Class JmolSymmetryScriptGeneratorH

Method Details

• 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:

• getDefaultOrientation

  public String getDefaultOrientation()

  Returns a Jmol script to set the default orientation for a structure

  Specified by:

  getDefaultOrientation in class JmolSymmetryScriptGenerator

  Returns:

  Jmol script

• getOrientationCount

  public int getOrientationCount()

  Description copied from class: JmolSymmetryScriptGenerator

  Returns the number of orientations available for this structure

  Specified by:

  getOrientationCount in class JmolSymmetryScriptGenerator

  Returns:

  number of orientations

• getOrientation

  public String getOrientation(int index)

  Description copied from class: JmolSymmetryScriptGenerator

  Returns a Jmol script that sets a specific orientation

  Specified by:

  getOrientation in class JmolSymmetryScriptGenerator

  Parameters:

  index - orientation index

  Returns:

  Jmol script

• getOrientationWithZoom

  public 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 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

• getTransformation

  public javax.vecmath.Matrix4d getTransformation()

  Description copied from class: JmolSymmetryScriptGenerator

  Returns transformation matrix to orient structure

  Specified by:

  getTransformation in class JmolSymmetryScriptGenerator

  Returns:

  transformation matrix

• setDefaultColoring

  public void setDefaultColoring(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 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

• hidePolyhedron

  public String hidePolyhedron()

  Specified by:

  hidePolyhedron in class JmolSymmetryScriptGenerator

• showPolyhedron

  public String showPolyhedron()

  Specified by:

  showPolyhedron in class JmolSymmetryScriptGenerator

• drawAxes

  public 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

• hideAxes

  public String hideAxes()

  Returns a Jmol script to hide axes

  Specified by:

  hideAxes in class JmolSymmetryScriptGenerator

  Returns:

  Jmol script

• showAxes

  public String showAxes()

  Returns a Jmol script to show axes

  Specified by:

  showAxes in class JmolSymmetryScriptGenerator

  Returns:

  Jmol script

• playOrientations

  public 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 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 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 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: