atoms ()
int	atomCount () const
const Atom *	atom (int index) const
Atom *	atom (int index)
void	addAtom (Atom *atom)
void	eraseAtom (Atom *atom)
void	eraseAtom (int index)
void	eraseAllAtoms ()
const std::vector< ref< Bond > > &	bonds () const
std::vector< ref< Bond > > &	bonds ()
int	bondCount () const
const Bond *	bond (int index) const
Bond *	bond (int index)
const Bond *	bond (Atom a1, Atom a2) 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< ref< Atom > > &	cycle (int i) const
	Returns the i-th cycle.
std::vector< ref< Atom > > &	cycle (int i)
	Returns the i-th cycle.
const std::vector< std::vector < ref< Atom > > > &	cycles () const
	Returns the list of cycles.
std::vector< std::vector< ref < Atom > > > &	cycles ()
	Returns the list of cycles.
void	prepareForRendering ()
	Generates the geometry representing the current molecule, atom and bond settings.
const ActorTree *	actorTree () const
	The ActorTree node containing the Actor[s] representing the molecule.
ActorTree *	actorTree ()
	The ActorTree node containing the Actor[s] representing the molecule.
void	setCPKAtomColors ()
	Sets all the atoms' color to their CPK color.
void	setAtomColors (const 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 fvec4 &color)
void	setAromaticRingColor (const fvec4 &color)
const fvec4 &	aromaticRingColor () const
float	lineWidth () const
bool	smoothLines () const
void	setLineWidth (float w)
void	setSmoothLines (bool smooth)
Transform *	transformTree ()
	The transform tree used by the generated bonds, atoms and labels.
const Transform *	transformTree () const
	The transform tree used by the generated bonds, atoms and labels.
const Text *	atomLabelTemplate () const
	The text settings to be used to render the atom labels.
Text *	atomLabelTemplate ()
	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 Effect *	atomLabelEffect () const
	The Effect used to render the atom labels.
Effect *	atomLabelEffect ()
	The Effect used to render the atom labels.
void	setMoleculeToActorMapEnabled (bool enabled)
	If enabled the atomToActorMap() and bondToActorMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
bool	isMoleculeToActorMapEnabled () const
	If enabled the atomToActorMap() and bondToActorMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
void	setActorToMoleculeMapEnabled (bool enabled)
	If enabled the actorToAtomMap() and actorToBondMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
bool	isActorToMoleculeMapEnabled () const
	If enabled the actorToAtomMap() and actorToBondMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
const std::map< ref< Atom > , ref< Actor > > &	atomToActorMap () const
	Maps an Atom to it's corresponding Actor.
const std::map< ref< Actor > , ref< Atom > > &	actorToAtomMap () const
	Maps an Actor to it's corresponding Atom.
const std::map< ref< Bond > , ref< Actor > > &	bondToActorMap () const
	Maps a Bond to it's corresponding Actor.
const std::map< ref< Actor > , ref< Bond > > &	actorToBondMap () const
	Maps an Actor to it's corresponding Bond.
std::map< ref< Atom >, ref < Actor > > &	atomToActorMap ()
	Maps an Atom to it's corresponding Actor.
std::map< ref< Actor >, ref < Atom > > &	actorToAtomMap ()
	Maps an Actor to it's corresponding Atom.
std::map< ref< Bond >, ref < Actor > > &	bondToActorMap ()
	Maps a Bond to it's corresponding Actor.
std::map< ref< Actor >, ref < Bond > > &	actorToBondMap ()
	Maps an Actor to it's corresponding Bond.
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, Transform tr)
Protected Attributes
fvec4	mAromaticRingColor
ref< ActorTree >	mActorTree
ref< Transform >	mTransformTree
std::vector< ref< Atom > >	mAtoms
std::vector< ref< Bond > >	mBonds
std::vector< std::vector< ref < Atom > > >	mCycles
std::map< ref< Atom >, ref < Actor > >	mAtomToActorMap
std::map< ref< Actor >, ref < Atom > >	mActorToAtomMap
std::map< ref< Bond >, ref < Actor > >	mBondToActorMap
std::map< ref< Actor >, ref < Bond > >	mActorToBondMap
String	mMoleculeName
ref< KeyValues >	mTags
ref< Text >	mAtomLabelTemplate
ref< Effect >	mAtomLabelEffect
unsigned int	mId
EMoleculeStyle	mMoleculeStyle
int	mAtomDetail
int	mBondDetail
float	mRingOffset
float	mLineWidth
bool	mSmoothLines
bool	mShowAtomNames
bool	mMoleculeToActorMapEnabled
bool	mActorToMoleculeMapEnabled

