org.biojava.nbio.structure.symmetry.core

Class AxisAligner

java.lang.Object

org.biojava.nbio.structure.symmetry.core.AxisAligner

Direct Known Subclasses:

HelixAxisAligner, RotationAxisAligner

public abstract class AxisAligner
extends Object

Constructor Summary

Constructors

Constructor and Description
AxisAligner()

Method Summary

Modifier and Type	Method and Description
abstract javax.vecmath.Point3d	getCentroid()
abstract javax.vecmath.Vector3d	getDimension()
abstract javax.vecmath.Matrix4d	getGeometicCenterTransformation() Returns a transformation matrix transform polyhedra for Cn structures.
abstract javax.vecmath.Point3d	getGeometricCenter() Returns the geometric center of polyhedron.
static AxisAligner	getInstance(QuatSymmetryResults results) Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)
abstract List<List<Integer>>	getOrbits()
abstract javax.vecmath.Vector3d[]	getPrincipalAxesOfInertia()
abstract javax.vecmath.Vector3d	getPrincipalRotationAxis()
abstract double	getRadius() Returns the radius for drawing polyhedra
abstract javax.vecmath.Matrix4d	getReverseTransformation()
abstract javax.vecmath.Matrix3d	getRotationMatrix()
abstract javax.vecmath.Vector3d	getRotationReferenceAxis()
abstract Subunits	getSubunits()
abstract String	getSymmetry()
abstract javax.vecmath.Matrix4d	getTransformation()

Methods inherited from class java.lang.Object

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

Constructor Detail

AxisAligner

public AxisAligner()

Method Detail

getInstance

public static AxisAligner getInstance(QuatSymmetryResults results)

Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)

Parameters:

results - symmetry results

Returns:

instance of AxisAligner

getSymmetry

public abstract String getSymmetry()

getTransformation

public abstract javax.vecmath.Matrix4d getTransformation()

getRotationMatrix

public abstract javax.vecmath.Matrix3d getRotationMatrix()

getReverseTransformation

public abstract javax.vecmath.Matrix4d getReverseTransformation()

getPrincipalRotationAxis

public abstract javax.vecmath.Vector3d getPrincipalRotationAxis()

getRotationReferenceAxis

public abstract javax.vecmath.Vector3d getRotationReferenceAxis()

getPrincipalAxesOfInertia

public abstract javax.vecmath.Vector3d[] getPrincipalAxesOfInertia()

getDimension

public abstract javax.vecmath.Vector3d getDimension()

getRadius

public abstract double getRadius()

Returns the radius for drawing polyhedra

Returns:

double radius

getGeometicCenterTransformation

public abstract 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.

Returns:

getGeometricCenter

public abstract 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.

Returns:

getCentroid

public abstract javax.vecmath.Point3d getCentroid()

getSubunits

public abstract Subunits getSubunits()

getOrbits

public abstract List<List<Integer>> getOrbits()