chemaxon.marvin.space
Class MolecularSurfaceComponent

java.lang.Object
  chemaxon.marvin.space.GraphicComponent
      chemaxon.marvin.space.MolecularSurfaceComponent

All Implemented Interfaces:

chemaxon.marvin.space.UsableObject, chemaxon.marvin.util.CallbackIface

public class MolecularSurfaceComponent
extends GraphicComponent
implements chemaxon.marvin.util.CallbackIface, chemaxon.marvin.space.UsableObject

Class that represents a surface of a molecule. The surface can be computed different ways, this class connects the molecule with the somehow-computed surface e.g. by handling coordinate-change of the molecule or by coloring the surface based on a molecular property.

Since:

Marvin 4.0.2

Version:

MarvinSpace 1.0

Author:

Judit Papp

Field Summary

protected int	atomCount
protected static boolean	AUTO_RESOLUTION_ENABLED
protected boolean	automaticSettingOfGridSize
protected byte[][]	customPaletteColors
static float	DEFAULT_ISOVALUE
static float	DEFAULT_PROBE_RADIUS
static float	DEFAULT_RESOLUTION
protected static float[]	highPrecisions
protected static float[]	lowPrecisions
protected static float[]	mediumPrecisions
protected int	paletteId
protected static int[]	precisionThresholds
static int	SURFACE_COLOR_GRID_MAPPING
static int	SURFACE_COLOR_PROPERTY_MAPPING
static int	SURFACE_COLOR_TYPE_ATOMTYPE
static int	SURFACE_COLOR_TYPE_B_FACTOR
static int	SURFACE_COLOR_TYPE_CHAIN
static int	SURFACE_COLOR_TYPE_CONSTANT
static int	SURFACE_COLOR_TYPE_EP
static int	SURFACE_COLOR_TYPE_RAINBOW
static int	SURFACE_COLOR_TYPE_RESIDUE
static int	SURFACE_COLOR_TYPE_SS
protected static boolean	SURFACE_SIMPLIFICATION_ENABLED
protected static int	SURFACE_SMOOTHNESS
static int	SURFACE_TYPE_BLOBBY
static int	SURFACE_TYPE_CONNOLLY
static int	SURFACE_TYPE_GAUSSIAN
static int	SURFACE_TYPE_SAS
static int	SURFACE_TYPE_VDW
protected int	surfaceColorType
protected float	surfaceGridPrecision
protected boolean	surfaceSimplificationEnabled
protected float	surfaceSimplificationTolerance
protected int	surfaceSmoothnessFactor
protected int	surfaceType

Fields inherited from class chemaxon.marvin.space.GraphicComponent

active, associatedComponents, boundingBox, color, 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

MolecularSurfaceComponent()
Creates a new instance of MolecularSurfaceComponent without setting anything.

MolecularSurfaceComponent(java.util.ArrayList molecules)
Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces and MoleculeVisualizers.

MolecularSurfaceComponent(java.util.ArrayList molecules, java.lang.String surfaceType)
Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces and MoleculeVisualizers.

MolecularSurfaceComponent(chemaxon.struc.MoleculeIterators.MoleculeInterface mi, chemaxon.marvin.modules.mprop.VolumetricData vd)
Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData, which usually comes from a Gaussian Cube file.

MolecularSurfaceComponent(chemaxon.struc.MoleculeIterators.MoleculeInterface mi, chemaxon.marvin.modules.mprop.VolumetricData vd, float isoValue)
Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData, which usually comes from a Gaussian Cube file.

Method Summary

java.lang.Object	callback(java.lang.String method, java.lang.Object arg)
void	draw() Draws the molecular surface, and recomputes it if the coordinates of the molecule have been changed.
protected void	drawSelection(int mode) Draws the component in the given mode (usually in selection mode), the rendering mode is for checking.
void	drawTransparentPart() Draws the surface if it was transparent or mesh.
java.awt.Color	getColor() Returns the constant color of the surface.
int	getColorType() Returns the color type of the surface.
int	getDrawType() Returns the drawing type of the molecular surface.
double	getMaximumMappedValue() Returns the maximum value of the mapped property on this surface.
double	getMinimumMappedValue() Returns the minimum value of the mapped property on this surface.
chemaxon.marvin.space.util.Palette	getPalette() Returns the used built-in palette.
java.lang.String	getPaletteString() Returns the string identifier of the used built-in palette.
double	getProbeRadius() Returns the probe radius the surface computing will use.
SurfaceComponent	getSurface() Returns the surface.
double	getSurfacePrecision() Returns the grid resolution from which the surface is computed.
boolean	getSurfaceSimplificationEnabled() Returns true if Surface Simplification is enabled.
int	getSurfaceSmoothnessFactor() Surfaces can be smoothed by the following algorithm: Paul Bourke: Surface Relaxation and Smoothing http://astronomy.swin.edu.au/~pbourke/modelling/relax/ This algorithm has a smoothness factor.
float	getSurfaceThreshold() Returns the isovalue/threshold of the surface.
int	getSurfaceType() Returns the type of the surface.
static int	getSurfaceType(java.lang.String type)
static java.lang.String	getSurfaceTypeString(int surfaceType)
boolean	hasTransparentPart() Returns true if the drawing type of the molecular surface was MESH_TYPE or TRANSPARENT_TYPE.
boolean	isColorMapperEnabled()
boolean	isControllable(java.lang.String type) Returns whether controling by the given type of controller is allowed to the component.
boolean	isVolumeVisible() Tells whether the volumetric data is shown or not.
void	mapPropertyToSurface(chemaxon.marvin.space.grid.Grid grid)
void	mapPropertyToSurface(chemaxon.marvin.modules.mprop.VolumetricData vd) Coloring surface based on the given grid.
void	onRemoveGraphicComponent()
void	receiveNotificationOnCoordinateChange(GraphicComponent gc) The molecule will notify the surface when its coordinates change.
void	refreshColoring()
void	resize(double x, double y, double z) Resizes the component according to given factors.
void	select() Sets the component to be selected.
void	setAtomPropertyList(java.util.ArrayList atomProperties) Sets a list of atomic properties that can be mapped as coloring on the surface.
void	setColor(java.awt.Color c) Sets the constant color of the component.
void	setDrawProperty(java.lang.String propertyName, java.lang.String propertyValue) This is the gate of draw properties from outside to the component.
void	setExclusiveDrawing(boolean b) Enables/disables exclusive drawing, see SurfaceComponent.setExclusiveColor(byte[]).
void	setGL(javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu) Sets the GL rendering environment.
void	setMolecules(java.util.ArrayList molecules) The surface will be the molecular surface of the given molecules.
void	setNegativeCriterium(double v) Sets the lowest negative value colored.
void	setPalette(byte[][] colors) Sets colors to be used by the color palette.
void	setPalette(int paletteId) Sets a built-in palette used during coloring the molecular surface.
void	setPaletteMaximum(double v) Sets the largest positive value colored.
void	setPaletteMinimum(double v) Sets the largest negative value colored.
void	setPositiveCriterium(double v) Sets the lowest positive value colored.
void	setProbeRadius(double r) Sets thwe probe radius that is the radius of a water molecule used in computing surfaces.
void	setProgressBar(chemaxon.marvin.space.ProgressBarInterface PB)
void	setRotateMatrix(float[] rotateMatrix) Sets the rotation matrix in order to get the proper mapping of a vector to the viewing plane.
void	setSurfacePrecision() Resolution will be set automatically according to the number of atoms and the rendering quality.
void	setSurfacePrecision(float v) Explicitly sets the grid resolution from which the surface is computed.
void	setSurfacePrecision(java.lang.String quality) Sets the surface precision by setting a quality.
void	setSurfaceSimplificationEnabled(boolean b) The number of surface polygons can be reduced by the following algorithm: Paul Bourke: Surface (polygonal) Simplification http://astronomy.swin.edu.au/~pbourke/modelling/surfsimp/ This method enables/disables simplification.
void	setSurfaceType(java.lang.String s) Sets the type of the surface and computes the surface with the necessary method.
void	setVisible(boolean state) Sets the surface to be visible/invisible.
void	showVolume(boolean b) For Gaussian Cube surfaces it can be enabled to visualize the volumetric data from which the surface is generated.
boolean	surfaceOf(GraphicComponent gc) Tells whether it is the molecular surface of the given component (molecule).
void	surfaceSimplification() Runs the (might be time-consuming) algorithm thst reduces the number of triangles of the surface.
void	translate(float[] v) Translates the component with the given translation vector.
void	updatePropertyMapping()

Methods inherited from class chemaxon.marvin.space.GraphicComponent

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

Field Detail

SURFACE_TYPE_VDW

public static final int SURFACE_TYPE_VDW

See Also:

Constant Field Values

SURFACE_TYPE_CONNOLLY

public static final int SURFACE_TYPE_CONNOLLY

See Also:

Constant Field Values

SURFACE_TYPE_SAS

public static final int SURFACE_TYPE_SAS

See Also:

Constant Field Values

SURFACE_TYPE_BLOBBY

public static final int SURFACE_TYPE_BLOBBY

See Also:

Constant Field Values

SURFACE_TYPE_GAUSSIAN

public static final int SURFACE_TYPE_GAUSSIAN

See Also:

Constant Field Values

highPrecisions

protected static final float[] highPrecisions

mediumPrecisions

protected static final float[] mediumPrecisions

lowPrecisions

protected static final float[] lowPrecisions

precisionThresholds

protected static final int[] precisionThresholds

SURFACE_SMOOTHNESS

protected static final int SURFACE_SMOOTHNESS

See Also:

Constant Field Values

SURFACE_SIMPLIFICATION_ENABLED

protected static final boolean SURFACE_SIMPLIFICATION_ENABLED

See Also:

Constant Field Values

AUTO_RESOLUTION_ENABLED

protected static final boolean AUTO_RESOLUTION_ENABLED

See Also:

Constant Field Values

DEFAULT_RESOLUTION

public static final float DEFAULT_RESOLUTION

See Also:

Constant Field Values

DEFAULT_PROBE_RADIUS

public static final float DEFAULT_PROBE_RADIUS

See Also:

Constant Field Values

DEFAULT_ISOVALUE

public static final float DEFAULT_ISOVALUE

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_CONSTANT

public static final int SURFACE_COLOR_TYPE_CONSTANT

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_ATOMTYPE

public static final int SURFACE_COLOR_TYPE_ATOMTYPE

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_RESIDUE

public static final int SURFACE_COLOR_TYPE_RESIDUE

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_CHAIN

public static final int SURFACE_COLOR_TYPE_CHAIN

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_EP

public static final int SURFACE_COLOR_TYPE_EP

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_SS

public static final int SURFACE_COLOR_TYPE_SS

See Also:

Constant Field Values

SURFACE_COLOR_GRID_MAPPING

public static final int SURFACE_COLOR_GRID_MAPPING

See Also:

Constant Field Values

SURFACE_COLOR_PROPERTY_MAPPING

public static final int SURFACE_COLOR_PROPERTY_MAPPING

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_B_FACTOR

public static final int SURFACE_COLOR_TYPE_B_FACTOR

See Also:

Constant Field Values

SURFACE_COLOR_TYPE_RAINBOW

public static final int SURFACE_COLOR_TYPE_RAINBOW

See Also:

Constant Field Values

paletteId

protected int paletteId

customPaletteColors

protected byte[][] customPaletteColors

surfaceGridPrecision

protected float surfaceGridPrecision

surfaceSmoothnessFactor

protected int surfaceSmoothnessFactor

surfaceSimplificationEnabled

protected boolean surfaceSimplificationEnabled

surfaceSimplificationTolerance

protected float surfaceSimplificationTolerance

automaticSettingOfGridSize

protected boolean automaticSettingOfGridSize

atomCount

protected int atomCount

surfaceType

protected int surfaceType

surfaceColorType

protected int surfaceColorType

Constructor Detail

MolecularSurfaceComponent

public MolecularSurfaceComponent()

Creates a new instance of MolecularSurfaceComponent without setting anything.

MolecularSurfaceComponent

public MolecularSurfaceComponent(chemaxon.struc.MoleculeIterators.MoleculeInterface mi,
                                 chemaxon.marvin.modules.mprop.VolumetricData vd)
                          throws java.lang.Exception

Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData, which usually comes from a Gaussian Cube file.

