Package 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

  • Field Details

  • Constructor Details

    • 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 Details

    • 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 String getDescription()
      Returns textual description.
      Overrides:
      getDescription in class GraphicComponent
      Returns:
      description that contains pharmacophore type name

    • 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 PharmacophorePoint in angstroms.

    • setRadius

      public void setRadius(float r)
      Sets the radius of the PharmaCophorePoint.
      Parameters:
      r - radius in angstroms

    • getColor

      public 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(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(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

    • 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(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 - rendering quality, see RENDERING_* constants

    • setDrawProperty

      public void setDrawProperty(String propertyName, 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