Class JmolSymmetryScriptGeneratorH

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String colorBySequenceCluster()
      Returns a Jmol script that colors subunits by their sequence cluster ids.
      java.lang.String colorBySubunit()
      Returns a Jmol script that colors the subunits of a structure by different colors
      java.lang.String colorBySymmetry()
      Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colors
      java.lang.String drawAxes()
      Returns a Jmol script that draws symmetry or inertia axes for a structure.
      java.lang.String drawPolyhedron()
      Returns a Jmol script that draws an invisible polyhedron around a structure.
      java.lang.String getDefaultOrientation()
      Returns a Jmol script to set the default orientation for a structure
      protected double getMaxExtension()
      Returns the maximum extension (length) of structure
      java.lang.String getOrientation​(int index)
      Returns a Jmol script that sets a specific orientation
      int getOrientationCount()
      Returns the number of orientations available for this structure
      java.lang.String getOrientationName​(int index)
      Returns the name of a specific orientation
      java.lang.String getOrientationWithZoom​(int index)
      Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron
      javax.vecmath.Matrix4d getTransformation()
      Returns transformation matrix to orient structure
      int getZoom()
      Returns the Jmol zoom to fit polyhedron and symmetry axes.
      java.lang.String hideAxes()
      Returns a Jmol script to hide axes
      java.lang.String hidePolyhedron()  
      java.lang.String playOrientations()
      Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
      void setDefaultColoring​(java.lang.String colorScript)
      Sets a default Jmol script used for coloring.
      void setOnTheFly​(boolean onTheFly)
      Sets the type of bioassembly to be colored.
      java.lang.String showAxes()
      Returns a Jmol script to show axes
      java.lang.String showPolyhedron()  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • JmolSymmetryScriptGeneratorH

        public JmolSymmetryScriptGeneratorH​(HelixAxisAligner helixAxisAligner,
                                            java.lang.String name)
    • Method Detail

      • setOnTheFly

        public void setOnTheFly​(boolean onTheFly)
        Description copied from class: JmolSymmetryScriptGenerator
        Sets the type of bioassembly to be colored. If set to true, it will generate a Jmol script for a bioassembly generated by Jmol on the fly. If set to false, it will generate Jmol script for a bioassembly file read by Jmol.
        Specified by:
        setOnTheFly in class JmolSymmetryScriptGenerator
      • getZoom

        public int getZoom()
        Description copied from class: JmolSymmetryScriptGenerator
        Returns the Jmol zoom to fit polyhedron and symmetry axes. This zoom level should be used so that the polyhedron and symmetry axes are not cutoff.
        Specified by:
        getZoom in class JmolSymmetryScriptGenerator
        Returns:
      • getOrientationWithZoom

        public java.lang.String getOrientationWithZoom​(int index)
        Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron
        Specified by:
        getOrientationWithZoom in class JmolSymmetryScriptGenerator
        Parameters:
        index - orientation index
        Returns:
        Jmol script
      • getOrientationName

        public java.lang.String getOrientationName​(int index)
        Returns the name of a specific orientation
        Specified by:
        getOrientationName in class JmolSymmetryScriptGenerator
        Parameters:
        index - orientation index
        Returns:
        name of orientation
      • setDefaultColoring

        public void setDefaultColoring​(java.lang.String colorScript)
        Description copied from class: JmolSymmetryScriptGenerator
        Sets a default Jmol script used for coloring. This method is used in local symmetry cases to color those subunits that are not related by symmetry.
        Specified by:
        setDefaultColoring in class JmolSymmetryScriptGenerator
      • drawPolyhedron

        public java.lang.String drawPolyhedron()
        Returns a Jmol script that draws an invisible polyhedron around a structure. Use showPolyhedron() and hidePolyhedron() to toggle visibility.
        Specified by:
        drawPolyhedron in class JmolSymmetryScriptGenerator
        Returns:
        Jmol script
      • drawAxes

        public java.lang.String drawAxes()
        Returns a Jmol script that draws symmetry or inertia axes for a structure. Use showAxes() and hideAxes() to toggle visibility.
        Specified by:
        drawAxes in class JmolSymmetryScriptGenerator
        Returns:
        Jmol script
      • playOrientations

        public java.lang.String playOrientations()
        Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
        Specified by:
        playOrientations in class JmolSymmetryScriptGenerator
        Returns:
        Jmol script
      • colorBySubunit

        public java.lang.String colorBySubunit()
        Returns a Jmol script that colors the subunits of a structure by different colors
        Specified by:
        colorBySubunit in class JmolSymmetryScriptGenerator
        Returns:
      • colorBySequenceCluster

        public java.lang.String colorBySequenceCluster()
        Returns a Jmol script that colors subunits by their sequence cluster ids.
        Specified by:
        colorBySequenceCluster in class JmolSymmetryScriptGenerator
        Returns:
        Jmol script
      • colorBySymmetry

        public java.lang.String colorBySymmetry()
        Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colors
        Specified by:
        colorBySymmetry in class JmolSymmetryScriptGenerator
        Returns:
        Jmol script
      • getMaxExtension

        protected double getMaxExtension()
        Returns the maximum extension (length) of structure
        Returns: