GLSimpleMoleculeView Class Reference

#include <glsimplemoleculeview.h>

Inheritance diagram for GLSimpleMoleculeView:

Detailed Description

This class shows a molecule in 3D using OpenGL.

It does not allow chaning of the molecule and is used in the program CrdView. Brabosphere uses the derived class GLMoleculeView with more features.

Definition at line 40 of file glsimplemoleculeview.h.

Public Types

enum DisplayStyle {
  None, Lines, Tubes, BallAndStick,
  VanDerWaals
}

enum DisplaySource { Molecule, Forces }

Public Slots

void updateAtomSet (const bool reset=false)

Updates the view under influence of changes in the atomset.

void selectAll (const bool update=true)

Selects all atoms.

void unselectAll (const bool update=true)

Unselects all atoms.

Public Member Functions

GLSimpleMoleculeView (AtomSet *atomset, QWidget *parent=0, const char *name=0)

~GLSimpleMoleculeView ()

The default destructor.

unsigned int displayStyle (const DisplaySource source) const

Returns the display style of a certain primitive.

bool isShowingElements () const

Returns whether the atom elements are shown.

bool isShowingNumbers () const

Returns whether the atom numbers are shown.

bool isShowingCharges (const unsigned int type) const

Returns whether the atomic charges of the specified type are shown.

unsigned int selectedAtoms () const

Returns the number of selected atoms.

void loadCML (QDomElement *root)

Loads the view settings from a QDomElement.

void saveCML (QDomElement *root)

Saves the view settings to a QDomElement.

void setDisplayStyle (const DisplaySource source, const unsigned int style)

Sets the display style for a certain primitive. Does not redraw the scene.

void setLabels (const bool element, const bool number, const unsigned int type)

Sets up showing of the atom labels. Does not redraw the scene.

Static Public Member Functions

static void setParameters (GLMoleculeParameters params)

Updates the OpenGL parameters and makes sure they are adapted at the next call to updateGL().

Protected Types

enum SelectionType {
  SELECTION_NONE, SELECTION_ATOM, SELECTION_BOND, SELECTION_ANGLE,
  SELECTION_TORSION, SELECTION_GROUP, SELECTION_BONDS, SELECTION_FORCES
}

enum ShapeTypes {
  SHAPE_ATOMS, SHAPE_BONDS, SHAPE_FORCES, SHAPE_LABELS,
  SHAPE_IC, SHAPE_SELECTION, SHAPE_NEXT
}

Protected Slots

void reorderShapes ()

Orders all drawn shapes according to their opacity.

Protected Member Functions

virtual void keyPressEvent (QKeyEvent *e)

Overridden from GLView::keyPressEvent.

virtual void initializeGL ()

Overridden from QGLWidget::initializeGL(). Initializes the OpenGL window.

virtual void drawItem (const unsigned int)

Draws the item shapes[index].

virtual void updateGLSettings ()

Updates the OpenGL settings.

virtual float boundingSphereRadius ()

Calculates the radius of the bounding sphere.

void clicked (const QPoint &position)

Implementation of GLView::clicked(). Handles mouse click events.

virtual void updateShapes ()

Updates the contents of the shapes vector.

Protected Attributes

GLfloat centerX

X-offset needed to center the molecule.

GLfloat centerY

Y-offset needed to center the moelcule.

GLfloat centerZ

Z-offset needed to center the molecule.

unsigned int selectionType

Keeps track of the type of selection.

std::list< unsigned int > selectionList

List that holds the selected atoms and their order.

std::vector< ShapeProperties > shapes

the list of shapes ordered by opacity.

Static Protected Attributes

static GLMoleculeParameters moleculeParameters

Holds the OpenGL molecule parameters.

Private Types

enum Directions { DIRECTION_X, DIRECTION_Y, DIRECTION_Z }

enum StartIndices {
  START_ATOMS = 100, START_BONDS = 1, START_FORCES = 2, START_SELECTEDATOMS = 3,
  START_SELECTEDBONDS = 4
}

Private Member Functions

GLuint makeObjects (const int numSlices)

Generates the shapes for the atoms and the bonds.

void changeObjects (const GLuint startList, const int numSlices)

Changes the quality of the atom and bond shapes.

void selectEntity (const QPoint position)

Selects the entity (atom, bond, etc.) pointed to by the mouse position.

void processSelection (const unsigned int id)

Changes the selection according to the change in selection of the entity with an ID id.

void centerMolecule ()

Calculates the translations needed to center the molecule.

void drawScene ()

Implementation of the pure virtual GLView::drawScene().

void drawAtoms ()

Draws the atoms in the OpenGL scene.

void drawBonds ()

Draws the bonds in the OpenGL scene in a format depending in the OpenGL parameters.

void drawLabels ()

Draws the element types and numbers.

void drawForces ()

Draws the forces.

void drawICValue ()

Draws the value for the currently selected internal coordinate.

void drawSelections ()

Draws the selected atoms and internal coordinates.

Private Attributes

int atomObject

The OpenGL atom shape object pointer.

int bondObject

The OpenGL bond shape object pointer.

int forceObjectLines

The OpenGL force shape object pointer for lines style.

int forceObjectTubes

The OpenGL force shape object pointer for tubes style.

unsigned int moleculeStyle

The rendering style of the molecule.

unsigned int forcesStyle

The rendering style of the forces.

bool showElements

Is true if elements should be shown.

bool showNumbers

Is true if atom numbers should be shown.

unsigned int chargeType

Determines the type of charges to be shown.

AtomSet * atoms

The list of atoms.

GLfloat selectionLineWidth

The linewidth for drawing selected bonds.

GLfloat selectionPointSize

The pointsize for drawing selected atoms.

float scaleFactor

scalefactor for scenes exceeding 50A in radius

QFont labelFont

The font used to render labels and other values.

Static Private Attributes

static const float cylinderHeight = 10.0f

The cylinder height. A too low value shows severe bugs in the Mesa OpenGL implementation.

Classes

struct ShapeProperties

Utility struct for sorting of shapes by decreasing opacity. More...

Member Enumeration Documentation

enum GLSimpleMoleculeView::DisplayStyle

Enumerator:

None

Lines

Tubes

BallAndStick

VanDerWaals

Definition at line 50 of file glsimplemoleculeview.h.

enum GLSimpleMoleculeView::DisplaySource

Enumerator:

Molecule

Forces

Definition at line 52 of file glsimplemoleculeview.h.

enum GLSimpleMoleculeView::SelectionType [protected]

Enumerator:

SELECTION_NONE

SELECTION_ATOM

SELECTION_BOND

SELECTION_ANGLE

SELECTION_TORSION

SELECTION_GROUP

SELECTION_BONDS

SELECTION_FORCES

Definition at line 78 of file glsimplemoleculeview.h.

enum GLSimpleMoleculeView::ShapeTypes [protected]

Enumerator:

SHAPE_ATOMS

SHAPE_BONDS

SHAPE_FORCES

SHAPE_LABELS

SHAPE_IC

SHAPE_SELECTION

SHAPE_NEXT

Definition at line 81 of file glsimplemoleculeview.h.

enum GLSimpleMoleculeView::Directions [private]

Enumerator:

DIRECTION_X

DIRECTION_Y

DIRECTION_Z

Definition at line 119 of file glsimplemoleculeview.h.

enum GLSimpleMoleculeView::StartIndices [private]

Enumerator:

START_ATOMS

START_BONDS

START_FORCES

START_SELECTEDATOMS

START_SELECTEDBONDS

Definition at line 120 of file glsimplemoleculeview.h.

Constructor & Destructor Documentation

GLSimpleMoleculeView::GLSimpleMoleculeView ( AtomSet * atomset,

QWidget * parent = 0,

const char * name = 0

)

Definition at line 59 of file glsimplemoleculeview.cpp.

