java.lang.Object

org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup

Direct Known Subclasses:: JmolSymmetryScriptGeneratorC1, JmolSymmetryScriptGeneratorCn, JmolSymmetryScriptGeneratorDn, JmolSymmetryScriptGeneratorI, JmolSymmetryScriptGeneratorO, JmolSymmetryScriptGeneratorT

public abstract class JmolSymmetryScriptGeneratorPointGroup extends JmolSymmetryScriptGenerator

Author:: Peter

Constructor Summary

Constructors

Constructor

Description

JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner rotationAxisAligner, String name)
Method Summary

Modifier and Type

Method

Description

String

colorBySequenceCluster()

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

String

colorBySubunit()

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

String

colorBySymmetry()

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

String

drawAxes()

Returns a Jmol script that draws symmetry or inertia axes for a structure.

String

drawPolyhedron()

Returns a Jmol script that draws an invisible polyhedron around a structure.

protected RotationAxisAligner

getAxisTransformation()

String

getDefaultOrientation()

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

protected double

getMaxExtension()

Returns the maximum extension (length) of structure

protected double

getMeanExtension()

Returns the mean extension (length) of structure

String

getOrientation(int index)

Returns a Jmol script that sets a specific orientation

int

getOrientationCount()

Returns the number of orientations available for this structure

String

getOrientationName(int index)

Returns the name of a specific orientation

String

getOrientationWithZoom(int index)

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

protected Polyhedron

getPolyhedron()

protected RotationGroup

getRotationGroup()

javax.vecmath.Matrix4d

getTransformation()

Returns transformation matrix to orient structure

abstract int

getZoom()

Returns the Jmol zoom to fit polyhedron and symmetry axes.

String

hideAxes()

Returns a Jmol script to hide axes

String

hidePolyhedron()

String

playOrientations()

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

protected void

setAxisTransformation(RotationAxisAligner axisTransformation)

void

setDefaultColoring(String colorScript)

Sets a default Jmol script used for coloring.

void

setOnTheFly(boolean onTheFly)

Sets the type of bioassembly to be colored.

protected void

setPolyhedron(Polyhedron polyhedron)

protected void

setRotationGroup(RotationGroup rotationGroup)

String

showAxes()

Returns a Jmol script to show axes

String

showPolyhedron()

Methods inherited from class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
f1Dot2, fDot2, getInstance, getInstantaneousOrientation, getJmolColor, getJmolColorScript, getJmolLigandScript, getJmolPoint, jMolFloat

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- JmolSymmetryScriptGeneratorPointGroup
  
  public JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner rotationAxisAligner, String name)
Method Details
- getZoom
  
  public abstract 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:
- 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
- getDefaultOrientation
  
  public String getDefaultOrientation()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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)
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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)
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  Returns a Jmol script to hide axes
  
  Specified by:
  
  hideAxes in class JmolSymmetryScriptGenerator
  
  Returns:
  
  Jmol script
- showAxes
  
  public String showAxes()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  Returns a Jmol script to show axes
  
  Specified by:
  
  showAxes in class JmolSymmetryScriptGenerator
  
  Returns:
  
  Jmol script
- playOrientations
  
  public String playOrientations()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  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()
  
  Description copied from class: JmolSymmetryScriptGenerator
  
  Returns a Jmol script that colors subunits to highlight the symmetry within a structure
  
  Specified by:
  
  colorBySymmetry in class JmolSymmetryScriptGenerator
  
  Returns:
  
  Jmol script
- getMaxExtension
  
  protected double getMaxExtension()
  
  Returns the maximum extension (length) of structure
  
  Returns:
- getMeanExtension
  
  protected double getMeanExtension()
  
  Returns the mean extension (length) of structure
  
  Returns:
- getAxisTransformation
  
  protected RotationAxisAligner getAxisTransformation()
  
  Returns:
  
  the axisTransformation
- setAxisTransformation
  
  protected void setAxisTransformation(RotationAxisAligner axisTransformation)
  
  Parameters:
  
  axisTransformation - the axisTransformation to set
- getRotationGroup
  
  protected RotationGroup getRotationGroup()
  
  Returns:
  
  the rotationGroup
- setRotationGroup
  
  protected void setRotationGroup(RotationGroup rotationGroup)
  
  Parameters:
  
  rotationGroup - the rotationGroup to set
- getPolyhedron
  
  protected Polyhedron getPolyhedron()
  
  Returns:
  
  the polyhedron
- setPolyhedron
  
  protected void setPolyhedron(Polyhedron polyhedron)
  
  Parameters:
  
  polyhedron - the polyhedron to set

Class JmolSymmetryScriptGeneratorPointGroup

Constructor Summary

Method Summary

Methods inherited from class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

Methods inherited from class java.lang.Object

Constructor Details

JmolSymmetryScriptGeneratorPointGroup

Method Details

getZoom

setOnTheFly

getDefaultOrientation

getOrientationCount

getOrientation

getOrientationWithZoom

getOrientationName

getTransformation

setDefaultColoring

drawPolyhedron

hidePolyhedron

showPolyhedron

drawAxes

hideAxes

showAxes

playOrientations

colorBySubunit

colorBySequenceCluster

colorBySymmetry

getMaxExtension

getMeanExtension

getAxisTransformation

setAxisTransformation

getRotationGroup

setRotationGroup

getPolyhedron

setPolyhedron