Throws:

java.lang.Exception

MolecularSurfaceComponent

public MolecularSurfaceComponent(chemaxon.struc.MoleculeIterators.MoleculeInterface mi,
                                 chemaxon.marvin.modules.mprop.VolumetricData vd,
                                 float isoValue)
                          throws java.lang.Exception

Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData, which usually comes from a Gaussian Cube file.

Throws:

java.lang.Exception

MolecularSurfaceComponent

public MolecularSurfaceComponent(java.util.ArrayList molecules)

Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces and MoleculeVisualizers. Does not compute a surface, setSurfaceType() should be called.

MolecularSurfaceComponent

public MolecularSurfaceComponent(java.util.ArrayList molecules,
                                 java.lang.String surfaceType)
                          throws java.lang.Exception

Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces and MoleculeVisualizers.

Parameters:

surfaceType - can be "van der Waals", "Solvent-accessible", "Connolly", "Blobby".

Throws:

java.lang.Exception

Method Detail

getSurfaceTypeString

public static java.lang.String getSurfaceTypeString(int surfaceType)

getSurfaceType

public static int getSurfaceType(java.lang.String type)

onRemoveGraphicComponent

public void onRemoveGraphicComponent()

Overrides:

onRemoveGraphicComponent in class GraphicComponent

setProgressBar

public void setProgressBar(chemaxon.marvin.space.ProgressBarInterface PB)

Overrides:

setProgressBar in class GraphicComponent

receiveNotificationOnCoordinateChange

public void receiveNotificationOnCoordinateChange(GraphicComponent gc)

The molecule will notify the surface when its coordinates change.

Overrides:

receiveNotificationOnCoordinateChange in class GraphicComponent

Parameters:

gc - component changing coordinates

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 resized.

Overrides:

isControllable in class GraphicComponent

Parameters:

type - control event type, Resize and Shift> are interpreted by this component

Returns:

true if type is either Resize or Shift

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.

Overrides:

resize in class GraphicComponent

Parameters:

x - size increment/decrement

y - size increment/decrement

z - size increment/decrement

surfaceOf

public boolean surfaceOf(GraphicComponent gc)

Tells whether it is the molecular surface of the given component (molecule).

setMolecules

public void setMolecules(java.util.ArrayList molecules)

The surface will be the molecular surface of the given molecules.

Parameters:

molecules - MoleculeInterfaces and MoleculeVisualizers (now every MoleculeVisualizer is also a MoleculeInterface)

draw

public void draw()

Draws the molecular surface, and recomputes it if the coordinates of the molecule have been changed.

Overrides:

draw in class GraphicComponent

drawTransparentPart

public void drawTransparentPart()

Draws the surface if it was transparent or mesh.

Overrides:

drawTransparentPart in class GraphicComponent

getColor

public java.awt.Color getColor()

Returns the constant color of the surface.

Specified by:

getColor in interface chemaxon.marvin.space.UsableObject

Overrides:

getColor in class GraphicComponent

setColor

public void setColor(java.awt.Color c)

Description copied from class: GraphicComponent

Sets the constant color of the component.

Specified by:

setColor in interface chemaxon.marvin.space.UsableObject

Overrides:

setColor in class GraphicComponent

getSurface

public SurfaceComponent getSurface()

Returns the surface.

getSurfaceType

public int getSurfaceType()

Returns the type of the surface. See {#SURFACE_TYPE_VDW}, {#SURFACE_TYPE_CONNOLLY}, {#SURFACE_TYPE_SAS}, {#SURFACE_TYPE_BLOBBY}, {#SURFACE_TYPE_GAUSSIAN} types. Type can be returned as String with {#getSurfaceTypeString(int)}.

setSurfaceType

public void setSurfaceType(java.lang.String s)
                    throws java.lang.Exception

Sets the type of the surface and computes the surface with the necessary method. SurfaceType can be "van der Waals", "Solvent-accessible", "Connolly", "Blobby".