GLSimpleMoleculeView::~GLSimpleMoleculeView ( )

The default destructor.

Definition at line 84 of file glsimplemoleculeview.cpp.

Member Function Documentation

unsigned int GLSimpleMoleculeView::displayStyle ( const DisplaySource source ) const

Returns the display style of a certain primitive.

Definition at line 92 of file glsimplemoleculeview.cpp.

bool GLSimpleMoleculeView::isShowingElements ( ) const

Returns whether the atom elements are shown.

Definition at line 102 of file glsimplemoleculeview.cpp.

bool GLSimpleMoleculeView::isShowingNumbers ( ) const

Returns whether the atom numbers are shown.

Definition at line 109 of file glsimplemoleculeview.cpp.

bool GLSimpleMoleculeView::isShowingCharges ( const unsigned int type ) const

Returns whether the atomic charges of the specified type are shown.

Definition at line 116 of file glsimplemoleculeview.cpp.

unsigned int GLSimpleMoleculeView::selectedAtoms ( ) const

Returns the number of selected atoms.

Definition at line 123 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::loadCML ( QDomElement * root )

Loads the view settings from a QDomElement.

Definition at line 129 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::saveCML ( QDomElement * root )

Saves the view settings to a QDomElement.

Definition at line 180 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::setDisplayStyle ( const DisplaySource source,

const unsigned int style

)

Sets the display style for a certain primitive. Does not redraw the scene.

Definition at line 202 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::setLabels ( const bool element,

const bool number,

const unsigned int type

)

Sets up showing of the atom labels. Does not redraw the scene.

Definition at line 223 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::setParameters ( GLMoleculeParameters params ) [static]

Updates the OpenGL parameters and makes sure they are adapted at the next call to updateGL().

Definition at line 236 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::updateAtomSet ( const bool reset = false ) [slot]

Updates the view under influence of changes in the atomset.
It has to be called under the following conditions:

a new coordinate set has been read

atoms have been added/removed/changes When reset = true, the scene will be reset completely

Definition at line 249 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::selectAll ( const bool update = true ) [slot]

Selects all atoms.

Definition at line 302 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::unselectAll ( const bool update = true ) [slot]

Unselects all atoms.

Definition at line 328 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::reorderShapes ( ) [protected, slot]

Orders all drawn shapes according to their opacity.

Definition at line 344 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::keyPressEvent ( QKeyEvent * e ) [protected, virtual]

Overridden from GLView::keyPressEvent.
Handles key presses for font changes (no public interface yet)
Reimplemented from GLView.
Reimplemented in GLMoleculeView.
Definition at line 356 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::initializeGL ( ) [protected, virtual]

Overridden from QGLWidget::initializeGL(). Initializes the OpenGL window.

Reimplemented from GLView.
Definition at line 377 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawItem ( const unsigned int ) [protected, virtual]

Draws the item shapes[index].
It should be overridden by a subclass to draw new shapes. It is not made pure virtual because implementation is not mandatory.
Reimplemented in GLMoleculeView.
Definition at line 419 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::updateGLSettings ( ) [protected, virtual]

Updates the OpenGL settings.
It is only called when an update is really needed (determined by staticUpdateIndex != updateIndex in GLView).
Reimplemented from GLView.
Definition at line 435 of file glsimplemoleculeview.cpp.

float GLSimpleMoleculeView::boundingSphereRadius ( ) [protected, virtual]

Calculates the radius of the bounding sphere.

Implements GLView.
Reimplemented in GLMoleculeView.
Definition at line 391 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::clicked ( const QPoint & position ) [protected, virtual]

Implementation of GLView::clicked(). Handles mouse click events.

Reimplemented from GLView.
Definition at line 428 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::updateShapes ( ) [protected, virtual]

Updates the contents of the shapes vector.

Reimplemented in GLMoleculeView.
Definition at line 475 of file glsimplemoleculeview.cpp.

GLuint GLSimpleMoleculeView::makeObjects ( const int numSlices ) [private]

Generates the shapes for the atoms and the bonds.

