Package org.biojava.nbio.structure.symmetry.jmolScript

Class JmolSymmetryScriptGenerator

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	Description
JmolSymmetryScriptGenerator()

Method Summary

Modifier and Type	Method	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()