MacroMoleculeComponent (JChem Base API documentation (c) 1998-2020 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.space.GraphicComponent
- - chemaxon.marvin.space.MacroMoleculeComponent

All Implemented Interfaces:

chemaxon.marvin.space.UsableObject
```
@PublicAPI
public class MacroMoleculeComponent
extends GraphicComponent
```
MacroMoleculeComponent is a visualizer of complex structures. It can individually display and handle protein chains, ligands, water and ions.

Since:

Marvin 4.0.2

Version:

MarvinSpace 1.0

Author:

Judit Papp

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static interface MacroMoleculeComponent.MoleculeVisualizer

Nested Classes
Modifier and Type	Class and Description
`static interface`	`MacroMoleculeComponent.MoleculeVisualizer`

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`B_FACTOR_MODE`
`protected static int`	`COMPONENT_TYPE_ATOM`
`protected static int`	`COMPONENT_TYPE_BOND`
`protected static int`	`COMPONENT_TYPE_MOLECULE`
`protected static int`	`COMPONENT_TYPE_RESIDUE`
`protected boolean`	`initialised`
`static int`	`RAINBOW_MODE`

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

Constructors
Modifier	Constructor and Description
`protected`	`MacroMoleculeComponent()` Creates a new instance of MacroMoleculeComponent
	`MacroMoleculeComponent(chemaxon.struc.MacroMolecule mol)` Creates a new instance of MacroMoleculeComponent

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`draw()` Draws the MacroMolecule as letting its visualizers draw its parts.
`void`	`draw2DPart()` Draws the 2D parts of its visualizers.
`protected void`	`drawSelection(int mode)` Draws the component in the given mode (usually in selection mode).
`void`	`drawTransparentPart()` Draws the transparent parts of its visualizers.
`void`	`exclusiveSelection()` Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
`void`	`extendSelection()` Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
`void`	`fadeSelected()` The selected visualizers will be hidden.
`void`	`fadeUnselected()` The unselected visualizers will be hidden.
`chemaxon.marvin.space.util.Palette`	`getBFactorPalette()` Returns the palette that is used when the coloring mode of the component is b-factor coloring.
`MacroMoleculeComponent.MoleculeVisualizer`	`getComponent(int cIdx)` Returns its visualizer with the given index.
`ComponentElement`	`getComponentElement()` Returns the previously picked but unprocessed ComponentElement or the whole component as a ComponentElement, if no picking happened.
`ComponentElement`	`getComponentElement(MacroMoleculeComponent.MoleculeVisualizer mv)` Returns the visualizer as a `ComponentElement`.
`java.util.Iterator<MacroMoleculeComponent.MoleculeVisualizer>`	`getComponentIterator()` Returns the Iterator of its visualizers.
`java.util.ArrayList<MacroMoleculeComponent.MoleculeVisualizer>`	`getComponents()` Returns its visualizers.
`void`	`getCoordinates(ComponentElement element, float[] c)` Sets the coordinates of the given ComponentElement in the given array.
`java.lang.String`	`getDescription(ComponentElement element)` Returns the short description of the given element.
`ComponentElement[]`	`getLabelInformation(java.lang.String labelType)` Collects the label information of the visualizers.
`chemaxon.struc.MacroMolecule`	`getMacroMolecule()` Returns the `MacroMolecule` this component visualizes.
`Molecule`	`getMolecule()` Returns the `Molecule` representation of the `MacroMolecule`.
`chemaxon.marvin.space.util.Palette`	`getRainbowPalette()` Returns the color palette that is used when the coloring mode of the component is rainbow coloring.
`chemaxon.marvin.space.UsableObject`	`getUsableObject(chemaxon.marvin.space.UOID id)` Returns the component that the given UOID identifies.
`chemaxon.marvin.space.UOID`	`getUsableObjectId(MacroMoleculeComponent.MoleculeVisualizer mv)`
`boolean`	`has2DPart()` Returns true if any of its visualizers have 2D part.
`boolean`	`hasSelectedElements()` Returns true if any of its visualizers have any selected part.
`boolean`	`hasTransparentPart()` Returns true if any of its visualizers have transparent part.
`void`	`hideSelected()` The selected visualizers will be hidden.
`void`	`hideUnselected()` The unselected visualizers will be hidden.
`void`	`invertSelection()` Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
`boolean`	`isControllable(java.lang.String type)` Returns whether controling by the given type of controller is allowed to the component.
`boolean`	`isVisible()` Returns true if any of its visualizers is visible.
`boolean`	`isVisible(ComponentElement element)` Returns true if the gien ComponentElement is visible.
`void`	`onRemoveGraphicComponent()`
`void`	`removeGraphicComponent(MacroMoleculeComponent.MoleculeVisualizer mv)`
`void`	`rotate(float[] vector, float[] center)` Rotates its selected ligand by changing its coordinates, and not just the view.
`void`	`select()` Sets all visualizers to be selected.
`void`	`selectComponentElementsInside(BoundingBox bb)` Visualizers lying in the given box will be selected.
`void`	`setDrawProperty(java.lang.String propertyName, java.lang.String propertyValue)` Sets a `draw property`.
`void`	`setDrawProperty(java.lang.String propertyName, java.lang.String propertyValue, MacroMoleculeComponent.MoleculeVisualizer mmv)` Sets the given draw property to the given visualizer.
`void`	`setGL(javax.media.opengl.GL2 gl, javax.media.opengl.glu.GLU glu)` Sets GL2 in all of its visualizers.
`void`	`setProgressBar(chemaxon.marvin.space.ProgressBarInterface progressBar)`
`void`	`setVisible(boolean state)` Sets all of the visualizers to visible/invisible.
`void`	`showFaded()` The faded visualizers will be fully visible again.
`protected double`	`touchObject(int hits)` Returns the z coordinate of the component being nearest to the viewing point.
`void`	`translate(float[] vector)` Translates its selected ligand by changing its coordinates, and not just the view.
`void`	`unSelect()` Sets all parts of all visualizers not to be selected.

Methods inherited from class chemaxon.marvin.space.GraphicComponent
addDrawProperties, associate, cleanup, drawBoundingBox, drawCoordinateAxes, exclusiveSelection, extendSelection, getAssociatedComponents, getBoundingBox, getBoundingSphereRadius, getCell, getColor, getCoordinates, getDescription, getDrawProperties, getDrawProperty, getGraphicComponent, getId, getLabelInformation, getName, getRenderingQuality, getZCoordinateTo2DPart, glColor, invertSelection, isGraphicComponent, isSelected, isSelected, locateObject, notifyCoordinateChange, notifyInvisibility, notifySelection, notifyUnSelection, notifyVisibility, pickObject, projectVector, receiveNotificationOnCoordinateChange, receiveNotificationOnInvisibility, receiveNotificationOnSelection, receiveNotificationOnUnSelection, receiveNotificationOnVisibility, removeAssociation, resize, rotate, rotate, select, setColor, setColor, setColor, setColor, setDrawProperties, setMotionMode, setName, setRenderingQuality, setRotateMatrix, storeDrawProperty, toString, unSelect

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - COMPONENT_TYPE_ATOM
```
protected static final int COMPONENT_TYPE_ATOM
```
    See Also:
    
    Constant Field Values
  - COMPONENT_TYPE_BOND
```
protected static final int COMPONENT_TYPE_BOND
```
    See Also:
    
    Constant Field Values
  - COMPONENT_TYPE_MOLECULE
```
protected static final int COMPONENT_TYPE_MOLECULE
```
    See Also:
    
    Constant Field Values
  - COMPONENT_TYPE_RESIDUE
```
protected static final int COMPONENT_TYPE_RESIDUE
```
    See Also:
    
    Constant Field Values
  - initialised
```
protected boolean initialised
```
  - RAINBOW_MODE
```
public static final int RAINBOW_MODE
```
    See Also:
    
