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

Inheritance diagram for BALL::VIEW::AddBackboneModel:

Classes
struct	ModelPart

Public Member Functions
	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 Types
enum	ModelTypes { TUBE, RIBBON, NUCLEIC_ACID }

Protected Member Functions
virtual void	calculateModelParts (Protein &protein)

virtual bool	collectPositions (vector< Residue * > residues)

virtual void	calculateGuidePoints_ ()

virtual void	assignModelType (ModelPart &part)

virtual void	createModel_ (Position set_pos, Position model_pos)

virtual void	createTube_ (Position set_pos, Position model_pos)

virtual void	createRibbon_ (Position set_pos, Position model_pos)

virtual void	refineGuidePoints_ ()

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	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
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

Detailed Description

AddBackboneModel class. The class AddBackboneModel is a model processor that creates a backbone 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 41 of file backboneModel.h.

Member Enumeration Documentation

enum BALL::VIEW::AddBackboneModel::ModelTypes

protected

Enumerator
TUBE
RIBBON
NUCLEIC_ACID

Definition at line 64 of file backboneModel.h.

Constructor & Destructor Documentation

BALL::VIEW::AddBackboneModel::AddBackboneModel ( )

Default Constructor.

BALL::VIEW::AddBackboneModel::AddBackboneModel ( const AddBackboneModel & add_Backbone_model )

Copy constructor.

virtual BALL::VIEW::AddBackboneModel::~AddBackboneModel ( )

virtual

Destructor.

Member Function Documentation

virtual void BALL::VIEW::AddBackboneModel::assignModelType ( ModelPart & part )

protectedvirtual

Reimplemented in BALL::VIEW::AddCartoonModel.

virtual void BALL::VIEW::AddBackboneModel::calculateGuidePoints_ ( )

protectedvirtual

virtual void BALL::VIEW::AddBackboneModel::calculateModelParts ( Protein & protein )

protectedvirtual

Reimplemented in BALL::VIEW::AddCartoonModel.

void BALL::VIEW::AddBackboneModel::calculateRibbonEllipse_	(	float	ribbon_width,
		float	ribbon_height
	)

inlineprotected

void BALL::VIEW::AddBackboneModel::calculateRibbonPoints_	(	Vector3	xn,
		Vector3	dir,
		vector< Vector3 > &	points
	)

inlineprotected

void BALL::VIEW::AddBackboneModel::calculateTubePoints_	(	Vector3	right,
		Vector3	dir,
		vector< Vector3 > &	points
	)

inlineprotected

virtual void BALL::VIEW::AddBackboneModel::clear ( )

virtual

Explicit default initialization. Calls ModelProcessor::clear.

Reimplemented from BALL::VIEW::ModelProcessor.

virtual void BALL::VIEW::AddBackboneModel::clear_ ( )

protectedvirtual

virtual bool BALL::VIEW::AddBackboneModel::collectPositions ( vector< Residue * > residues )

protectedvirtual

virtual bool BALL::VIEW::AddBackboneModel::createGeometricObjects ( )

virtual

Method to create geometric objects. This method is called in Representation::update() after all operator() was called for all Composites. To be overloaded in derived classes

Reimplemented from BALL::VIEW::ModelProcessor.

virtual void BALL::VIEW::AddBackboneModel::createModel_	(	Position	set_pos,
		Position	model_pos
	)

protectedvirtual

Reimplemented in BALL::VIEW::AddCartoonModel.

virtual void BALL::VIEW::AddBackboneModel::createRibbon_	(	Position	set_pos,
		Position	model_pos
	)

protectedvirtual

virtual void BALL::VIEW::AddBackboneModel::createTube_	(	Position	set_pos,
		Position	model_pos
	)

protectedvirtual

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

virtual

Internal value dump. Dump the current state to the output ostream s with dumping depth depth. Calls ModelProcessor::dump.

Parameters

s	output stream where to output the state
depth	the dumping depth

Reimplemented from BALL::VIEW::ModelProcessor.

void BALL::VIEW::AddBackboneModel::evaluateBSpline	(	const Vector3 &	v1,
		const Vector3 &	v2,
		const Vector3 &	v3,
		float	x,
		Vector3 &	result
	)

inlineprotected

float BALL::VIEW::AddBackboneModel::getTubeRadius ( ) const

inline

Definition at line 115 of file backboneModel.h.

virtual void BALL::VIEW::AddBackboneModel::interpolate_ ( )

protectedvirtual

virtual Processor::Result BALL::VIEW::AddBackboneModel::operator() ( Composite & composite )

virtual

Operator method. This method iterates over each Composite object reachable in the Composite tree. If a Composite is of kind Atom and has the substring CA in its name (this method collects only CA-atoms) than that atom is stored for later processing in the finish method.