Detailed Description

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

See also:

Definition at line 64 of file Molecule.hpp.

Constructor & Destructor Documentation

Molecule::Molecule ( )

Definition at line 38 of file Molecule.cpp.

References vl::EN_BLEND, mAtomLabelEffect, reset(), and VL_DEBUG_SET_OBJECT_NAME.

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

Definition at line 70 of file Molecule.hpp.

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

Definition at line 71 of file Molecule.hpp.

Member Function Documentation

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

Definition at line 76 of file Molecule.cpp.

References atom(), vl::Bond::atom1(), vl::Bond::atom2(), atoms(), bond(), bonds(), cycle(), mAromaticRingColor, mAtomDetail, mBondDetail, mCycles, mLineWidth, mMoleculeName, mMoleculeStyle, mRingOffset, mSmoothLines, mTags, and reset().

void Molecule::reset ( )

Definition at line 50 of file Molecule.cpp.

References vl::KeyValues::clear(), vl::String::clear(), mActorToAtomMap, mActorToBondMap, mActorToMoleculeMapEnabled, mActorTree, mAromaticRingColor, mAtomDetail, mAtoms, mAtomToActorMap, mBondDetail, mBonds, mBondToActorMap, mCycles, mId, mLineWidth, mMoleculeName, mMoleculeStyle, mMoleculeToActorMapEnabled, mRingOffset, vl::MS_BallAndStick, mShowAtomNames, mSmoothLines, and tags().

Referenced by Molecule(), and operator=().

void vl::Molecule::setMoleculeName ( const String & name ) [inline]

Definition at line 76 of file Molecule.hpp.

const String vl::Molecule::moleculeName ( ) const [inline]

Definition at line 77 of file Molecule.hpp.

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

Definition at line 79 of file Molecule.hpp.

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

Definition at line 80 of file Molecule.hpp.

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

Definition at line 82 of file Molecule.hpp.

Referenced by reset().

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

Definition at line 83 of file Molecule.hpp.

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

Definition at line 85 of file Molecule.hpp.

Referenced by addAtom(), eraseAtom(), vl::RingExtractor::keepMinimalCycles(), operator=(), setAtomColors(), setAtomRadii(), setAtomTypeVisible(), setCalculatedAtomRadii(), setCovalentAtomRadii(), setCPKAtomColors(), setEmpiricalAtomRadii(), and setVanDerWaalsAtomRadii().

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

Definition at line 86 of file Molecule.hpp.

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

Definition at line 88 of file Molecule.hpp.

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

const Atom * Molecule::atom ( int index ) const

Definition at line 115 of file Molecule.cpp.

References mAtoms.

Referenced by vl::RingExtractor::bootstrap(), computeAtomAdjacency(), eraseAtom(), eraseBond(), incidentBonds(), operator=(), and setAtomTypeVisible().

Atom * Molecule::atom ( int index )

Definition at line 117 of file Molecule.cpp.

References mAtoms.

void Molecule::addAtom ( Atom * atom )

Definition at line 119 of file Molecule.cpp.

References atoms(), and prepareAtomInsert().

void Molecule::eraseAtom ( Atom * atom )

Definition at line 141 of file Molecule.cpp.

References atom(), atoms(), eraseBond(), and incidentBonds().

void Molecule::eraseAtom ( int index )

Definition at line 132 of file Molecule.cpp.

References atom(), atoms(), eraseBond(), and incidentBonds().

void Molecule::eraseAllAtoms ( )

Definition at line 125 of file Molecule.cpp.

References mAtoms, mBonds, and mCycles.

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

Definition at line 96 of file Molecule.hpp.

Referenced by addBond(), bond(), eraseAllBonds(), eraseBond(), operator=(), setAromaticBondsColor(), and setBondRadii().

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

Definition at line 97 of file Molecule.hpp.

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

Definition at line 99 of file Molecule.hpp.

Referenced by computeAtomAdjacency(), and incidentBonds().

const Bond * Molecule::bond ( int index ) const

Definition at line 167 of file Molecule.cpp.

References mBonds.

Referenced by addBond(), bond(), computeAtomAdjacency(), eraseBond(), incidentBonds(), vl::RingExtractor::keepAromaticCycles(), and operator=().

Bond * Molecule::bond ( int index )

Definition at line 169 of file Molecule.cpp.

References mBonds.

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

Definition at line 171 of file Molecule.cpp.

References vl::Bond::atom1(), vl::Bond::atom2(), bond(), bonds(), and NULL.

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

Definition at line 179 of file Molecule.cpp.

References vl::Bond::atom1(), vl::Bond::atom2(), bond(), bonds(), and NULL.

void Molecule::addBond ( Bond * bond )

Definition at line 187 of file Molecule.cpp.

References bonds(), and prepareBondInsert().

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

Definition at line 157 of file Molecule.cpp.

References bond(), bonds(), vl::ref< T >::get(), and prepareBondInsert().

void Molecule::eraseBond ( Bond * bond )

Definition at line 193 of file Molecule.cpp.

References bond(), and bonds().

Referenced by eraseAtom(), and eraseBond().

void Molecule::eraseBond ( int bond )

Definition at line 205 of file Molecule.cpp.

References bonds().

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

Definition at line 209 of file Molecule.cpp.

References vl::Bond::atom1(), vl::Bond::atom2(), bond(), and bonds().

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

Definition at line 222 of file Molecule.cpp.

References atom(), and eraseBond().

void Molecule::eraseAllBonds ( )

Definition at line 207 of file Molecule.cpp.

References bonds().

void Molecule::computeAtomAdjacency ( )

Definition at line 224 of file Molecule.cpp.

References vl::Atom::adjacentAtoms(), atom(), vl::Bond::atom1(), vl::Bond::atom2(), atomCount(), bond(), and bondCount().

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

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

Definition at line 235 of file Molecule.cpp.

References atom(), vl::Bond::atom1(), vl::Bond::atom2(), bond(), and bondCount().

Referenced by eraseAtom().

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

Returns the i-th cycle.

Definition at line 116 of file Molecule.hpp.

Referenced by vl::RingExtractor::keepAromaticCycles(), vl::RingExtractor::keepPlanarCycles(), operator=(), vl::RingExtractor::removeDoubles(), and vl::RingExtractor::sortCycles().

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

Returns the i-th cycle.

Definition at line 118 of file Molecule.hpp.

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

Returns the list of cycles.

Definition at line 121 of file Molecule.hpp.

Referenced by vl::RingExtractor::depthFirstVisit(), vl::RingExtractor::keepAromaticCycles(), vl::RingExtractor::keepMinimalCycles(), vl::RingExtractor::keepPlanarCycles(), vl::RingExtractor::removeDoubles(), and vl::RingExtractor::sortCycles().

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

Returns the list of cycles.

Definition at line 123 of file Molecule.hpp.

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().

Definition at line 185 of file Molecule_rendering.cpp.

References vl::MS_AtomsOnly, vl::MS_BallAndStick, vl::MS_Sticks, and vl::MS_Wireframe.

