#include <BALL/VIEW/MODELS/cartoonModel.h>

Inheritance diagram for BALL::VIEW::AddCartoonModel:

Public Types
enum	Types { STRAND = NUCLEIC_ACID + 1, HELIX }

Public Types inherited from BALL::UnaryFunctor< Composite, Processor::Result >
typedef Processor::Result	result_type

typedef Composite	argument_type

typedef Composite &	argument_reference

typedef const Composite &	const_argument_reference

typedef Composite *	argument_pointer

typedef const Composite *	const_argument_pointer

Public Member Functions
	AddCartoonModel ()
	Default Constructor. More...

	AddCartoonModel (const AddCartoonModel &cartoon_model)
	Copy constructor. More...

virtual	~AddCartoonModel ()
	Destructor. More...

void	setHelixRadius (float radius)

float	getHelixRadius () const

void	setArrowWidth (float width)

float	getArrowWidth () const

void	setStrandHeight (float heigth)

float	getStrandHeight () const

void	setStrandWidth (float w)

float	getStrandWidth () const

void	setDNABaseRadius (float r)

float	getDNABaseRadius () const

void	setDNAHelixRadius (float r)

float	getDNAHelixRadius () const

void	setDNALadderRadius (float r)

float	getDNALadderRadius () const

void	setDrawDNAAsLadderModel (bool state)

bool	drawDNAAsLadderModel ()

void	enableRibbons (bool state)

bool	ribbonsEnabled () const

Public Member Functions inherited from BALL::VIEW::AddBackboneModel
	AddBackboneModel ()
	Default Constructor. More...

	AddBackboneModel (const AddBackboneModel &add_Backbone_model)
	Copy constructor. More...

virtual	~AddBackboneModel ()
	Destructor. More...

virtual void	clear ()

virtual bool	start ()

virtual Processor::Result	operator() (Composite &composite)

virtual void	dump (std::ostream &s=std::cout, Size depth=0) const

void	setTubeRadius (float radius)

float	getTubeRadius () const

virtual bool	createGeometricObjects ()

void	setRibbonMode (bool state)

bool	ribbonModeEnabled () const

Public Member Functions inherited from BALL::VIEW::ModelProcessor
	ModelProcessor ()

	ModelProcessor (const ModelProcessor &model_processor)

virtual	~ModelProcessor ()

virtual bool	isValid () const

virtual void	clearComposites ()

GeometricObjectList &	getGeometricObjects ()
	Return the list with the created geometric objects. More...

const GeometricObjectList &	getGeometricObjects () const
	Return the list with the created geometric objects. More...

void	setDrawingPrecision (Index precision)

Index	getDrawingPrecision () const

void	setSurfaceDrawingPrecision (float precision)

float	getSurfaceDrawingPrecision () const

Public Member Functions inherited from BALL::UnaryProcessor< Composite >
	UnaryProcessor ()

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

virtual bool	finish ()

Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE	PropertyManager ()
	Default constructor. More...

BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor. More...

virtual	~PropertyManager ()
	Destructor. More...

virtual void	destroy ()
	Clears all properties. More...

void	set (const PropertyManager &property_manager)

const PropertyManager &	operator= (const PropertyManager &property_manager)

void	get (PropertyManager &property_manager) const

void	swap (PropertyManager &property_manager)

BitVector &	getBitVector ()

const BitVector &	getBitVector () const

	operator BitVector & ()

void	setProperty (Property property)

void	clearProperty (Property property)

void	toggleProperty (Property property)

Size	countProperties () const

const NamedProperty &	getNamedProperty (Position index) const

NamedProperty &	getNamedProperty (Position index)

void	setProperty (const NamedProperty &property)

void	setProperty (const std::string &name)

void	setProperty (const std::string &name, bool value)

void	setProperty (const std::string &name, int value)

void	setProperty (const std::string &name, unsigned int value)

void	setProperty (const std::string &name, float value)

void	setProperty (const std::string &name, double value)

void	setProperty (const std::string &name, const std::string &value)

void	setProperty (const std::string &name, const PersistentObject &value)

const NamedProperty &	getProperty (const std::string &name) const

NamedPropertyIterator	beginNamedProperty ()

NamedPropertyIterator	endNamedProperty ()

void	clearProperty (const std::string &name)

Size	countNamedProperties () const

bool	hasProperty (Property property) const
	Query for an unnamed property. More...

bool	hasProperty (const std::string &name) const
	Query for a named property. More...

bool	operator== (const PropertyManager &pm) const

bool	operator!= (const PropertyManager &pm) const
	Inequality operator. More...

void	write (PersistenceManager &pm) const
	Persistent stream writing. More...

bool	read (PersistenceManager &pm)
	Persistent stream reading. More...

