BALL  1.4.1
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Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BALL::VIEW::AddCartoonModel Class Reference

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

Inheritance diagram for BALL::VIEW::AddCartoonModel:
BALL::VIEW::AddBackboneModel BALL::VIEW::ModelProcessor BALL::UnaryProcessor< Composite > BALL::PropertyManager BALL::UnaryFunctor< Composite, Processor::Result >

Public Types

enum  Types { STRAND = NUCLEIC_ACID + 1, HELIX }

Public Member Functions

 AddCartoonModel ()
 Default Constructor.
 AddCartoonModel (const AddCartoonModel &cartoon_model)
 Copy constructor.
virtual ~AddCartoonModel ()
 Destructor.
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.
 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
- Public Member Functions inherited from BALL::VIEW::ModelProcessor
 ModelProcessor ()
 ModelProcessor (const ModelProcessor &model_processor)
virtual ~ModelProcessor ()
virtual bool isValid () const
virtual void clearComposites ()
GeometricObjectListgetGeometricObjects ()
 Return the list with the created geometric objects.
const GeometricObjectListgetGeometricObjects () const
 Return the list with the created geometric objects.
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.
BALL_INLINE PropertyManager (const PropertyManager &property_manager)
 Copy constructor.
virtual ~PropertyManager ()
 Destructor.
virtual void destroy ()
 Clears all properties.
void set (const PropertyManager &property_manager)
const PropertyManageroperator= (const PropertyManager &property_manager)
void get (PropertyManager &property_manager) const
void swap (PropertyManager &property_manager)
BitVectorgetBitVector ()
const BitVectorgetBitVector () const
 operator BitVector & ()
void setProperty (Property property)
void clearProperty (Property property)
void toggleProperty (Property property)
Size countProperties () const
const NamedPropertygetNamedProperty (Position index) const
NamedPropertygetNamedProperty (Position index)
void setProperty (const NamedProperty &property)
void setProperty (const string &name)
void setProperty (const string &name, bool value)
void setProperty (const string &name, int value)
void setProperty (const string &name, unsigned int value)
void setProperty (const string &name, float value)
void setProperty (const string &name, double value)
void setProperty (const string &name, const string &value)
void setProperty (const string &name, const PersistentObject &value)
const NamedPropertygetProperty (const string &name) const
NamedPropertyIterator beginNamedProperty ()
NamedPropertyIterator endNamedProperty ()
void clearProperty (const string &name)
Size countNamedProperties () const
bool hasProperty (Property property) const
 Query for an unnamed property.
bool hasProperty (const string &name) const
 Query for a named property.
bool operator== (const PropertyManager &pm) const
bool operator!= (const PropertyManager &pm) const
 Inequality operator.
void write (PersistenceManager &pm) const
 Persistent stream writing.
bool read (PersistenceManager &pm)
 Persistent stream reading.

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)
MeshcreateDoubleRing_ (const vector< Vector3 > &positions)
Meshcreate6Ring_ (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_
Proteinlast_protein_
vector< vector< Index > > ss_
Size slides_
Position middle_slide_
Position middle_ribbon_
Angle slides_angle_
Matrix4x4 temp_matrix_
vector< floatxs_
vector< floatys_
- 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

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.