Parameters

composite the Composite object that will be processed

Reimplemented from BALL::UnaryProcessor< Composite >.

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

inlineprotectedvirtual

Reimplemented in BALL::VIEW::AddCartoonModel.

Definition at line 144 of file backboneModel.h.

virtual void BALL::VIEW::AddBackboneModel::refineModelParts_ ( )

protectedvirtual

bool BALL::VIEW::AddBackboneModel::residuesAreConnected_	(	Residue &	residue1,
		Residue &	residue2
	)

inlineprotected

bool BALL::VIEW::AddBackboneModel::ribbonModeEnabled ( ) const

inline

Definition at line 126 of file backboneModel.h.

void BALL::VIEW::AddBackboneModel::setRibbonMode ( bool state )

inline

Definition at line 122 of file backboneModel.h.

void BALL::VIEW::AddBackboneModel::setTubeRadius ( float radius )

inline

Definition at line 111 of file backboneModel.h.

virtual bool BALL::VIEW::AddBackboneModel::start ( )

virtual

start method

Reimplemented from BALL::UnaryProcessor< Composite >.

Member Data Documentation

vector<vector<Vector3> > BALL::VIEW::AddBackboneModel::backbone_

protected

Definition at line 173 of file backboneModel.h.

bool BALL::VIEW::AddBackboneModel::care_for_SS_

protected

Definition at line 168 of file backboneModel.h.

Chain BALL::VIEW::AddBackboneModel::dummy_chain_

protected

Definition at line 178 of file backboneModel.h.

Protein BALL::VIEW::AddBackboneModel::dummy_protein_

protected

Definition at line 177 of file backboneModel.h.

SecondaryStructure BALL::VIEW::AddBackboneModel::dummy_ss_

protected

Definition at line 179 of file backboneModel.h.

vector<vector<vector<Vector3> > > BALL::VIEW::AddBackboneModel::guide_points_

protected

Definition at line 171 of file backboneModel.h.

vector<vector<vector<Vector3> > > BALL::VIEW::AddBackboneModel::interpolated_points_

protected

Definition at line 172 of file backboneModel.h.

Size BALL::VIEW::AddBackboneModel::interpolation_steps_

protected

Definition at line 163 of file backboneModel.h.

Protein* BALL::VIEW::AddBackboneModel::last_protein_

protected

Definition at line 181 of file backboneModel.h.

Position BALL::VIEW::AddBackboneModel::middle_ribbon_

protected

Definition at line 186 of file backboneModel.h.

Position BALL::VIEW::AddBackboneModel::middle_slide_

protected

Definition at line 185 of file backboneModel.h.

vector<vector<ModelPart> > BALL::VIEW::AddBackboneModel::model_parts_

protected

Definition at line 175 of file backboneModel.h.

Size BALL::VIEW::AddBackboneModel::number_of_ribbons_

protected

Definition at line 165 of file backboneModel.h.

vector<vector<Vector3> > BALL::VIEW::AddBackboneModel::offsets_

protected

Definition at line 174 of file backboneModel.h.

HashSet<Residue*> BALL::VIEW::AddBackboneModel::residues_to_be_rendered_

protected

Definition at line 180 of file backboneModel.h.

float BALL::VIEW::AddBackboneModel::ribbon_height_

protected

Definition at line 167 of file backboneModel.h.

bool BALL::VIEW::AddBackboneModel::ribbon_mode_

protected

Definition at line 169 of file backboneModel.h.

float BALL::VIEW::AddBackboneModel::ribbon_width_

protected

Definition at line 166 of file backboneModel.h.

Size BALL::VIEW::AddBackboneModel::slides_

protected

Definition at line 184 of file backboneModel.h.

Angle BALL::VIEW::AddBackboneModel::slides_angle_

protected

Definition at line 187 of file backboneModel.h.

vector<vector<Index> > BALL::VIEW::AddBackboneModel::ss_

protected

Definition at line 182 of file backboneModel.h.

Matrix4x4 BALL::VIEW::AddBackboneModel::temp_matrix_

protected

Definition at line 188 of file backboneModel.h.

float BALL::VIEW::AddBackboneModel::tube_radius_

protected

Definition at line 160 of file backboneModel.h.

vector<float> BALL::VIEW::AddBackboneModel::xs_

protected

Definition at line 189 of file backboneModel.h.

vector<float> BALL::VIEW::AddBackboneModel::ys_

protected

Definition at line 189 of file backboneModel.h.

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation