BALL::VIEW::AddBackboneModel Class Reference
[Model Processors]

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

Inheritance diagram for BALL::VIEW::AddBackboneModel:

List of all members.

Classes
struct	ModelPart
Public Member Functions
	AddBackboneModel ()
	Default Constructor.
	AddBackboneModel (const AddBackboneModel &add_Backbone_model)
	Copy constructor.
virtual	~AddBackboneModel ()
	Destructor.
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
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_

---

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.

---

Member Enumeration Documentation

enum BALL::VIEW::AddBackboneModel::ModelTypes [protected]

Enumerator:

TUBE
RIBBON
NUCLEIC_ACID

---

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

)

[protected, virtual]

Reimplemented in BALL::VIEW::AddCartoonModel.

virtual void BALL::VIEW::AddBackboneModel::calculateGuidePoints_

(

)

[protected, virtual]

virtual void BALL::VIEW::AddBackboneModel::calculateModelParts

(

Protein &

protein

)

[protected, virtual]

Reimplemented in BALL::VIEW::AddCartoonModel.

void BALL::VIEW::AddBackboneModel::calculateRibbonEllipse_	(	float	ribbon_width,
		float	ribbon_height
	)			[inline, protected]

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

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

virtual void BALL::VIEW::AddBackboneModel::clear

(

)

[virtual]

Explicit default initialization. Calls ModelProcessor::clear.

Reimplemented from BALL::VIEW::ModelProcessor.

virtual void BALL::VIEW::AddBackboneModel::clear_

(

)

[protected, virtual]

virtual bool BALL::VIEW::AddBackboneModel::collectPositions

(

vector< Residue * >

residues

)

[protected, virtual]

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
	)			[protected, virtual]

Reimplemented in BALL::VIEW::AddCartoonModel.

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

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

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
	)			[inline, protected]

float BALL::VIEW::AddBackboneModel::getTubeRadius

(

)

const [inline]

virtual void BALL::VIEW::AddBackboneModel::interpolate_

(

)

[protected, virtual]

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_

(

)

[inline, protected, virtual]

Reimplemented in BALL::VIEW::AddCartoonModel.

virtual void BALL::VIEW::AddBackboneModel::refineModelParts_

(

)

[protected, virtual]

bool BALL::VIEW::AddBackboneModel::residuesAreConnected_	(	Residue &	residue1,
		Residue &	residue2
	)			[inline, protected]

bool BALL::VIEW::AddBackboneModel::ribbonModeEnabled

(

)

const [inline]

void BALL::VIEW::AddBackboneModel::setRibbonMode

(

bool

state

)

[inline]

void BALL::VIEW::AddBackboneModel::setTubeRadius

(

float

radius

)

[inline]

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]

bool BALL::VIEW::AddBackboneModel::care_for_SS_ [protected]

Chain BALL::VIEW::AddBackboneModel::dummy_chain_ [protected]

Protein BALL::VIEW::AddBackboneModel::dummy_protein_ [protected]

SecondaryStructure BALL::VIEW::AddBackboneModel::dummy_ss_ [protected]

vector<vector<vector<Vector3> > > BALL::VIEW::AddBackboneModel::guide_points_ [protected]

vector<vector<vector<Vector3> > > BALL::VIEW::AddBackboneModel::interpolated_points_ [protected]

Size BALL::VIEW::AddBackboneModel::interpolation_steps_ [protected]

Protein* BALL::VIEW::AddBackboneModel::last_protein_ [protected]

Position BALL::VIEW::AddBackboneModel::middle_ribbon_ [protected]

Position BALL::VIEW::AddBackboneModel::middle_slide_ [protected]

vector<vector<ModelPart> > BALL::VIEW::AddBackboneModel::model_parts_ [protected]

Size BALL::VIEW::AddBackboneModel::number_of_ribbons_ [protected]

vector<vector<Vector3> > BALL::VIEW::AddBackboneModel::offsets_ [protected]

HashSet<Residue*> BALL::VIEW::AddBackboneModel::residues_to_be_rendered_ [protected]

float BALL::VIEW::AddBackboneModel::ribbon_height_ [protected]

bool BALL::VIEW::AddBackboneModel::ribbon_mode_ [protected]

float BALL::VIEW::AddBackboneModel::ribbon_width_ [protected]

Reimplemented in BALL::VIEW::AddCartoonModel.

Size BALL::VIEW::AddBackboneModel::slides_ [protected]

Angle BALL::VIEW::AddBackboneModel::slides_angle_ [protected]

vector<vector<Index> > BALL::VIEW::AddBackboneModel::ss_ [protected]

Matrix4x4 BALL::VIEW::AddBackboneModel::temp_matrix_ [protected]

float BALL::VIEW::AddBackboneModel::tube_radius_ [protected]

vector<float> BALL::VIEW::AddBackboneModel::xs_ [protected]

vector<float> BALL::VIEW::AddBackboneModel::ys_ [protected]