Class JmolSymmetryScriptGenerator
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
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- Direct Known Subclasses:
JmolSymmetryScriptGeneratorH
,JmolSymmetryScriptGeneratorPointGroup
public abstract class JmolSymmetryScriptGenerator extends Object
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Constructor Summary
Constructors Constructor Description JmolSymmetryScriptGenerator()
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods 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 colorsabstract String
colorBySymmetry()
Returns a Jmol script that colors subunits to highlight the symmetry within a structureabstract 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 structurestatic 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 instantaneouslyprotected 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 orientationabstract int
getOrientationCount()
Returns the number of orientations available for this structureabstract String
getOrientationName(int index)
Returns the name of a specific orientationabstract String
getOrientationWithZoom(int index)
Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedronabstract javax.vecmath.Matrix4d
getTransformation()
Returns transformation matrix to orient structureabstract int
getZoom()
Returns the Jmol zoom to fit polyhedron and symmetry axes.abstract String
hideAxes()
Returns a Jmol script to hide axesabstract String
hidePolyhedron()
protected static float
jMolFloat(double f)
Returns a lower precision floating point number for Jmolabstract String
playOrientations()
Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientationsabstract 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 axesabstract String
showPolyhedron()
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Constructor Detail
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JmolSymmetryScriptGenerator
public JmolSymmetryScriptGenerator()
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Method Detail
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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
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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:
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getDefaultOrientation
public abstract String getDefaultOrientation()
Returns a Jmol script to set the default orientation for a structure- Returns:
- Jmol script
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getOrientationCount
public abstract int getOrientationCount()
Returns the number of orientations available for this structure- Returns:
- number of orientations
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getOrientation
public abstract String getOrientation(int index)
Returns a Jmol script that sets a specific orientation- Parameters:
index
- orientation index- Returns:
- Jmol script
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getInstantaneousOrientation
public String getInstantaneousOrientation(int index)
Returns a Jmol script that sets a specific orientation instantaneously- Parameters:
index
- orientation index- Returns:
- Jmol script
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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
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getOrientationName
public abstract String getOrientationName(int index)
Returns the name of a specific orientation- Parameters:
index
- orientation index- Returns:
- name of orientation
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getTransformation
public abstract javax.vecmath.Matrix4d getTransformation()
Returns transformation matrix to orient structure- Returns:
- transformation matrix
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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
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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.
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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
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hidePolyhedron
public abstract String hidePolyhedron()
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showPolyhedron
public abstract String showPolyhedron()
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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
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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
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colorBySubunit
public abstract String colorBySubunit()
Returns a Jmol script that colors the subunits of a structure by different colors- Returns:
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colorBySequenceCluster
public abstract String colorBySequenceCluster()
Returns a Jmol script that colors subunits by their sequence cluster ids.- Returns:
- Jmol script
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colorBySymmetry
public abstract String colorBySymmetry()
Returns a Jmol script that colors subunits to highlight the symmetry within a structure- Returns:
- Jmol script
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getJmolColorScript
protected static String getJmolColorScript(Map<javax.vecmath.Color4f,List<String>> map)
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getJmolColor
protected static String getJmolColor(javax.vecmath.Color4f color)
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getJmolPoint
protected static String getJmolPoint(javax.vecmath.Tuple3d point)
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jMolFloat
protected static float jMolFloat(double f)
Returns a lower precision floating point number for Jmol- Parameters:
f
-- Returns:
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getJmolLigandScript
protected static String getJmolLigandScript()
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