Package chemaxon.marvin.space

Class PharmacophoreArrow

java.lang.Object

chemaxon.marvin.space.GraphicComponent

chemaxon.marvin.space.PharmacophoreArrow

All Implemented Interfaces:

chemaxon.marvin.space.UsableObject

@PublicAPI
public class PharmacophoreArrow
extends GraphicComponent
implements chemaxon.marvin.space.UsableObject

PharmacophoreArrow provides an extension of PharmacophorePoint to represent pharmacophores by introducing directionality. The direction, the length and the thickness of the arrow can be changed.

Since:

Marvin 4.0.2

Field Summary

Fields

Modifier and Type	Field	Description
static String[]	DRAW_TYPES

Fields inherited from class chemaxon.marvin.space.GraphicComponent

active, associatedComponents, boundingBox, COMPONENT_TYPE_ENTIRE, drawProperties, drawType, gl, glu, graphicCell, irm, modifiesOrigin, motionMode, mousex, mousey, name, pickedItem, RENDERING_QUALITY_HIGH, RENDERING_QUALITY_LOW, RENDERING_QUALITY_MEDIUM, renderingQuality, rm, uoid, visible

Constructor Summary

Constructors

Constructor	Description
PharmacophoreArrow()	Creates a new instance of PharmacophoreArrow.
PharmacophoreArrow(double x, double y, double z)	Creates a PharmacophoreArrow at the given position.
PharmacophoreArrow(ComponentElement ce)	Creates a PharmacophoreArrow at the position of the given ComponentElement getting the coordinates by getCoordinates().

Method Summary

Modifier and Type	Method	Description
void	cleanup()
void	draw()	Draws the component if it is opaque.
void	drawTransparentPart()	Draws transparent parts of the component if there is any.
Color	getColor()	Returns the color of the component.
void	getCoordinates(ComponentElement item, float[] c)	Gets the position of the component.
String	getDescription()	Returns a descriptive text.
String	getDrawType()	Returns the name of the drawing type.
String	getName()	Returns the name of the component.
double	getRadius()	Returns the radius of the arrow.
boolean	hasTransparentPart()	See GraphicComponent.hasTransparentPart().
void	initDraw()
boolean	isControllable(String type)	Returns whether controling by the given type of controller is allowed to the component.
boolean	isHighlighted()	Returns true if the component is highlighted.
void	onRemoveGraphicComponent()
protected void	pickObject(int offset, double[] maxZ, float[] modelview)	Sets GraphicComponent.pickedItem to be the picked part of the component.
void	resize(double x, double y, double z)	Resizes the component according to the given factors in each direction.
void	rotate(float[] v, float[] center)	Rotates the component around the 3 axis, x, y, z, and given center.
void	select()	Sets the component to be selected.
void	setDrawProperty(String propertyName, String propertyValue)	Sets a draw property.
void	setDrawType(String type)	Sets current drawing type.
void	setHighlighted(boolean flag)	Sets the component to be highlighted.
void	setPosition(double x, double y, double z)	Sets the position of the PharmacophoreArrow.
void	setRadius(double r)	Sets the radius of the arrow.
void	setRenderingQuality(int quality)	Sets the rendering quality, see RENDERING_* constants.
void	setRenderingQuality(String quality)	Sets the rendering quality and calls setRenderingQuality(int).
String	toString()
void	translate(float[] v)	Translates the component with the parameter as a translation vector.
void	unSelect()	Sets the component to be unselected.

Methods inherited from class chemaxon.marvin.space.GraphicComponent

addDrawProperties, associate, draw2DPart, drawBoundingBox, drawCoordinateAxes, drawSelection, exclusiveSelection, exclusiveSelection, extendSelection, extendSelection, fadeSelected, fadeUnselected, getAssociatedComponents, getBoundingBox, getBoundingSphereRadius, getCell, getComponentElement, getCoordinates, getDescription, getDrawProperties, getDrawProperty, getGraphicComponent, getId, getLabelInformation, getLabelInformation, getRenderingQuality, getUsableObject, getZCoordinateTo2DPart, glColor, has2DPart, hasSelectedElements, hideSelected, hideUnselected, invertSelection, invertSelection, isGraphicComponent, isSelected, isSelected, isVisible, isVisible, locateObject, notifyCoordinateChange, notifyInvisibility, notifySelection, notifyUnSelection, notifyVisibility, projectVector, receiveNotificationOnCoordinateChange, receiveNotificationOnInvisibility, receiveNotificationOnSelection, receiveNotificationOnUnSelection, receiveNotificationOnVisibility, removeAssociation, rotate, rotate, select, selectComponentElementsInside, setColor, setColor, setColor, setColor, setDrawProperties, setGL, setMotionMode, setName, setProgressBar, setRotateMatrix, setVisible, showFaded, storeDrawProperty, touchObject, unSelect

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface chemaxon.marvin.space.UsableObject

getGraphicComponent, getId, isGraphicComponent, isSelected, isVisible, setColor, setName, setVisible

Field Detail

DRAW_TYPES

public static final String[] DRAW_TYPES

Constructor Detail

PharmacophoreArrow

public PharmacophoreArrow()

Creates a new instance of PharmacophoreArrow. It will be placed at the origin by default, its position can be set by setPosition().

PharmacophoreArrow

public PharmacophoreArrow(ComponentElement ce)

Creates a PharmacophoreArrow at the position of the given ComponentElement getting the coordinates by getCoordinates().

Parameters:

ce - reference to a component to get the coordinates

PharmacophoreArrow

public PharmacophoreArrow(double x,
                          double y,
                          double z)

Creates a PharmacophoreArrow at the given position.

Parameters:

x - coordinate

y - coordinate

z - coordinate

Method Detail

onRemoveGraphicComponent

public void onRemoveGraphicComponent()

Overrides:

onRemoveGraphicComponent in class GraphicComponent

setPosition

public void setPosition(double x,
                        double y,
                        double z)

Sets the position of the PharmacophoreArrow.

Parameters:

x - first coordinate

y - second coordinate

z - third coordinate

getCoordinates

public void getCoordinates(ComponentElement item,
                           float[] c)

Gets the position of the component.

Overrides:

getCoordinates in class GraphicComponent

Parameters:

item - ignored here (since PharmacophoreArrow is not subdivided further into smaller constituting elements)

c - output parameter to store 3 coordinates (must be allocated by caller)

getDescription

public String getDescription()

Returns a descriptive text.

Overrides:

getDescription in class GraphicComponent

Returns:

"Pharmacophore arrow"

getName

public String getName()

Description copied from class: GraphicComponent

Returns the name of the component.

Specified by:

getName in interface chemaxon.marvin.space.UsableObject

Overrides:

getName in class GraphicComponent

Returns:

name that is getClass.getName() by default.

toString

public String toString()

Specified by:

toString in interface chemaxon.marvin.space.UsableObject

Overrides:

toString in class GraphicComponent

getRadius

public double getRadius()

Returns the radius of the arrow.

setRadius

public void setRadius(double r)

Sets the radius of the arrow.

getColor

public Color getColor()

Returns the color of the component.

Specified by:

getColor in interface chemaxon.marvin.space.UsableObject

Overrides:

getColor in class GraphicComponent

select

public void select()

Sets the component to be selected.

Specified by:

select in interface chemaxon.marvin.space.UsableObject

Overrides:

select in class GraphicComponent

unSelect

public void unSelect()

Sets the component to be unselected.

Specified by:

unSelect in interface chemaxon.marvin.space.UsableObject

Overrides:

unSelect in class GraphicComponent

isHighlighted

public boolean isHighlighted()

Returns true if the component is highlighted.

setHighlighted

public void setHighlighted(boolean flag)

Sets the component to be highlighted. The highlighted component will appear brighter.

translate

public void translate(float[] v)

Translates the component with the parameter as a translation vector.

Overrides:

translate in class GraphicComponent

Parameters:

v - The translation vector.

rotate

public void rotate(float[] v,
                   float[] center)

Rotates the component around the 3 axis, x, y, z, and given center.

Overrides:

rotate in class GraphicComponent

Parameters:

v - Measurement of the rotation around the 3 axis, x, y, z.

center - Center of the rotation.

resize

public void resize(double x,
                   double y,
                   double z)

Resizes the component according to the given factors in each direction.

Overrides:

resize in class GraphicComponent

isControllable

public boolean isControllable(String type)

Returns whether controling by the given type of controller is allowed to the component. This component is allowed to be translated and resized.

Overrides:

isControllable in class GraphicComponent

Parameters:

type - "Shift", "Rotate", "Resize"

Returns:

is the component aloowed to be controlled or not

hasTransparentPart

public boolean hasTransparentPart()

See GraphicComponent.hasTransparentPart(). Returns true if the drawing type is not DRAW_TYPE_FILLED.

Overrides:

hasTransparentPart in class GraphicComponent

Returns:

will the component draw with transparency

drawTransparentPart

public void drawTransparentPart()

Draws transparent parts of the component if there is any.

Overrides:

drawTransparentPart in class GraphicComponent

draw

public void draw()

Draws the component if it is opaque.

Overrides:

draw in class GraphicComponent

initDraw

public void initDraw()

pickObject

protected void pickObject(int offset,
                          double[] maxZ,
                          float[] modelview)

Description copied from class: GraphicComponent

Sets GraphicComponent.pickedItem to be the picked part of the component.

Overrides:

pickObject in class GraphicComponent

Parameters:

offset - Integer used in the name stack to identify the part of the component.

maxZ - Stores the z coordinate of the part with maximum z coordinate in the actual picking. It has to be set if the part with the current offset has greater z coordinate than the stored one. Example to compute: int aIdx = GeomCalc.newVector( picked.x(), picked.y(), picked.z() ); GeomCalc.multVectorWithMatrix(aIdx, modelview); z coordinate: maxZ[0] = GeomCalc.getZ(aIdx)

modelview - Is to compute the proper z coordinate.

cleanup

public void cleanup()

Overrides:

cleanup in class GraphicComponent

setDrawType

public void setDrawType(String type)

Sets current drawing type.

Parameters:

type - Solid, Mesh or Transparent

getDrawType

public String getDrawType()

Returns the name of the drawing type.

Returns:

Solid, Mesh or Transparent

setRenderingQuality

public void setRenderingQuality(String quality)

Sets the rendering quality and calls setRenderingQuality(int).

Parameters:

quality - Can be "High", "Medium", "Low".

setRenderingQuality

public void setRenderingQuality(int quality)

Sets the rendering quality, see RENDERING_* constants. Sets the precision of the drawn arrow.

Overrides:

setRenderingQuality in class GraphicComponent

Parameters:

quality -

setDrawProperty

public void setDrawProperty(String propertyName,
                            String propertyValue)

Sets a draw property.
Accepts:

• "Quality" -- "High", "Medium", "Low"
• "PharmacophoreArrow.DrawType" -- "Mesh", "Solid", "Transparent"

Specified by:

setDrawProperty in interface chemaxon.marvin.space.UsableObject

Overrides:

setDrawProperty in class GraphicComponent

Parameters:

propertyName - identifier of the draw property

propertyValue - value of the draw property as a String