org.biojava.nbio.structure.symmetry.jmolScript

Class JmolSymmetryScriptGeneratorPointGroup

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 and Description
JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner rotationAxisAligner, String name)

Method Summary

Methods

Modifier and Type	Method and 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, getJmolColor, getJmolColorScript, getJmolLigandScript, getJmolPoint, jMolFloat

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

JmolSymmetryScriptGeneratorPointGroup

public JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner rotationAxisAligner,
                                     String name)

Method Detail

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