JmolSymmetryScriptGenerator (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator

Direct Known Subclasses:

JmolSymmetryScriptGeneratorH, JmolSymmetryScriptGeneratorPointGroup
```
public abstract class JmolSymmetryScriptGenerator
extends Object
```

Constructor Summary

Constructors
Constructor and Description

JmolSymmetryScriptGenerator()

Constructors
Constructor and Description
`JmolSymmetryScriptGenerator()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`abstract String`	`colorBySequenceCluster()` Returns a Jmol script that colors subunits by their sequence cluster ids.
`abstract String`	`colorBySubunit()` Returns a Jmol script that colors the subunits of a structure by different colors
`abstract String`	`colorBySymmetry()` Returns a Jmol script that colors subunits to highlight the symmetry within a structure
`abstract String`	`drawAxes()` Returns a Jmol script that draws symmetry or inertia axes for a structure.
`abstract String`	`drawPolyhedron()` Returns a Jmol script that draws an invisible polyhedron around a structure.
`protected static String`	`f1Dot2(float number)`
`protected static String`	`fDot2(double number)`
`abstract String`	`getDefaultOrientation()` Returns a Jmol script to set the default orientation for a structure
`static JmolSymmetryScriptGenerator`	`getInstance(AxisAligner axisAligner, String name)` Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)
`String`	`getInstantaneousOrientation(int index)` Returns a Jmol script that sets a specific orientation instantaneously
`protected static String`	`getJmolColor(javax.vecmath.Color4f color)`
`protected static String`	`getJmolColorScript(Map<javax.vecmath.Color4f,List<String>> map)`
`protected static String`	`getJmolLigandScript()`
`protected static String`	`getJmolPoint(javax.vecmath.Tuple3d point)`
`abstract String`	`getOrientation(int index)` Returns a Jmol script that sets a specific orientation
`abstract int`	`getOrientationCount()` Returns the number of orientations available for this structure
`abstract String`	`getOrientationName(int index)` Returns the name of a specific orientation
`abstract String`	`getOrientationWithZoom(int index)` Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron
`abstract javax.vecmath.Matrix4d`	`getTransformation()` Returns transformation matrix to orient structure
`abstract int`	`getZoom()` Returns the Jmol zoom to fit polyhedron and symmetry axes.
`abstract String`	`hideAxes()` Returns a Jmol script to hide axes
`abstract String`	`hidePolyhedron()`
`protected static float`	`jMolFloat(double f)` Returns a lower precision floating point number for Jmol
`abstract String`	`playOrientations()` Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
`abstract void`	`setDefaultColoring(String colorScript)` Sets a default Jmol script used for coloring.
`abstract void`	`setOnTheFly(boolean onTheFly)` Sets the type of bioassembly to be colored.
`abstract String`	`showAxes()` Returns a Jmol script to show axes
`abstract String`	`showPolyhedron()`

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

- Constructor Detail
  - JmolSymmetryScriptGenerator
```
public JmolSymmetryScriptGenerator()
```
- Method Detail
  - 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()
```

Class JmolSymmetryScriptGenerator

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

JmolSymmetryScriptGenerator

Method Detail

getInstance

getZoom

getDefaultOrientation

getOrientationCount

getOrientation

getInstantaneousOrientation

getOrientationWithZoom

getOrientationName

getTransformation

setDefaultColoring

setOnTheFly

drawPolyhedron

hidePolyhedron

showPolyhedron

drawAxes

hideAxes

showAxes

playOrientations

colorBySubunit

colorBySequenceCluster

colorBySymmetry

getJmolColorScript

getJmolColor

getJmolPoint

f1Dot2

fDot2

jMolFloat

getJmolLigandScript