Class RotationAxisAligner
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.axis.AxisAligner
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- org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner
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public class RotationAxisAligner extends AxisAligner
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Constructor Summary
Constructors Constructor Description RotationAxisAligner(QuatSymmetryResults results)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description javax.vecmath.Point3d
getCentroid()
javax.vecmath.Vector3d
getDimension()
javax.vecmath.Matrix4d
getGeometicCenterTransformation()
Returns a transformation matrix transform polyhedra for Cn structures.javax.vecmath.Point3d
getGeometricCenter()
Returns the geometric center of polyhedron.List<List<Integer>>
getOrbits()
javax.vecmath.Vector3d[]
getPrincipalAxesOfInertia()
javax.vecmath.Vector3d
getPrincipalRotationAxis()
double
getRadius()
Returns the radius for drawing the minor rotation axis in the xy-planejavax.vecmath.Matrix4d
getReverseTransformation()
RotationGroup
getRotationGroup()
javax.vecmath.Matrix3d
getRotationMatrix()
javax.vecmath.Vector3d
getRotationReferenceAxis()
QuatSymmetrySubunits
getSubunits()
String
getSymmetry()
javax.vecmath.Matrix4d
getTransformation()
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Methods inherited from class org.biojava.nbio.structure.symmetry.axis.AxisAligner
getInstance
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Constructor Detail
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RotationAxisAligner
public RotationAxisAligner(QuatSymmetryResults results)
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Method Detail
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getSymmetry
public String getSymmetry()
- Specified by:
getSymmetry
in classAxisAligner
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getTransformation
public javax.vecmath.Matrix4d getTransformation()
- Specified by:
getTransformation
in classAxisAligner
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getRotationMatrix
public javax.vecmath.Matrix3d getRotationMatrix()
- Specified by:
getRotationMatrix
in classAxisAligner
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getReverseTransformation
public javax.vecmath.Matrix4d getReverseTransformation()
- Specified by:
getReverseTransformation
in classAxisAligner
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getPrincipalRotationAxis
public javax.vecmath.Vector3d getPrincipalRotationAxis()
- Specified by:
getPrincipalRotationAxis
in classAxisAligner
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getRotationReferenceAxis
public javax.vecmath.Vector3d getRotationReferenceAxis()
- Specified by:
getRotationReferenceAxis
in classAxisAligner
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getPrincipalAxesOfInertia
public javax.vecmath.Vector3d[] getPrincipalAxesOfInertia()
- Specified by:
getPrincipalAxesOfInertia
in classAxisAligner
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getDimension
public javax.vecmath.Vector3d getDimension()
- Specified by:
getDimension
in classAxisAligner
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getRadius
public double getRadius()
Returns the radius for drawing the minor rotation axis in the xy-plane- Specified by:
getRadius
in classAxisAligner
- Returns:
- double radius in xy-plane
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getGeometicCenterTransformation
public javax.vecmath.Matrix4d getGeometicCenterTransformation()
Returns a transformation matrix transform polyhedra for Cn structures. The center in this matrix is the geometric center, rather then the centroid. In Cn structures those are usually not the same.- Specified by:
getGeometicCenterTransformation
in classAxisAligner
- Returns:
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getGeometricCenter
public javax.vecmath.Point3d getGeometricCenter()
Returns the geometric center of polyhedron. In the case of the Cn point group, the centroid and geometric center are usually not identical.- Specified by:
getGeometricCenter
in classAxisAligner
- Returns:
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getCentroid
public javax.vecmath.Point3d getCentroid()
- Specified by:
getCentroid
in classAxisAligner
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getSubunits
public QuatSymmetrySubunits getSubunits()
- Specified by:
getSubunits
in classAxisAligner
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getRotationGroup
public RotationGroup getRotationGroup()
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