JmolSymmetryScriptGeneratorPointGroup (biojava 5.3.0 API)

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)

Constructors
Constructor and Description
`JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner rotationAxisAligner, String name)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete 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, 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 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

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 Detail

JmolSymmetryScriptGeneratorPointGroup

Method Detail

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