Throws:

java.lang.Exception

getSurfaceSmoothnessFactor

public int getSurfaceSmoothnessFactor()

Surfaces can be smoothed by the following algorithm: Paul Bourke: Surface Relaxation and Smoothing http://astronomy.swin.edu.au/~pbourke/modelling/relax/ This algorithm has a smoothness factor. If the factor is 0, the algorithm will not have effect.

setSurfaceSimplificationEnabled

public void setSurfaceSimplificationEnabled(boolean b)

The number of surface polygons can be reduced by the following algorithm: Paul Bourke: Surface (polygonal) Simplification http://astronomy.swin.edu.au/~pbourke/modelling/surfsimp/ This method enables/disables simplification. If this is enabled, computing surface will require more time, but displaying will be much easier and faster, and data will cost less memory.

getSurfaceSimplificationEnabled

public boolean getSurfaceSimplificationEnabled()

Returns true if Surface Simplification is enabled. See setSurfaceSimplificationEnabled(boolean) for details.

getSurfaceThreshold

public float getSurfaceThreshold()

Returns the isovalue/threshold of the surface.

getProbeRadius

public double getProbeRadius()

Returns the probe radius the surface computing will use. Connolly and Solvent-accesible surfaces use a so-called probe radius, which approximates the radius of a water molecule.

setProbeRadius

public void setProbeRadius(double r)

Sets thwe probe radius that is the radius of a water molecule used in computing surfaces.

setVisible

public void setVisible(boolean state)

Sets the surface to be visible/invisible.

Specified by:

setVisible in interface chemaxon.marvin.space.UsableObject

Overrides:

setVisible in class GraphicComponent

Parameters:

state - of visibility

getSurfacePrecision

public double getSurfacePrecision()

Returns the grid resolution from which the surface is computed.

setSurfacePrecision

public void setSurfacePrecision(java.lang.String quality)
                         throws java.lang.Exception

Sets the surface precision by setting a quality. Grid resolution from which the surface is computed will be set according to the given quality.

Parameters:

quality - can be "High", "Medium", "Low"

Throws:

java.lang.Exception

setSurfacePrecision

public void setSurfacePrecision(float v)

Explicitly sets the grid resolution from which the surface is computed.

setSurfacePrecision

public void setSurfacePrecision()

Resolution will be set automatically according to the number of atoms and the rendering quality. Larger number of atoms means lower precision.

setDrawProperty

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

This is the gate of draw properties from outside to the component. See also GraphicComponent.setDrawProperty(String, String). Accepts:

• "Surface.DrawType" -- "Dot", "Mesh", "Solid", "Transparent"
• "Surface.ColorType" "Constant", "AtomType", "ResidueType", "ChainType", "ElectrostaticPotential"
• "Surface.Color" -- java.awt.Color value as String
• "CarbonColorStyle" -- Integer value as String
  (Carbon color is 0: lightgray, 1: darkgray, 2: green, 3:cyan)

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

Throws:

java.lang.Exception

refreshColoring

public void refreshColoring()
                     throws java.lang.Exception

Throws:

java.lang.Exception

getDrawType

public int getDrawType()

Returns the drawing type of the molecular surface. See SurfaceComponent.getDrawType().

hasTransparentPart

public boolean hasTransparentPart()

Returns true if the drawing type of the molecular surface was MESH_TYPE or TRANSPARENT_TYPE.

Overrides:

hasTransparentPart in class GraphicComponent

Returns:

will the component draw with transparency

getColorType

public int getColorType()

Returns the color type of the surface. See SURFACE_COLOR_TYPE_CONSTANT, SURFACE_COLOR_TYPE_ATOMTYPE, SURFACE_COLOR_TYPE_RESIDUE, SURFACE_COLOR_TYPE_CHAIN, SURFACE_COLOR_TYPE_EP}

setPalette

public void setPalette(int paletteId)

Sets a built-in palette used during coloring the molecular surface.

Parameters:

paletteId - id of the palette, see SurfaceColoring.COLOR_MAPPER_RAINBOW, SurfaceColoring.COLOR_MAPPER_BLUE_TO_GREEN, etc.

setPalette

public void setPalette(byte[][] colors)

Sets colors to be used by the color palette.

Parameters:

colors - array of byte[3] colors

setExclusiveDrawing

public void setExclusiveDrawing(boolean b)

Enables/disables exclusive drawing, see SurfaceComponent.setExclusiveColor(byte[]).

Parameters:

b -

isVolumeVisible

public boolean isVolumeVisible()

Tells whether the volumetric data is shown or not. Note that the volume can be visible independently of the surface.

Returns:

true if the surface is a Gaussian Cube surface, and the volumetric data is visible.

showVolume

public void showVolume(boolean b)

For Gaussian Cube surfaces it can be enabled to visualize the volumetric data from which the surface is generated.