bool	isValid () const

void	dump (std::ostream &s=std::cout, Size depth=0) const

Protected Member Functions
void	insertTriangle_ (Position v1, Position v2, Position v3, Mesh &mesh)

void	drawStrand_ (const Vector3 &start, Vector3 &right, Vector3 &hn, float arrow_width, Position &last_vertices, Mesh &mesh)

void	calculateComplementaryBases_ (const Composite &composite)

bool	assignNucleotideAtoms_ (Residue &r, Size nr_atoms, String atom_names[10], Atom *atoms[10])

void	drawRiboseAtoms_ (const Atom atom1, const Atom atom2, const Vector3 &v1, const Vector3 &v2)

void	calculateModelParts (Protein &protein)

void	assignModelType (ModelPart &part)

void	createModel_ (Position set_pos, Position part_pos)

void	createStrand_ (Position set_pos, Position part_pos)

void	createHelix_ (Position set_first, Position part_pos)

void	createTubeHelix_ (Position set_first, Position part_pos)

void	createWatsonCrickModel_ (Position set_pos, Position part_pos)

void	createSimpleNucleicAcid_ (Position set_pos, Position part_pos)

void	renderNucleotideOutline_ (const vector< Vector3 > &positions, Vector3 uv, Mesh &mesh)

Mesh *	createDoubleRing_ (const vector< Vector3 > &positions)

Mesh *	create6Ring_ (vector< Vector3 > positions)

virtual void	refineGuidePoints_ ()

Protected Member Functions inherited from BALL::VIEW::AddBackboneModel
virtual bool	collectPositions (vector< Residue * > residues)

virtual void	calculateGuidePoints_ ()

virtual void	createTube_ (Position set_pos, Position model_pos)

virtual void	createRibbon_ (Position set_pos, Position model_pos)

virtual void	interpolate_ ()

virtual void	refineModelParts_ ()

virtual void	clear_ ()

void	evaluateBSpline (const Vector3 &v1, const Vector3 &v2, const Vector3 &v3, float x, Vector3 &result)

bool	residuesAreConnected_ (Residue &residue1, Residue &residue2)

void	calculateTubePoints_ (Vector3 right, Vector3 dir, vector< Vector3 > &points)

void	calculateRibbonPoints_ (Vector3 xn, Vector3 dir, vector< Vector3 > &points)

void	calculateRibbonEllipse_ (float ribbon_width, float ribbon_height)

Protected Attributes
float	helix_radius_

float	helix_height_

float	helix_width_

float	arrow_width_

float	strand_width_

float	strand_height_

float	DNA_helix_radius_

float	DNA_ladder_radius_

float	DNA_base_radius_

float	ribbon_width_

float	ribbon_radius_

bool	draw_DNA_as_ladder_

bool	draw_ribbon_

HashMap< const Residue , const Residue >	complementary_bases_

Protected Attributes inherited from BALL::VIEW::AddBackboneModel
float	tube_radius_

Size	interpolation_steps_

Size	number_of_ribbons_

float	ribbon_width_

float	ribbon_height_

bool	care_for_SS_

bool	ribbon_mode_

vector< vector< vector < Vector3 > > >	guide_points_

vector< vector< vector < Vector3 > > >	interpolated_points_

vector< vector< Vector3 > >	backbone_

vector< vector< Vector3 > >	offsets_

vector< vector< ModelPart > >	model_parts_

Protein	dummy_protein_

Chain	dummy_chain_

SecondaryStructure	dummy_ss_

HashSet< Residue * >	residues_to_be_rendered_

Protein *	last_protein_

vector< vector< Index > >	ss_

Size	slides_

Position	middle_slide_

Position	middle_ribbon_

Angle	slides_angle_

Matrix4x4	temp_matrix_

vector< float >	xs_

vector< float >	ys_

Protected Attributes inherited from BALL::VIEW::ModelProcessor
GeometricObjectList	geometric_objects_

Index	drawing_precision_

float	surface_drawing_precision_

Additional Inherited Members
Protected Types inherited from BALL::VIEW::AddBackboneModel
enum	ModelTypes { TUBE, RIBBON, NUCLEIC_ACID }

Detailed Description

AddCartoonModel class. The class AddCartoonModel is a model processor that creates a Cartoon model through the CA-atoms of the processed Composite object. For information about the processor concept see Processor in the BALL documentation.

Definition at line 28 of file cartoonModel.h.

Member Enumeration Documentation

enum BALL::VIEW::AddCartoonModel::Types

Enumerator
STRAND
HELIX

Definition at line 33 of file cartoonModel.h.

Constructor & Destructor Documentation

BALL::VIEW::AddCartoonModel::AddCartoonModel ( )

Default Constructor.

BALL::VIEW::AddCartoonModel::AddCartoonModel ( const AddCartoonModel & cartoon_model )

Copy constructor.

virtual BALL::VIEW::AddCartoonModel::~AddCartoonModel ( )

virtual

Destructor.

Member Function Documentation

void BALL::VIEW::AddCartoonModel::assignModelType ( ModelPart & part )

protectedvirtual

Reimplemented from BALL::VIEW::AddBackboneModel.

bool BALL::VIEW::AddCartoonModel::assignNucleotideAtoms_	(	Residue &	r,
		Size	nr_atoms,
		String	atom_names[10],
		Atom *	atoms[10]
	)

protected

void BALL::VIEW::AddCartoonModel::calculateComplementaryBases_ ( const Composite & composite )

protected

void BALL::VIEW::AddCartoonModel::calculateModelParts ( Protein & protein )

protectedvirtual

Reimplemented from BALL::VIEW::AddBackboneModel.

