Class JmolSymmetryScriptGeneratorH
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
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- org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
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public class JmolSymmetryScriptGeneratorH extends JmolSymmetryScriptGenerator
- Author:
- Peter
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Constructor Summary
Constructors Constructor Description JmolSymmetryScriptGeneratorH(HelixAxisAligner helixAxisAligner, String name)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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 colorsString
colorBySymmetry()
Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colorsString
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.String
getDefaultOrientation()
Returns a Jmol script to set the default orientation for a structureprotected double
getMaxExtension()
Returns the maximum extension (length) of structureString
getOrientation(int index)
Returns a Jmol script that sets a specific orientationint
getOrientationCount()
Returns the number of orientations available for this structureString
getOrientationName(int index)
Returns the name of a specific orientationString
getOrientationWithZoom(int index)
Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedronjavax.vecmath.Matrix4d
getTransformation()
Returns transformation matrix to orient structureint
getZoom()
Returns the Jmol zoom to fit polyhedron and symmetry axes.String
hideAxes()
Returns a Jmol script to hide axesString
hidePolyhedron()
String
playOrientations()
Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientationsvoid
setDefaultColoring(String colorScript)
Sets a default Jmol script used for coloring.void
setOnTheFly(boolean onTheFly)
Sets the type of bioassembly to be colored.String
showAxes()
Returns a Jmol script to show axesString
showPolyhedron()
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Methods inherited from class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
f1Dot2, fDot2, getInstance, getInstantaneousOrientation, getJmolColor, getJmolColorScript, getJmolLigandScript, getJmolPoint, jMolFloat
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Constructor Detail
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JmolSymmetryScriptGeneratorH
public JmolSymmetryScriptGeneratorH(HelixAxisAligner helixAxisAligner, String name)
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Method Detail
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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 classJmolSymmetryScriptGenerator
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getZoom
public 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 classJmolSymmetryScriptGenerator
- Returns:
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getDefaultOrientation
public String getDefaultOrientation()
Returns a Jmol script to set the default orientation for a structure- Specified by:
getDefaultOrientation
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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getOrientationCount
public int getOrientationCount()
Description copied from class:JmolSymmetryScriptGenerator
Returns the number of orientations available for this structure- Specified by:
getOrientationCount
in classJmolSymmetryScriptGenerator
- Returns:
- number of orientations
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getOrientation
public String getOrientation(int index)
Description copied from class:JmolSymmetryScriptGenerator
Returns a Jmol script that sets a specific orientation- Specified by:
getOrientation
in classJmolSymmetryScriptGenerator
- Parameters:
index
- orientation index- Returns:
- Jmol script
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getOrientationWithZoom
public String getOrientationWithZoom(int index)
Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron- Specified by:
getOrientationWithZoom
in classJmolSymmetryScriptGenerator
- Parameters:
index
- orientation index- Returns:
- Jmol script
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getOrientationName
public String getOrientationName(int index)
Returns the name of a specific orientation- Specified by:
getOrientationName
in classJmolSymmetryScriptGenerator
- Parameters:
index
- orientation index- Returns:
- name of orientation
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getTransformation
public javax.vecmath.Matrix4d getTransformation()
Description copied from class:JmolSymmetryScriptGenerator
Returns transformation matrix to orient structure- Specified by:
getTransformation
in classJmolSymmetryScriptGenerator
- Returns:
- transformation matrix
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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 classJmolSymmetryScriptGenerator
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drawPolyhedron
public String drawPolyhedron()
Returns a Jmol script that draws an invisible polyhedron around a structure. Use showPolyhedron() and hidePolyhedron() to toggle visibility.- Specified by:
drawPolyhedron
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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hidePolyhedron
public String hidePolyhedron()
- Specified by:
hidePolyhedron
in classJmolSymmetryScriptGenerator
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showPolyhedron
public String showPolyhedron()
- Specified by:
showPolyhedron
in classJmolSymmetryScriptGenerator
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drawAxes
public String drawAxes()
Returns a Jmol script that draws symmetry or inertia axes for a structure. Use showAxes() and hideAxes() to toggle visibility.- Specified by:
drawAxes
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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hideAxes
public String hideAxes()
Returns a Jmol script to hide axes- Specified by:
hideAxes
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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showAxes
public String showAxes()
Returns a Jmol script to show axes- Specified by:
showAxes
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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playOrientations
public String playOrientations()
Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations- Specified by:
playOrientations
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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colorBySubunit
public String colorBySubunit()
Returns a Jmol script that colors the subunits of a structure by different colors- Specified by:
colorBySubunit
in classJmolSymmetryScriptGenerator
- Returns:
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colorBySequenceCluster
public String colorBySequenceCluster()
Returns a Jmol script that colors subunits by their sequence cluster ids.- Specified by:
colorBySequenceCluster
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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colorBySymmetry
public String colorBySymmetry()
Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colors- Specified by:
colorBySymmetry
in classJmolSymmetryScriptGenerator
- Returns:
- Jmol script
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getMaxExtension
protected double getMaxExtension()
Returns the maximum extension (length) of structure- Returns:
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