Definition at line 518 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::changeObjects ( const GLuint startList,

const int numSlices

) [private]

Changes the quality of the atom and bond shapes.

Definition at line 527 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::selectEntity ( const QPoint position ) [private]

Selects the entity (atom, bond, etc.) pointed to by the mouse position.

Definition at line 586 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::processSelection ( const unsigned int id ) [private]

Changes the selection according to the change in selection of the entity with an ID id.

Definition at line 644 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::centerMolecule ( ) [private]

Calculates the translations needed to center the molecule.
The center of mass cannot be used, just the largest extents of the molecule.
Definition at line 693 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawScene ( ) [private, virtual]

Implementation of the pure virtual GLView::drawScene().
Changed from protected to private as subclasses should implement drawItem. Does the drawing of the OpenGL scene (called from paintGL). The default state is lighting enabled. If certain routine need to disable lighting they are required to enable it again at the end.
Implements GLView.
Definition at line 733 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawAtoms ( ) [private]

Draws the atoms in the OpenGL scene.

Definition at line 814 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawBonds ( ) [private]

Draws the bonds in the OpenGL scene in a format depending in the OpenGL parameters.
if bonds don't need to be selected individually, all bonds can be stored together in an OpenGL display list.
Definition at line 852 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawLabels ( ) [private]

Draws the element types and numbers.

Definition at line 972 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawForces ( ) [private]

Draws the forces.
If forces don't need to be selected individually, all forces can be stored together in an OpenGL display list.
Definition at line 1021 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawICValue ( ) [private]

Draws the value for the currently selected internal coordinate.

Definition at line 1104 of file glsimplemoleculeview.cpp.

void GLSimpleMoleculeView::drawSelections ( ) [private]

Draws the selected atoms and internal coordinates.

Definition at line 1247 of file glsimplemoleculeview.cpp.

Member Data Documentation

GLfloat GLSimpleMoleculeView::centerX [protected]

X-offset needed to center the molecule.

Definition at line 107 of file glsimplemoleculeview.h.

GLfloat GLSimpleMoleculeView::centerY [protected]

Y-offset needed to center the moelcule.

Definition at line 108 of file glsimplemoleculeview.h.

GLfloat GLSimpleMoleculeView::centerZ [protected]

Z-offset needed to center the molecule.

Definition at line 109 of file glsimplemoleculeview.h.

unsigned int GLSimpleMoleculeView::selectionType [protected]

Keeps track of the type of selection.

Definition at line 110 of file glsimplemoleculeview.h.

std::list<unsigned int> GLSimpleMoleculeView::selectionList [protected]

List that holds the selected atoms and their order.

Definition at line 111 of file glsimplemoleculeview.h.

std::vector<ShapeProperties> GLSimpleMoleculeView::shapes [protected]

the list of shapes ordered by opacity.

Definition at line 112 of file glsimplemoleculeview.h.

GLMoleculeParameters GLSimpleMoleculeView::moleculeParameters [static, protected]

Initial value:
{5, 1.0f, 0.2f, 0.2f, BallAndStick, Tubes, 1000, false, true, 0x00FF00, 0x00FFFF, 0xFFFF00, 50, 0xFFFF0, false, 100}
Holds the OpenGL molecule parameters.

Definition at line 115 of file glsimplemoleculeview.h.

int GLSimpleMoleculeView::atomObject [private]

The OpenGL atom shape object pointer.

Definition at line 137 of file glsimplemoleculeview.h.

int GLSimpleMoleculeView::bondObject [private]

The OpenGL bond shape object pointer.

Definition at line 138 of file glsimplemoleculeview.h.

int GLSimpleMoleculeView::forceObjectLines [private]

The OpenGL force shape object pointer for lines style.

Definition at line 139 of file glsimplemoleculeview.h.

int GLSimpleMoleculeView::forceObjectTubes [private]

The OpenGL force shape object pointer for tubes style.