Mesh* BALL::VIEW::AddCartoonModel::create6Ring_ ( vector< Vector3 > positions )

protected

Mesh* BALL::VIEW::AddCartoonModel::createDoubleRing_ ( const vector< Vector3 > & positions )

protected

void BALL::VIEW::AddCartoonModel::createHelix_	(	Position	set_first,
		Position	part_pos
	)

protected

void BALL::VIEW::AddCartoonModel::createModel_	(	Position	set_pos,
		Position	part_pos
	)

protectedvirtual

Reimplemented from BALL::VIEW::AddBackboneModel.

void BALL::VIEW::AddCartoonModel::createSimpleNucleicAcid_	(	Position	set_pos,
		Position	part_pos
	)

protected

void BALL::VIEW::AddCartoonModel::createStrand_	(	Position	set_pos,
		Position	part_pos
	)

protected

void BALL::VIEW::AddCartoonModel::createTubeHelix_	(	Position	set_first,
		Position	part_pos
	)

protected

void BALL::VIEW::AddCartoonModel::createWatsonCrickModel_	(	Position	set_pos,
		Position	part_pos
	)

protected

bool BALL::VIEW::AddCartoonModel::drawDNAAsLadderModel ( )

inline

Definition at line 111 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::drawRiboseAtoms_	(	const Atom *	atom1,
		const Atom *	atom2,
		const Vector3 &	v1,
		const Vector3 &	v2
	)

protected

void BALL::VIEW::AddCartoonModel::drawStrand_	(	const Vector3 &	start,
		Vector3 &	right,
		Vector3 &	hn,
		float	arrow_width,
		Position &	last_vertices,
		Mesh &	mesh
	)

inlineprotected

void BALL::VIEW::AddCartoonModel::enableRibbons ( bool state )

inline

Definition at line 115 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::getArrowWidth ( ) const

inline

Definition at line 63 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::getDNABaseRadius ( ) const

inline

Definition at line 87 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::getDNAHelixRadius ( ) const

inline

Definition at line 95 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::getDNALadderRadius ( ) const

inline

Definition at line 103 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::getHelixRadius ( ) const

inline

Definition at line 55 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::getStrandHeight ( ) const

inline

Definition at line 71 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::getStrandWidth ( ) const

inline

Definition at line 79 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::insertTriangle_	(	Position	v1,
		Position	v2,
		Position	v3,
		Mesh &	mesh
	)

protected

virtual void BALL::VIEW::AddCartoonModel::refineGuidePoints_ ( )

protectedvirtual

Reimplemented from BALL::VIEW::AddBackboneModel.

void BALL::VIEW::AddCartoonModel::renderNucleotideOutline_	(	const vector< Vector3 > &	positions,
		Vector3	uv,
		Mesh &	mesh
	)

protected

bool BALL::VIEW::AddCartoonModel::ribbonsEnabled ( ) const

inline

Definition at line 119 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setArrowWidth ( float width )

inline

Definition at line 59 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setDNABaseRadius ( float r )

inline

Definition at line 83 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setDNAHelixRadius ( float r )

inline

Definition at line 91 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setDNALadderRadius ( float r )

inline

Definition at line 99 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setDrawDNAAsLadderModel ( bool state )

inline

Definition at line 107 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setHelixRadius ( float radius )

inline

Definition at line 51 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setStrandHeight ( float heigth )

inline

Definition at line 67 of file cartoonModel.h.

void BALL::VIEW::AddCartoonModel::setStrandWidth ( float w )

inline

Definition at line 75 of file cartoonModel.h.

Member Data Documentation

float BALL::VIEW::AddCartoonModel::arrow_width_

protected

Definition at line 156 of file cartoonModel.h.

HashMap<const Residue*, const Residue*> BALL::VIEW::AddCartoonModel::complementary_bases_

protected

Definition at line 168 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::DNA_base_radius_

protected

Definition at line 161 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::DNA_helix_radius_

protected

Definition at line 159 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::DNA_ladder_radius_

protected

Definition at line 160 of file cartoonModel.h.

bool BALL::VIEW::AddCartoonModel::draw_DNA_as_ladder_

protected

Definition at line 165 of file cartoonModel.h.

bool BALL::VIEW::AddCartoonModel::draw_ribbon_

protected

Definition at line 166 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::helix_height_

protected

Definition at line 154 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::helix_radius_

protected

Definition at line 153 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::helix_width_

protected

Definition at line 155 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::ribbon_radius_

protected

Definition at line 163 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::ribbon_width_

protected

Definition at line 162 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::strand_height_

protected

Definition at line 158 of file cartoonModel.h.

float BALL::VIEW::AddCartoonModel::strand_width_

protected

Definition at line 157 of file cartoonModel.h.

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation