org.biojava.nbio.structure.symmetry.internal

Class SymmetryAxes

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

public class SymmetryAxes
extends Object

Data Structure that stores all the symmetry axis that describe the symmetry of a structure. Generalizes to all types of symmetry, the classic ones (Cn, Dn) and any hierarchical or local symmetries.

It also stores the parts of the structure (symmetric units) involved in each axis, in addition to the way to calculate them.

This is intended to provide a general axis support for the multiple repeat alignment optimization and the axis display in Jmol. This object is related to a MultipleAlignment object that defines the symmetric units.

Since:

4.2.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
SymmetryAxes() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addAxis(javax.vecmath.Matrix4d axis, List<List<Integer>> superposition, List<Integer> repeats, Integer division) Adds a new axis of symmetry.
List<javax.vecmath.Matrix4d>	getElementaryAxes() Return all elementary axes of symmetry of the structure, that is, the axes stored in the List as unique and from which all the symmetry axes are constructed.
List<List<Integer>>	getRepeatRelation(Integer index) Return the repeat superposition relation needed to obtain the axis of symmetry (which repeats and in which order have to be superimposed to obtain the axis).
javax.vecmath.Matrix4d	getRepeatTransform(int repeat) Return the transformation that needs to be applied to a determinate repeat so that all get superimposed to the same point.
List<javax.vecmath.Matrix4d>	getSymmetryAxes() Deprecated. because it does not work as expected for open symmetry
void	updateAxis(Integer index, javax.vecmath.Matrix4d newAxis) Updates an axis of symmetry, after the superposition changed.

Methods inherited from class java.lang.Object

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

Constructor Detail

SymmetryAxes

public SymmetryAxes()

Constructor. Initializes variables only.

Method Detail

addAxis

public void addAxis(javax.vecmath.Matrix4d axis,
                    List<List<Integer>> superposition,
                    List<Integer> repeats,
                    Integer division)

Adds a new axis of symmetry. The repeats that participate in this axis and their superposition relation should also be indicated.

Parameters:

axis - the new axis of symmetry found

superposition - repeats participating and superposition relation

repeats - number of times the transformation is applied to every repeat. index1=repeat, index2=times.

division - number of parts that this axis divides the structure in

Throws:

IllegalArgumentException - if the repeat relation is in the wrong format: should be double List of equal sizes.

updateAxis

public void updateAxis(Integer index,
                       javax.vecmath.Matrix4d newAxis)

Updates an axis of symmetry, after the superposition changed.

Parameters:

index - old axis index

newAxis -

getElementaryAxes

public List<javax.vecmath.Matrix4d> getElementaryAxes()

Return all elementary axes of symmetry of the structure, that is, the axes stored in the List as unique and from which all the symmetry axes are constructed.

Returns:

axes elementary axes of symmetry.

getRepeatRelation

public List<List<Integer>> getRepeatRelation(Integer index)

Return the repeat superposition relation needed to obtain the axis of symmetry (which repeats and in which order have to be superimposed to obtain the axis).

Parameters:

index - the axis index

Returns:

the double List of repeat relations, or null if the axis is not already stored.

getRepeatTransform

public javax.vecmath.Matrix4d getRepeatTransform(int repeat)

Return the transformation that needs to be applied to a determinate repeat so that all get superimposed to the same point.

Parameters:

repeat - the repeat index

Returns:

transformation matrix for the repeat

getSymmetryAxes

@Deprecated
public List<javax.vecmath.Matrix4d> getSymmetryAxes()

Deprecated. because it does not work as expected for open symmetry

Return all symmetry axes of of the structure: the set of axes that describe all parts of the structure. This combines the elementary axes to generate all possible axes. The axes are returned in the repeat order.

Returns:

axes all symmetry axes of the structure.