Definition at line 140 of file glsimplemoleculeview.h.

unsigned int GLSimpleMoleculeView::moleculeStyle [private]

The rendering style of the molecule.

Definition at line 141 of file glsimplemoleculeview.h.

unsigned int GLSimpleMoleculeView::forcesStyle [private]

The rendering style of the forces.

Definition at line 142 of file glsimplemoleculeview.h.

bool GLSimpleMoleculeView::showElements [private]

Is true if elements should be shown.

Definition at line 143 of file glsimplemoleculeview.h.

bool GLSimpleMoleculeView::showNumbers [private]

Is true if atom numbers should be shown.

Definition at line 144 of file glsimplemoleculeview.h.

unsigned int GLSimpleMoleculeView::chargeType [private]

Determines the type of charges to be shown.

Definition at line 145 of file glsimplemoleculeview.h.

AtomSet* GLSimpleMoleculeView::atoms [private]

The list of atoms.

Reimplemented in GLMoleculeView.
Definition at line 146 of file glsimplemoleculeview.h.

GLfloat GLSimpleMoleculeView::selectionLineWidth [private]

The linewidth for drawing selected bonds.

Definition at line 147 of file glsimplemoleculeview.h.

GLfloat GLSimpleMoleculeView::selectionPointSize [private]

The pointsize for drawing selected atoms.

Definition at line 148 of file glsimplemoleculeview.h.

float GLSimpleMoleculeView::scaleFactor [private]

scalefactor for scenes exceeding 50A in radius

Definition at line 149 of file glsimplemoleculeview.h.

QFont GLSimpleMoleculeView::labelFont [private]

The font used to render labels and other values.

Definition at line 150 of file glsimplemoleculeview.h.

const float GLSimpleMoleculeView::cylinderHeight = 10.0f [static, private]

The cylinder height. A too low value shows severe bugs in the Mesa OpenGL implementation.

Definition at line 153 of file glsimplemoleculeview.h.

