chemaxon.marvin.space

Class PharmacophorePoint

java.lang.Object

chemaxon.marvin.space.GraphicComponent

chemaxon.marvin.space.PharmacophorePoint

All Implemented Interfaces:

chemaxon.marvin.space.UsableObject

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

Simple spherical representation of a pharmacophoric point/area. Three properties are considered: location, radius and pharmacophore point type. Current implementation provides wired in types: acceptor, donor, anionic, cationic, hydrophobic, aromatic and excluded.
At present PharmacophorePoint serves mere visualisation purposes. The graphical representation in the MarvinSpace canvas is a translucent sphere.

Since:

Marvin 4.0.2

Version:

MarvinSpace 1.0

Author:

Judit Papp

Field Summary

Fields

Modifier and Type	Field and Description
static int	ACCEPTOR_TYPE
static int	ANIONIC_TYPE
static int	AROMATIC_TYPE
static int	CATIONIC_TYPE
static float	DEFAULT_RADIUS
static int	DONOR_TYPE
static java.lang.String[]	DRAW_TYPES
static int	EXCLUDED_TYPE
static int	HYDROPHOBIC_TYPE
protected boolean	needRecreateBall
protected boolean	needRecreateDisplayList
static int	UNKONWN_TYPE

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

Method Summary

Modifier and Type	Method and Description
void	cleanup()
void	draw() Draws the entire component if it is opaque.
void	drawTransparentPart() Draws transparent parts of the component if there is any.
java.awt.Color	getColor() Returns the color of the PharmacophorePoint.
void	getCoordinates(ComponentElement item, float[] c) Gets the position of the pharmacophore point.
java.lang.String	getDescription() Returns textual description.
java.lang.String	getDrawType() Returns the name of the drawing type.
java.lang.String	getName() Returns the name of the component.
double	getRadius() Returns the radius of the PharmacophorePoint in angstroms.
boolean	hasTransparentPart() Checks is component has transparent part.
void	initDraw() Initializes all internal data structure needed for drawing the component.
boolean	isAcceptor() Checks if actual pharmacophore type includes ACCEPTOR_TYPE.
boolean	isAnionic() Check if actual pharmacophore type includes ANIONIC_TYPE.
boolean	isAromatic() Checks if actual pharmacophore type includes AROMATIC_TYPE.
boolean	isCationic() Check if actual pharmacophore type includes CATIONIC_TYPE.
boolean	isControllable(java.lang.String type) Returns whether controling by the given type of controller is allowed to the component.
boolean	isDonor() Checks if actual pharmacophore type includes DONOR_TYPE.
boolean	isExcluded() Check if actual pharmacophore type is EXCLUDED_TYPE.
boolean	isHighlighted() Returns true if the component is highlighted.
boolean	isHydrophobic() Checks if actual pharmacophore type includes HYDROPHOBIC_TYPE.
protected void	pickObject(int offset, double[] maxZ, float[] modelview) Sets GraphicComponent.pickedItem to the pharmacophore point.
void	resize(double x, double y, double z) Resizes the component according to given factors.
void	select() Sets the component to be selected.
void	setAcceptor(boolean flag) Sets or clears the acceptor property of the PharmacophorePoint.
void	setAnionic(boolean flag) Sets or clears the anionic property of the PharmacophorePoint.
void	setAromatic(boolean flag) Sets or clears the aromatic property of the PharmacophorePoint.
void	setCationic(boolean flag) Sets or clears the cationic property of the PharmacophorePoint.
void	setDonor(boolean flag) Sets or clears the donor property of the PharmacophorePoint.
void	setDrawProperty(java.lang.String propertyName, java.lang.String propertyValue) Sets drawing properties specific to PharmacophoreSphere.
void	setDrawType(java.lang.String type) Sets current drawing type.
void	setExcluded(boolean flag) Sets or clears the excluded property of the PharmacophorePoint.
void	setHighlighted(boolean flag) Sets the highlighted state of the pharmacophore point.
void	setHydrophobic(boolean flag) Sets or clears the hydrophobic property of the PharmacophorePoint.
void	setPosition(double x, double y, double z) Sets the position of the PharmacophorePoint.
void	setRadius(float r) Sets the radius of the PharmaCophorePoint.
void	setRenderingQuality(int quality) Sets the rendering quality, see GraphicComponent.RENDERING_QUALITY_HIGH constants.
void	setRenderingQuality(java.lang.String quality) Sets the rendering quality and calls setRenderingQuality(int).
java.lang.String	toString()
void	translate(float[] v) Translates the component with the given 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, onRemoveGraphicComponent, projectVector, receiveNotificationOnCoordinateChange, receiveNotificationOnInvisibility, receiveNotificationOnSelection, receiveNotificationOnUnSelection, receiveNotificationOnVisibility, removeAssociation, rotate, 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

DEFAULT_RADIUS

public static final float DEFAULT_RADIUS

See Also:

Constant Field Values

DRAW_TYPES

public static final java.lang.String[] DRAW_TYPES

UNKONWN_TYPE

public static final int UNKONWN_TYPE

See Also:

Constant Field Values

ACCEPTOR_TYPE

public static final int ACCEPTOR_TYPE

See Also:

Constant Field Values

DONOR_TYPE

public static final int DONOR_TYPE

See Also:

Constant Field Values

ANIONIC_TYPE

public static final int ANIONIC_TYPE

See Also:

Constant Field Values

CATIONIC_TYPE

public static final int CATIONIC_TYPE

See Also:

Constant Field Values

HYDROPHOBIC_TYPE

public static final int HYDROPHOBIC_TYPE

See Also:

Constant Field Values

AROMATIC_TYPE

public static final int AROMATIC_TYPE

See Also:

Constant Field Values

EXCLUDED_TYPE

public static final int EXCLUDED_TYPE

See Also:

Constant Field Values

needRecreateBall

protected boolean needRecreateBall

needRecreateDisplayList

protected boolean needRecreateDisplayList

Constructor Detail

PharmacophorePoint

public PharmacophorePoint()

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

PharmacophorePoint

public PharmacophorePoint(ComponentElement ce)

Creates a PharmacophorePoint at the position of the given ComponentElement getting the coordinates by getCoordinates(). Radius is set to by default.

Parameters:

ce - a visible component around which the pharmacophore sphere is placed

PharmacophorePoint

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

Creates a PharmacophorePoint at the given position. Radius is set to by default.

Parameters:

x - first coordinate of the pharmacophore point to create

y - second coordinate of the pharmacophore point to create

z - third coordinate of the pharmacophore point to create

Method Detail

setPosition

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

Sets the position of the PharmacophorePoint. Size is not affected.

getCoordinates

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

Gets the position of the pharmacophore point. The position of the pharmacophore point is the centre of the sphere.

Overrides:

getCoordinates in class GraphicComponent

Parameters:

item - not used

c - coordinates of the pharmacophore point are stored in this array, it has to be pre-allocated by the caller of this method

getDescription

public java.lang.String getDescription()

Returns textual description.

Overrides:

getDescription in class GraphicComponent

Returns:

description that contains pharmacophore type name

getName

public java.lang.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 java.lang.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 PharmacophorePoint in angstroms.

setRadius

public void setRadius(float r)

Sets the radius of the PharmaCophorePoint.

Parameters:

r - radius in angstroms

getColor

public java.awt.Color getColor()

Returns the color of the PharmacophorePoint. The color depends on the type of the PharmacophorePoint, and in case of multiple types, the individual colors are mixed. Note, that current implementation uses wired in colors.

• Anionic - Dark red
• Cationic - Dark blue
• Acceptor - Red
• Donor - Blue
• Hydrophobe - Yellow
• Aromatic - Green
• Excluded - Gray

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 highlighted state of the pharmacophore point. The highlighted component appears brighter.

Parameters:

flag - highligth indicator

translate

public void translate(float[] v)

Translates the component with the given translation vector.

Overrides:

translate in class GraphicComponent

Parameters:

v - 3D translation vector

resize

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

Resizes the component according to given factors. Due to spherical representation only one direction is considered. The sphere cannot be resized arbitrarily, the upper limit is 10 Angstrom.

Overrides:

resize in class GraphicComponent

Parameters:

x - ignored

y - size increment/decrement

z - ignored

isControllable

public boolean isControllable(java.lang.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 - control event type, Shift and Resize are interpreted by this component

Returns:

true if type is either Shift or Resize

hasTransparentPart

public boolean hasTransparentPart()

Checks is component has transparent part. For detailed discussion see GraphicComponent.hasTransparentPart().

Overrides:

hasTransparentPart in class GraphicComponent

Returns:

true if the current drawing type is not DRAW_TYPE_FILLED.

drawTransparentPart

public void drawTransparentPart()

Draws transparent parts of the component if there is any. Note, that PharmacophorePoint has no subpart, thus the whole component is either transparent or opaque.

Overrides:

drawTransparentPart in class GraphicComponent

draw

public void draw()

Draws the entire component if it is opaque.

Overrides:

draw in class GraphicComponent

initDraw

public void initDraw()

Initializes all internal data structure needed for drawing the component. It is called prior to draw().

pickObject

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

Sets GraphicComponent.pickedItem to the pharmacophore point.

Overrides:

pickObject in class GraphicComponent

Parameters:

offset - see GraphicComponent.pickObject(int,double[],float[])

maxZ - see GraphicComponent.pickObject(int,double[],float[])

modelview - see GraphicComponent.pickObject(int,double[],float[])

setDrawType

public void setDrawType(java.lang.String type)

Sets current drawing type.

Parameters:

type - Solid, Mesh or Transparent

getDrawType

public java.lang.String getDrawType()

Returns the name of the drawing type.

Returns:

Solid, Mesh or Transparent

isAcceptor

public boolean isAcceptor()

Checks if actual pharmacophore type includes ACCEPTOR_TYPE. Types are not exclusive, a PharmacophorePoint can have multiple types, though certain combinations are senseless (like ANIONIC_TYPE and CATIONIC_TYPE at the same time).

Returns:

true if current type includes ACCEPTOR_TYPE

setAcceptor

public void setAcceptor(boolean flag)

Sets or clears the acceptor property of the PharmacophorePoint.

Parameters:

flag - if true, current pharmacophore type will include ACCEPTOR_TYPE otherwise it will not be an acceptor

isDonor

public boolean isDonor()

Checks if actual pharmacophore type includes DONOR_TYPE. Types are not exclusive, a PharmacophorePoint can have multiple types.

Returns:

true if current type includes ADONOR_TYPE

setDonor

public void setDonor(boolean flag)

Sets or clears the donor property of the PharmacophorePoint.

Parameters:

flag - if true, current pharmacophore type will include DONOR_TYPE otherwise it will not be a donor

isHydrophobic

public boolean isHydrophobic()

Checks if actual pharmacophore type includes HYDROPHOBIC_TYPE. Types are not exclusive, a PharmacophorePoint can have multiple types.

Returns:

true if current type includes HYDROPHOBIC_TYPE

setHydrophobic

public void setHydrophobic(boolean flag)

Sets or clears the hydrophobic property of the PharmacophorePoint.

Parameters:

flag - if true, current pharmacophore type will include HYDROPHOBIC_TYPE otherwise it will not be hydrophobic

isAromatic

public boolean isAromatic()

Checks if actual pharmacophore type includes AROMATIC_TYPE. Types are not exclusive, a PharmacophorePoint can have multiple types.

Returns:

true if current type includes AROMATIC_TYPE

setAromatic

public void setAromatic(boolean flag)

Sets or clears the aromatic property of the PharmacophorePoint.

Parameters:

flag - if true, current pharmacophore type will include AROMATIC_TYPE otherwise it will not be aromatic

isAnionic

public boolean isAnionic()

Check if actual pharmacophore type includes ANIONIC_TYPE. Types are not exclusive, a PharmacophorePoint can have multiple types.

Returns:

true if current type includes ANIONIC_TYPE

setAnionic

public void setAnionic(boolean flag)

Sets or clears the anionic property of the PharmacophorePoint.

Parameters:

flag - if true, current pharmacophore type will include ANIONIC_TYPE otherwise it will not be anionic

isCationic

public boolean isCationic()

Check if actual pharmacophore type includes CATIONIC_TYPE. Types are not exclusive, a PharmacophorePoint can have multiple types.

Returns:

true if current type includes CATIONIC_TYPE

setCationic

public void setCationic(boolean flag)

Sets or clears the cationic property of the PharmacophorePoint.

Parameters:

flag - if true, current pharmacophore type will include CATIONIC_TYPE otherwise it will not be cationic

isExcluded

public boolean isExcluded()

Check if actual pharmacophore type is EXCLUDED_TYPE. This can be used to represent excluded volumes.

Returns:

true if current type is EXCLUDED_TYPE

setExcluded

public void setExcluded(boolean flag)

Sets or clears the excluded property of the PharmacophorePoint.

Parameters:

flag - if true, current pharmacophore type will be set to EXCLUDED_TYPE otherwise it will not be an excluded volume

setRenderingQuality

public void setRenderingQuality(java.lang.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 GraphicComponent.RENDERING_QUALITY_HIGH constants. Sets the precision (resolution) of the drawn sphere.

Overrides:

setRenderingQuality in class GraphicComponent

Parameters:

quality -

setDrawProperty

public void setDrawProperty(java.lang.String propertyName,
                            java.lang.String propertyValue)

Sets drawing properties specific to PharmacophoreSphere. Generic properties are processed by GraphicComponent.setDrawProperty(String, String).
Specific properties accepted:

• "Quality" -- "High", "Medium", "Low"
• "PharmacophorePoint.DrawType" -- "Mesh", "Solid", "Transparent"
• "Acceptor" -- Boolean value as String
• "Donor" -- Boolean value as String
• "Hydrophobe" -- Boolean value as String
• "Aromatic" -- Boolean value as String
• "Anionic" -- Boolean value as String
• "Cationic" -- Boolean value as String
• "Excluded" -- Boolean value as String

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

cleanup

public void cleanup()

Overrides:

cleanup in class GraphicComponent