Package chemaxon.marvin.space

Class MacroMoleculeComponent

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

  • Field Details

    • COMPONENT_TYPE_ATOM

      protected static final int COMPONENT_TYPE_ATOM
      See Also:

    • COMPONENT_TYPE_BOND

      protected static final int COMPONENT_TYPE_BOND
      See Also:

    • COMPONENT_TYPE_MOLECULE

      protected static final int COMPONENT_TYPE_MOLECULE
      See Also:

    • COMPONENT_TYPE_RESIDUE

      protected static final int COMPONENT_TYPE_RESIDUE
      See Also:

    • initialised

      protected boolean initialised

    • RAINBOW_MODE

      public static final int RAINBOW_MODE
      See Also:

    • B_FACTOR_MODE

      public static final int B_FACTOR_MODE
      See Also:

  • Constructor Details

    • MacroMoleculeComponent

      protected MacroMoleculeComponent()
      Creates a new instance of MacroMoleculeComponent

    • MacroMoleculeComponent

      public MacroMoleculeComponent(chemaxon.struc.MacroMolecule mol)
      Creates a new instance of MacroMoleculeComponent

  • Method Details

    • 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 Iterator<MacroMoleculeComponent.MoleculeVisualizer> getComponentIterator()
      Returns the Iterator of its visualizers.

    • getComponents

      public 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(com.jogamp.opengl.GL2 gl, com.jogamp.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 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(String labelType)
      Collects the label information of the visualizers.
      Overrides:
      getLabelInformation in class GraphicComponent
      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(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(String propertyName, 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(String propertyName, 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