Generated on Fri May 19 14:31:57 2006 for Brabosphere by

1.4.6-NO


Public Types
enum	DisplayStyle { None, Lines, Tubes, BallAndStick, VanDerWaals }
enum	DisplaySource { Molecule, Forces }
Public Slots
void	updateAtomSet (const bool reset=false)
	Updates the view under influence of changes in the atomset.
void	selectAll (const bool update=true)
	Selects all atoms.
void	unselectAll (const bool update=true)
	Unselects all atoms.
Public Member Functions
	GLSimpleMoleculeView (AtomSet atomset, QWidget parent=0, const char *name=0)
	~GLSimpleMoleculeView ()
	The default destructor.
unsigned int	displayStyle (const DisplaySource source) const
	Returns the display style of a certain primitive.
bool	isShowingElements () const
	Returns whether the atom elements are shown.
bool	isShowingNumbers () const
	Returns whether the atom numbers are shown.
bool	isShowingCharges (const unsigned int type) const
	Returns whether the atomic charges of the specified type are shown.
unsigned int	selectedAtoms () const
	Returns the number of selected atoms.
void	loadCML (QDomElement *root)
	Loads the view settings from a QDomElement.
void	saveCML (QDomElement *root)
	Saves the view settings to a QDomElement.
void	setDisplayStyle (const DisplaySource source, const unsigned int style)
	Sets the display style for a certain primitive. Does not redraw the scene.
void	setLabels (const bool element, const bool number, const unsigned int type)
	Sets up showing of the atom labels. Does not redraw the scene.
Static Public Member Functions
static void	setParameters (GLMoleculeParameters params)
	Updates the OpenGL parameters and makes sure they are adapted at the next call to updateGL().
Protected Types
enum	SelectionType { SELECTION_NONE, SELECTION_ATOM, SELECTION_BOND, SELECTION_ANGLE, SELECTION_TORSION, SELECTION_GROUP, SELECTION_BONDS, SELECTION_FORCES }
enum	ShapeTypes { SHAPE_ATOMS, SHAPE_BONDS, SHAPE_FORCES, SHAPE_LABELS, SHAPE_IC, SHAPE_SELECTION, SHAPE_NEXT }
Protected Slots
void	reorderShapes ()
	Orders all drawn shapes according to their opacity.
Protected Member Functions
virtual void	keyPressEvent (QKeyEvent *e)
	Overridden from GLView::keyPressEvent.
virtual void	initializeGL ()
	Overridden from QGLWidget::initializeGL(). Initializes the OpenGL window.
virtual void	drawItem (const unsigned int)
	Draws the item shapes[index].
virtual void	updateGLSettings ()
	Updates the OpenGL settings.
virtual float	boundingSphereRadius ()
	Calculates the radius of the bounding sphere.
void	clicked (const QPoint &position)
	Implementation of GLView::clicked(). Handles mouse click events.
virtual void	updateShapes ()
	Updates the contents of the shapes vector.
Protected Attributes
GLfloat	centerX
	X-offset needed to center the molecule.
GLfloat	centerY
	Y-offset needed to center the moelcule.
GLfloat	centerZ
	Z-offset needed to center the molecule.
unsigned int	selectionType
	Keeps track of the type of selection.
std::list< unsigned int >	selectionList
	List that holds the selected atoms and their order.
std::vector< ShapeProperties >	shapes
	the list of shapes ordered by opacity.
Static Protected Attributes
static GLMoleculeParameters	moleculeParameters
	Holds the OpenGL molecule parameters.
Private Types
enum	Directions { DIRECTION_X, DIRECTION_Y, DIRECTION_Z }
enum	StartIndices { START_ATOMS = 100, START_BONDS = 1, START_FORCES = 2, START_SELECTEDATOMS = 3, START_SELECTEDBONDS = 4 }
Private Member Functions
GLuint	makeObjects (const int numSlices)
	Generates the shapes for the atoms and the bonds.
void	changeObjects (const GLuint startList, const int numSlices)
	Changes the quality of the atom and bond shapes.
void	selectEntity (const QPoint position)
	Selects the entity (atom, bond, etc.) pointed to by the mouse position.
void	processSelection (const unsigned int id)
	Changes the selection according to the change in selection of the entity with an ID id.
void	centerMolecule ()
	Calculates the translations needed to center the molecule.
void	drawScene ()
	Implementation of the pure virtual GLView::drawScene().
void	drawAtoms ()
	Draws the atoms in the OpenGL scene.
void	drawBonds ()
	Draws the bonds in the OpenGL scene in a format depending in the OpenGL parameters.
void	drawLabels ()
	Draws the element types and numbers.
void	drawForces ()
	Draws the forces.
void	drawICValue ()
	Draws the value for the currently selected internal coordinate.
void	drawSelections ()
	Draws the selected atoms and internal coordinates.
Private Attributes
int	atomObject
	The OpenGL atom shape object pointer.
int	bondObject
	The OpenGL bond shape object pointer.
int	forceObjectLines
	The OpenGL force shape object pointer for lines style.
int	forceObjectTubes
	The OpenGL force shape object pointer for tubes style.
unsigned int	moleculeStyle
	The rendering style of the molecule.
unsigned int	forcesStyle
	The rendering style of the forces.
bool	showElements
	Is true if elements should be shown.
bool	showNumbers
	Is true if atom numbers should be shown.
unsigned int	chargeType
	Determines the type of charges to be shown.
AtomSet *	atoms
	The list of atoms.
GLfloat	selectionLineWidth
	The linewidth for drawing selected bonds.
GLfloat	selectionPointSize
	The pointsize for drawing selected atoms.
float	scaleFactor
	scalefactor for scenes exceeding 50A in radius
QFont	labelFont
	The font used to render labels and other values.
Static Private Attributes
static const float	cylinderHeight = 10.0f
	The cylinder height. A too low value shows severe bugs in the Mesa OpenGL implementation.
Classes
struct	ShapeProperties
	Utility struct for sorting of shapes by decreasing opacity. More...