Package org.biojava.nbio.structure.symmetry.core

Class RotationAxisAligner

java.lang.Object
org.biojava.nbio.structure.symmetry.core.AxisAligner
org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
public class RotationAxisAligner extends AxisAligner

  • Constructor Details

  • Method Details

    • getSymmetry

      public String getSymmetry()
      Specified by:
      getSymmetry in class AxisAligner

    • getTransformation

      public javax.vecmath.Matrix4d getTransformation()
      Specified by:
      getTransformation in class AxisAligner

    • getRotationMatrix

      public javax.vecmath.Matrix3d getRotationMatrix()
      Specified by:
      getRotationMatrix in class AxisAligner

    • getReverseTransformation

      public javax.vecmath.Matrix4d getReverseTransformation()
      Specified by:
      getReverseTransformation in class AxisAligner

    • getPrincipalRotationAxis

      public javax.vecmath.Vector3d getPrincipalRotationAxis()
      Specified by:
      getPrincipalRotationAxis in class AxisAligner

    • getRotationReferenceAxis

      public javax.vecmath.Vector3d getRotationReferenceAxis()
      Specified by:
      getRotationReferenceAxis in class AxisAligner

    • getPrincipalAxesOfInertia

      public javax.vecmath.Vector3d[] getPrincipalAxesOfInertia()
      Specified by:
      getPrincipalAxesOfInertia in class AxisAligner

    • getDimension

      public javax.vecmath.Vector3d getDimension()
      Specified by:
      getDimension in class AxisAligner

    • getRadius

      public double getRadius()
      Returns the radius for drawing the minor rotation axis in the xy-plane
      Specified by:
      getRadius in class AxisAligner
      Returns:
      double radius in xy-plane

    • 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 class AxisAligner
      Returns:

    • 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 class AxisAligner
      Returns:

    • getCentroid

      public javax.vecmath.Point3d getCentroid()
      Specified by:
      getCentroid in class AxisAligner

    • getSubunits

      public Subunits getSubunits()
      Specified by:
      getSubunits in class AxisAligner

    • getRotationGroup

      public RotationGroup getRotationGroup()

    • getOrbits

      public List<List<Integer>> getOrbits()
      Specified by:
      getOrbits in class AxisAligner