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