public abstract class JmolSymmetryScriptGeneratorPointGroup extends JmolSymmetryScriptGenerator
Constructor and Description |
---|
JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner rotationAxisAligner,
String name) |
Modifier and Type | Method and Description |
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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() |
f1Dot2, fDot2, getInstance, getInstantaneousOrientation, getJmolColor, getJmolColorScript, getJmolLigandScript, getJmolPoint, jMolFloat
public JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner rotationAxisAligner, String name)
public abstract int getZoom()
JmolSymmetryScriptGenerator
getZoom
in class JmolSymmetryScriptGenerator
public void setOnTheFly(boolean onTheFly)
JmolSymmetryScriptGenerator
setOnTheFly
in class JmolSymmetryScriptGenerator
public String getDefaultOrientation()
JmolSymmetryScriptGenerator
getDefaultOrientation
in class JmolSymmetryScriptGenerator
public int getOrientationCount()
JmolSymmetryScriptGenerator
getOrientationCount
in class JmolSymmetryScriptGenerator
public String getOrientation(int index)
JmolSymmetryScriptGenerator
getOrientation
in class JmolSymmetryScriptGenerator
index
- orientation indexpublic String getOrientationWithZoom(int index)
JmolSymmetryScriptGenerator
getOrientationWithZoom
in class JmolSymmetryScriptGenerator
index
- orientation indexpublic String getOrientationName(int index)
JmolSymmetryScriptGenerator
getOrientationName
in class JmolSymmetryScriptGenerator
index
- orientation indexpublic javax.vecmath.Matrix4d getTransformation()
JmolSymmetryScriptGenerator
getTransformation
in class JmolSymmetryScriptGenerator
public void setDefaultColoring(String colorScript)
JmolSymmetryScriptGenerator
setDefaultColoring
in class JmolSymmetryScriptGenerator
public String drawPolyhedron()
JmolSymmetryScriptGenerator
drawPolyhedron
in class JmolSymmetryScriptGenerator
public String hidePolyhedron()
hidePolyhedron
in class JmolSymmetryScriptGenerator
public String showPolyhedron()
showPolyhedron
in class JmolSymmetryScriptGenerator
public String drawAxes()
JmolSymmetryScriptGenerator
drawAxes
in class JmolSymmetryScriptGenerator
public String hideAxes()
JmolSymmetryScriptGenerator
hideAxes
in class JmolSymmetryScriptGenerator
public String showAxes()
JmolSymmetryScriptGenerator
showAxes
in class JmolSymmetryScriptGenerator
public String playOrientations()
JmolSymmetryScriptGenerator
playOrientations
in class JmolSymmetryScriptGenerator
public String colorBySubunit()
JmolSymmetryScriptGenerator
colorBySubunit
in class JmolSymmetryScriptGenerator
public String colorBySequenceCluster()
JmolSymmetryScriptGenerator
colorBySequenceCluster
in class JmolSymmetryScriptGenerator
public String colorBySymmetry()
JmolSymmetryScriptGenerator
colorBySymmetry
in class JmolSymmetryScriptGenerator
protected double getMaxExtension()
protected double getMeanExtension()
protected RotationAxisAligner getAxisTransformation()
protected void setAxisTransformation(RotationAxisAligner axisTransformation)
axisTransformation
- the axisTransformation to setprotected RotationGroup getRotationGroup()
protected void setRotationGroup(RotationGroup rotationGroup)
rotationGroup
- the rotationGroup to setprotected Polyhedron getPolyhedron()
protected void setPolyhedron(Polyhedron polyhedron)
polyhedron
- the polyhedron to setCopyright © 2000–2018 BioJava. All rights reserved.