Parameters:

b -

setNegativeCriterium

public void setNegativeCriterium(double v)
                          throws java.lang.Exception

Sets the lowest negative value colored. Vertices having larger negative value (nearer to zero) won't be colored.

Throws:

java.lang.Exception

setPositiveCriterium

public void setPositiveCriterium(double v)
                          throws java.lang.Exception

Sets the lowest positive value colored. Vertices having lower positive value (nearer to zero) won't be colored.

Throws:

java.lang.Exception

setPaletteMinimum

public void setPaletteMinimum(double v)
                       throws java.lang.Exception

Sets the largest negative value colored. Vertices having lower negative value (farther from zero) won't be colored.

Throws:

java.lang.Exception

setPaletteMaximum

public void setPaletteMaximum(double v)
                       throws java.lang.Exception

Sets the largest positive value colored. Vertices having larger positive value (farther from zero) won't be colored.

Throws:

java.lang.Exception

getPalette

public chemaxon.marvin.space.util.Palette getPalette()

Returns the used built-in palette.

Returns:

the actually used palette object

getPaletteString

public java.lang.String getPaletteString()

Returns the string identifier of the used built-in palette.

Returns:

a string that identifies the built-in palette by ColorPaletteUtil.getBuiltInPalette(Object)

getMinimumMappedValue

public double getMinimumMappedValue()

Returns the minimum value of the mapped property on this surface.

getMaximumMappedValue

public double getMaximumMappedValue()

Returns the maximum value of the mapped property on this surface.

isColorMapperEnabled

public boolean isColorMapperEnabled()

mapPropertyToSurface

public void mapPropertyToSurface(chemaxon.marvin.modules.mprop.VolumetricData vd)
                          throws java.lang.Exception

Coloring surface based on the given grid.

Parameters:

vd - property grid

Throws:

java.lang.Exception

mapPropertyToSurface

public void mapPropertyToSurface(chemaxon.marvin.space.grid.Grid grid)
                          throws java.lang.Exception

Throws:

java.lang.Exception

updatePropertyMapping

public void updatePropertyMapping()
                           throws java.lang.Exception

Throws:

java.lang.Exception

setAtomPropertyList

public void setAtomPropertyList(java.util.ArrayList atomProperties)

Sets a list of atomic properties that can be mapped as coloring on the surface.

Parameters:

atomProperties -

select

public void select()

Description copied from class: GraphicComponent

Sets the component to be selected. See also unSelect().

Specified by:

select in interface chemaxon.marvin.space.UsableObject

Overrides:

select in class GraphicComponent

surfaceSimplification

public void surfaceSimplification()
                           throws java.lang.Exception

Runs the (might be time-consuming) algorithm thst reduces the number of triangles of the surface. Note that this method is irreversible, and can greatly deform the surface when invoked many times. Usually reducing the number of triangles one time does not change the characteristic (shape) of the surface too much, but reduces the number of triangles by 40-70% so drawing can be much faster after that.

Throws:

java.lang.Exception

setGL

public void setGL(javax.media.opengl.GL gl,
                  javax.media.opengl.glu.GLU glu)

Description copied from class: GraphicComponent

Sets the GL rendering environment. Without this being set the component cannot draw itself.

Overrides:

setGL in class GraphicComponent

Parameters:

gl - Interface to OpenGL

glu - Interface to OpenGL

drawSelection

protected void drawSelection(int mode)

Description copied from class: GraphicComponent

Draws the component in the given mode (usually in selection mode), the rendering mode is for checking.

Overrides:

drawSelection in class GraphicComponent

Parameters:

mode - GL_RENDER or GL_SELECT

setRotateMatrix

public void setRotateMatrix(float[] rotateMatrix)

Description copied from class: GraphicComponent

Sets the rotation matrix in order to get the proper mapping of a vector to the viewing plane.

Overrides:

setRotateMatrix in class GraphicComponent

Parameters:

rotateMatrix - float array having 16 elements representing a 4 by 4 rotation matrix

callback

public java.lang.Object callback(java.lang.String method,
                                 java.lang.Object arg)

Specified by:

callback in interface chemaxon.marvin.util.CallbackIface