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

Class HelixAxisAligner

java.lang.Object
org.biojava.nbio.structure.symmetry.core.AxisAligner
org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
public class HelixAxisAligner 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()
      Description copied from class: AxisAligner
      Returns the radius for drawing polyhedra
      Specified by:
      getRadius in class AxisAligner
      Returns:
      double radius

    • getGeometicCenterTransformation

      public javax.vecmath.Matrix4d getGeometicCenterTransformation()
      Description copied from class: AxisAligner
      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()
      Description copied from class: AxisAligner
      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

    • getHelixLayers

      public HelixLayers getHelixLayers()

    • getOrbits

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

    • calcCenterOfRotation

      public javax.vecmath.Point3d calcCenterOfRotation()