    Constant Field Values
  - B_FACTOR_MODE
```
public static final int B_FACTOR_MODE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MacroMoleculeComponent
```
protected MacroMoleculeComponent()
```
    Creates a new instance of MacroMoleculeComponent
  - MacroMoleculeComponent
```
public MacroMoleculeComponent(chemaxon.struc.MacroMolecule mol)
```
    Creates a new instance of MacroMoleculeComponent
- Method Detail
  - removeGraphicComponent
```
public void removeGraphicComponent(MacroMoleculeComponent.MoleculeVisualizer mv)
```
  - onRemoveGraphicComponent
```
public void onRemoveGraphicComponent()
```
    Overrides:
    
    onRemoveGraphicComponent in class GraphicComponent
  - setProgressBar
```
public void setProgressBar(chemaxon.marvin.space.ProgressBarInterface progressBar)
```
    Overrides:
    
    setProgressBar in class GraphicComponent
  - getMolecule
```
public Molecule getMolecule()
```
    Returns the Molecule representation of the MacroMolecule. For example it can be necessary at copying molecules. Note that information about molecule parts such as chains, ligands, water, ions, etc will be lost. To have a more complex representation see {#getMacroMolecule()}.
    
    Returns:
    
    Molecule
  - getMacroMolecule
```
public chemaxon.struc.MacroMolecule getMacroMolecule()
```
    Returns the MacroMolecule this component visualizes. It stores the information about chains, ligands, water, ions, etc. To get it in simple Molecule representation see {#getMolecule()}.
    
    Returns:
    
    the macromolecule
  - draw
```
public void draw()
```
    Draws the MacroMolecule as letting its visualizers draw its parts.
    
    Overrides:
    
    draw in class GraphicComponent
  - has2DPart
```
public boolean has2DPart()
```
    Returns true if any of its visualizers have 2D part.
    
    Overrides:
    
    has2DPart in class GraphicComponent
    
    Returns:
    
    will the component draw in plane
  - draw2DPart
```
public void draw2DPart()
```
    Draws the 2D parts of its visualizers.
    
    Overrides:
    
    draw2DPart in class GraphicComponent
  - hasTransparentPart
```
public boolean hasTransparentPart()
```
    Returns true if any of its visualizers have transparent part.
    
    Overrides:
    
    hasTransparentPart in class GraphicComponent
    
    Returns:
    
    will the component draw with transparency
  - drawTransparentPart
```
public void drawTransparentPart()
```
    Draws the transparent parts of its visualizers.
    
    Overrides:
    
    drawTransparentPart in class GraphicComponent
  - getRainbowPalette
```
public chemaxon.marvin.space.util.Palette getRainbowPalette()
```
    Returns the color palette that is used when the coloring mode of the component is rainbow coloring. Note that this palette is configured to this macromolecule, because colors are get from atom indices.
    
    Returns:
    
    Palette with properly set colors, minimum and maximum values
  - getBFactorPalette
```
public chemaxon.marvin.space.util.Palette getBFactorPalette()
```
    Returns the palette that is used when the coloring mode of the component is b-factor coloring.
    
    Returns:
    
    Palette with properly set colors, minimum and maximum values
  - getComponentIterator
```
public java.util.Iterator<MacroMoleculeComponent.MoleculeVisualizer> getComponentIterator()
```
    Returns the Iterator of its visualizers.
  - getComponents
```
public java.util.ArrayList<MacroMoleculeComponent.MoleculeVisualizer> getComponents()
```
    Returns its visualizers.
  - getComponent
```
public MacroMoleculeComponent.MoleculeVisualizer getComponent(int cIdx)
```
    Returns its visualizer with the given index.
  - setGL
```
public void setGL(javax.media.opengl.GL2 gl,
                  javax.media.opengl.glu.GLU glu)
```
    Sets GL2 in all of its visualizers.
    
    Overrides:
    
    setGL in class GraphicComponent
    
    Parameters:
    
    gl - Interface to OpenGL
    
    glu - Interface to OpenGL
  - drawSelection
```
protected void drawSelection(int mode)
```
    Draws the component in the given mode (usually in selection mode).
    
    Overrides:
    
    drawSelection in class GraphicComponent
    
    Parameters:
    
    mode - GL_RENDER or GL_SELECT
  - getCoordinates
```
public void getCoordinates(ComponentElement element,
                           float[] c)
```
    Sets the coordinates of the given ComponentElement in the given array.
    
    Overrides:
    
    getCoordinates in class GraphicComponent
    
    Parameters:
    
    element - specific part of the component
    
    c - allocated array where coordinates will be put
