Package org.biojava.nbio.structure.symmetry.axis

Class HelixAxisAligner

java.lang.Object

org.biojava.nbio.structure.symmetry.axis.AxisAligner

org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

public class HelixAxisAligner
extends AxisAligner

Constructor Summary

Constructors

Constructor	Description
HelixAxisAligner(QuatSymmetryResults results)

Method Summary

Modifier and Type	Method	Description
javax.vecmath.Point3d	calcCenterOfRotation()
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.
HelixLayers	getHelixLayers()
List<List<Integer>>	getOrbits()
javax.vecmath.Vector3d[]	getPrincipalAxesOfInertia()
javax.vecmath.Vector3d	getPrincipalRotationAxis()
double	getRadius()	Returns the radius for drawing polyhedra
javax.vecmath.Matrix4d	getReverseTransformation()
javax.vecmath.Matrix3d	getRotationMatrix()
javax.vecmath.Vector3d	getRotationReferenceAxis()
QuatSymmetrySubunits	getSubunits()
String	getSymmetry()
javax.vecmath.Matrix4d	getTransformation()

Methods inherited from class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getInstance

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

HelixAxisAligner

public HelixAxisAligner(QuatSymmetryResults results)

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 QuatSymmetrySubunits 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()