Class JmolSymmetryScriptGenerator

Method Details

• getInstance

  public static JmolSymmetryScriptGenerator getInstance(AxisAligner axisAligner, String name)

  Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)

  Parameters:

  axisAligner -

  rotationGroup -

  Returns:

  instance of JmolSymmetryScriptGenerator

• getZoom

  public abstract int getZoom()

  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.

  Returns:

• getDefaultOrientation

  public abstract String getDefaultOrientation()

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

  Returns:

  Jmol script

• getOrientationCount

  public abstract int getOrientationCount()

  Returns the number of orientations available for this structure

  Returns:

  number of orientations

• getOrientation

  public abstract String getOrientation(int index)

  Returns a Jmol script that sets a specific orientation

  Parameters:

  index - orientation index

  Returns:

  Jmol script

• getInstantaneousOrientation

  public String getInstantaneousOrientation(int index)

  Returns a Jmol script that sets a specific orientation instantaneously

  Parameters:

  index - orientation index

  Returns:

  Jmol script

• getOrientationWithZoom

  public abstract String getOrientationWithZoom(int index)

  Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron

  Parameters:

  index - orientation index

  Returns:

  Jmol script

• getOrientationName

  public abstract String getOrientationName(int index)

  Returns the name of a specific orientation

  Parameters:

  index - orientation index

  Returns:

  name of orientation

• getTransformation

  public abstract javax.vecmath.Matrix4d getTransformation()

  Returns transformation matrix to orient structure

  Returns:

  transformation matrix

• setDefaultColoring

  public abstract void setDefaultColoring(String colorScript)

  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.

  Parameters:

  colorScript -

• setOnTheFly

  public abstract void setOnTheFly(boolean onTheFly)

  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.

• drawPolyhedron

  public abstract String drawPolyhedron()

  Returns a Jmol script that draws an invisible polyhedron around a structure. Use showPolyhedron() and hidePolyhedron() to toggle visibility.

  Returns:

  Jmol script

• hidePolyhedron

  public abstract String hidePolyhedron()

• showPolyhedron

  public abstract String showPolyhedron()

• drawAxes

  public abstract String drawAxes()

  Returns a Jmol script that draws symmetry or inertia axes for a structure. Use showAxes() and hideAxes() to toggle visibility.

  Returns:

  Jmol script

• hideAxes

  public abstract String hideAxes()

  Returns a Jmol script to hide axes

  Returns:

  Jmol script

• showAxes

  public abstract String showAxes()

  Returns a Jmol script to show axes

  Returns:

  Jmol script

• playOrientations

  public abstract String playOrientations()

  Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations

  Returns:

  Jmol script

• colorBySubunit

  public abstract String colorBySubunit()

  Returns a Jmol script that colors the subunits of a structure by different colors

  Returns:

• colorBySequenceCluster

  public abstract String colorBySequenceCluster()

  Returns a Jmol script that colors subunits by their sequence cluster ids.

  Returns:

  Jmol script

• colorBySymmetry

  public abstract String colorBySymmetry()

  Returns a Jmol script that colors subunits to highlight the symmetry within a structure

  Returns:

  Jmol script

• getJmolColorScript

  protected static String getJmolColorScript(Map<javax.vecmath.Color4f,List<String>> map)

• getJmolColor

  protected static String getJmolColor(javax.vecmath.Color4f color)

• getJmolPoint

  protected static String getJmolPoint(javax.vecmath.Tuple3d point)

• f1Dot2

  protected static String f1Dot2(float number)

• fDot2

  protected static String fDot2(double number)

• jMolFloat

  protected static float jMolFloat(double f)

  Returns a lower precision floating point number for Jmol

  Parameters:

  f -

  Returns:

• getJmolLigandScript

  protected static String getJmolLigandScript()