  - getComponentElement
```
public ComponentElement getComponentElement()
```
    Returns the previously picked but unprocessed ComponentElement or the whole component as a ComponentElement, if no picking happened.
    
    Overrides:
    
    getComponentElement in class GraphicComponent
    
    Returns:
    
    picked part of the component
  - getComponentElement
```
public ComponentElement getComponentElement(MacroMoleculeComponent.MoleculeVisualizer mv)
```
    Returns the visualizer as a ComponentElement. This is useful for the visualizers themselves thence they can figure out their index inside the macromolecule.
    
    Parameters:
    
    mv - visualizer of the macromolecule
    
    Returns:
    
    the visualizer as a COMPONENT_TYPE_MOLECULE type ComponentElement
  - getUsableObjectId
```
public chemaxon.marvin.space.UOID getUsableObjectId(MacroMoleculeComponent.MoleculeVisualizer mv)
```
  - getUsableObject
```
public chemaxon.marvin.space.UsableObject getUsableObject(chemaxon.marvin.space.UOID id)
```
    Description copied from class: GraphicComponent
    
    Returns the component that the given UOID identifies.
    
    Overrides:
    
    getUsableObject in class GraphicComponent
    
    Parameters:
    
    id - identifier of the component or a part of the component
    
    Returns:
    
    the component or the specific part of the component
  - getDescription
```
public java.lang.String getDescription(ComponentElement element)
```
    Returns the short description of the given element.
    
    Overrides:
    
    getDescription in class GraphicComponent
    
    Parameters:
    
    element - specific part of the component
    
    Returns:
    
    short description as String
  - getLabelInformation
```
public ComponentElement[] getLabelInformation(java.lang.String labelType)
```
    Collects the label information of the visualizers.
    
    Overrides:
    
    getLabelInformation in class GraphicComponent
    
    Parameters:
    
    labelType -
    
    Returns:
    
    all label information merged into one array
  - isVisible
```
public boolean isVisible()
```
    Returns true if any of its visualizers is visible.
    
    Specified by:
    
    isVisible in interface chemaxon.marvin.space.UsableObject
    
    Overrides:
    
    isVisible in class GraphicComponent
    
    Returns:
    
    visibility of the component
  - isVisible
```
public boolean isVisible(ComponentElement element)
```
    Returns true if the gien ComponentElement is visible.
    
    Overrides:
    
    isVisible in class GraphicComponent
    
    Parameters:
    
    element - part of the component
    
    Returns:
    
    visibility of the part of the component
  - setVisible
```
public void setVisible(boolean state)
```
    Sets all of the visualizers to visible/invisible.
    
    Specified by:
    
    setVisible in interface chemaxon.marvin.space.UsableObject
    
    Overrides:
    
    setVisible in class GraphicComponent
    
    Parameters:
    
    state - of visibility
  - showFaded
```
public void showFaded()
```
    The faded visualizers will be fully visible again.
    
    Overrides:
    
    showFaded in class GraphicComponent
  - hideSelected
```
public void hideSelected()
```
    The selected visualizers will be hidden.
    
    Overrides:
    
    hideSelected in class GraphicComponent
  - hideUnselected
```
public void hideUnselected()
```
    The unselected visualizers will be hidden.
    
    Overrides:
    
    hideUnselected in class GraphicComponent
  - fadeSelected
```
public void fadeSelected()
```
    The selected visualizers will be hidden.
    
    Overrides:
    
    fadeSelected in class GraphicComponent
  - fadeUnselected
```
public void fadeUnselected()
```
    The unselected visualizers will be hidden.
    
    Overrides:
    
    fadeUnselected in class GraphicComponent
  - exclusiveSelection
```
public void exclusiveSelection()
```
    Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
    
    Overrides:
    
    exclusiveSelection in class GraphicComponent
  - extendSelection
```
public void extendSelection()
```
    Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
    
    Overrides:
    
    extendSelection in class GraphicComponent
  - invertSelection
```
public void invertSelection()
```
    Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
    
    Overrides:
    
    invertSelection in class GraphicComponent
  - select
```
public void select()
```
    Sets all visualizers to be selected. See also unSelect().
    
    Specified by:
    
    select in interface chemaxon.marvin.space.UsableObject
    
    Overrides:
    
    select in class GraphicComponent
  - unSelect
```
public void unSelect()
```
    Sets all parts of all visualizers not to be selected.
    
    Specified by:
    
    unSelect in interface chemaxon.marvin.space.UsableObject
    
    Overrides:
    
    unSelect in class GraphicComponent
  - selectComponentElementsInside
```
public void selectComponentElementsInside(BoundingBox bb)
```
    Visualizers lying in the given box will be selected.
    
    Overrides:
    
    selectComponentElementsInside in class GraphicComponent
    
    Parameters:
    
    bb - given box represented by a BoundingBox
  - hasSelectedElements
```
public boolean hasSelectedElements()
```
    Returns true if any of its visualizers have any selected part.
    
    Overrides:
    
    hasSelectedElements in class GraphicComponent
    
    Returns:
    
    is any part of the component selected
  - touchObject
```
protected double touchObject(int hits)
```
    Returns the z coordinate of the component being nearest to the viewing point. This equals with the maximum z coordinate, because we are looking down the negative z axis.
    
    Overrides:
    
    touchObject in class GraphicComponent
    
    Parameters:
    
    hits - Number of hits at the previous hit.
    
    Returns:
    
    z coordinate of the nearest picked object
  - 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 controlled if any of its visualizers is allowed.
    
    Overrides:
    
    isControllable in class GraphicComponent
    
    Parameters:
    
    type - "Shift", "Rotate", "Resize"
    
    Returns:
    
    is the component aloowed to be controlled or not
  - translate
```
public void translate(float[] vector)
```
    Translates its selected ligand by changing its coordinates, and not just the view.
    
    Overrides:
    
    translate in class GraphicComponent
    
    Parameters:
    
    vector - The translation vector.
  - rotate
```
public void rotate(float[] vector,
                   float[] center)
```
    Rotates its selected ligand by changing its coordinates, and not just the view.
    
    Overrides:
    
    rotate in class GraphicComponent
    
    Parameters:
    
    vector - Measurement of the rotation around the 3 axis, x, y, z.
    
    center - Center of the rotation.
  - setDrawProperty
```
public void setDrawProperty(java.lang.String propertyName,
                            java.lang.String propertyValue)
```
    Sets a draw property.
    Gives all proper draw properties to its visualizers.
    Accepts the properties below:
    - "DrawType" -- "Wire", "Stick", "Ball", "BallAndStick", "StickAndBall", "BallAndWire", "WireAndBall", "Spacefill"
    - "ColorType" -- "Constant", "CPK"
    - "Quality" -- "High", "Medium", "Low"
    - Hierarchical properties e.g. "Ligand.DrawType", "Water.Quality"
    - "Ligand.*"
    - "MacroMolecule.*"
    - "Water.*"
    - "Ion.*"
    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
  - setDrawProperty
```
public void setDrawProperty(java.lang.String propertyName,
                            java.lang.String propertyValue,
                            MacroMoleculeComponent.MoleculeVisualizer mmv)
```
    Sets the given draw property to the given visualizer.
    
    Parameters:
    
    propertyName - Name of the property to pass.
    
    propertyValue - Value of the property to pass.
    
    mmv - Visualizer of a certain part of the MacroMolecule

Class MacroMoleculeComponent

Nested Class Summary

Field Summary

Fields inherited from class chemaxon.marvin.space.GraphicComponent

Constructor Summary

Method Summary

Methods inherited from class chemaxon.marvin.space.GraphicComponent

Methods inherited from class java.lang.Object

Field Detail

COMPONENT_TYPE_ATOM

COMPONENT_TYPE_BOND

COMPONENT_TYPE_MOLECULE

COMPONENT_TYPE_RESIDUE

initialised

RAINBOW_MODE

B_FACTOR_MODE

Constructor Detail

MacroMoleculeComponent

MacroMoleculeComponent

Method Detail

removeGraphicComponent

onRemoveGraphicComponent

setProgressBar

getMolecule

getMacroMolecule

draw

has2DPart

draw2DPart

hasTransparentPart

drawTransparentPart

getRainbowPalette

getBFactorPalette

getComponentIterator

getComponents

getComponent

setGL

drawSelection

getCoordinates

getComponentElement

getComponentElement

getUsableObjectId

getUsableObject

getDescription

getLabelInformation

isVisible

isVisible

setVisible

showFaded

hideSelected

hideUnselected

fadeSelected

fadeUnselected

exclusiveSelection

extendSelection

invertSelection

select

unSelect

selectComponentElementsInside

hasSelectedElements

touchObject

isControllable

translate

rotate

setDrawProperty

setDrawProperty