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

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

Definition at line 131 of file Molecule.hpp.

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

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

Definition at line 133 of file Molecule.hpp.

void Molecule::setCPKAtomColors ( )

Sets all the atoms' color to their CPK color.

Definition at line 243 of file Molecule.cpp.

References vl::atomInfo(), atoms(), and vl::atomType().

void Molecule::setAtomColors ( const fvec4 & color )

Sets all the atoms' color to the specified color.

Definition at line 249 of file Molecule.cpp.

References atoms().

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

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

Definition at line 255 of file Molecule.cpp.

References vl::atomInfo(), atoms(), and vl::atomType().

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

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

Definition at line 261 of file Molecule.cpp.

References vl::atomInfo(), atoms(), and vl::atomType().

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

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

Definition at line 267 of file Molecule.cpp.

References vl::atomInfo(), atoms(), and vl::atomType().

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

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

Definition at line 273 of file Molecule.cpp.

References vl::atomInfo(), atoms(), and vl::atomType().

void Molecule::setAtomRadii ( float radius )

Sets all the atoms' radii to the specified one.

Definition at line 279 of file Molecule.cpp.

References atoms().

void Molecule::setBondRadii ( float radius )

Sets all the bonds' radii to the specified one.

Definition at line 285 of file Molecule.cpp.

References bonds().

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

Definition at line 291 of file Molecule.cpp.

References atom(), atoms(), vl::Atom::atomType(), and vl::Atom::setVisible().

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

The rendering style of the molecule.

Definition at line 156 of file Molecule.hpp.

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

The rendering style of the molecule.

Definition at line 158 of file Molecule.hpp.

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

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

Definition at line 161 of file Molecule.hpp.

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

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

Definition at line 163 of file Molecule.hpp.

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

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

Definition at line 166 of file Molecule.hpp.

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

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

Definition at line 168 of file Molecule.hpp.

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

Definition at line 170 of file Molecule.hpp.

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

Definition at line 171 of file Molecule.hpp.

void Molecule::setAromaticBondsColor ( const fvec4 & color )

Definition at line 298 of file Molecule.cpp.

References bonds(), and vl::BT_Aromatic.

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

Definition at line 174 of file Molecule.hpp.

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

Definition at line 175 of file Molecule.hpp.

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

Definition at line 177 of file Molecule.hpp.

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

Definition at line 178 of file Molecule.hpp.

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

Definition at line 180 of file Molecule.hpp.

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

Definition at line 181 of file Molecule.hpp.

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

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

Definition at line 184 of file Molecule.hpp.

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

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

Definition at line 186 of file Molecule.hpp.

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

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

Definition at line 189 of file Molecule.hpp.

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

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

Definition at line 191 of file Molecule.hpp.

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

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

Definition at line 194 of file Molecule.hpp.

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

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

Definition at line 196 of file Molecule.hpp.

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

The Effect used to render the atom labels.

Definition at line 199 of file Molecule.hpp.

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

The Effect used to render the atom labels.

Definition at line 201 of file Molecule.hpp.

void vl::Molecule::setMoleculeToActorMapEnabled ( bool enabled ) [inline]

If enabled the atomToActorMap() and bondToActorMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).

Definition at line 204 of file Molecule.hpp.

bool vl::Molecule::isMoleculeToActorMapEnabled ( ) const [inline]

If enabled the atomToActorMap() and bondToActorMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).

Definition at line 206 of file Molecule.hpp.

void vl::Molecule::setActorToMoleculeMapEnabled ( bool enabled ) [inline]

If enabled the actorToAtomMap() and actorToBondMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).

Definition at line 209 of file Molecule.hpp.

bool vl::Molecule::isActorToMoleculeMapEnabled ( ) const [inline]

If enabled the actorToAtomMap() and actorToBondMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).

Definition at line 211 of file Molecule.hpp.

const std::map< ref<Atom>, ref<Actor> >& vl::Molecule::atomToActorMap ( ) const [inline]