SymmetryAxes (biojava 5.0.0 API)

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.
Hierarchical symmetry can be visualized as a tree, where each level has a fixed branching factor. Each level of the tree is associated with a transformation operator, whose order determines the degree of nodes at that level of the tree. Leaves of the tree implicitly represent aligned repeats (indexed 0 to n-1), so care must be taken to keep external references to the repeats (e.g. rows of a MultipleAlignment in the same order implied by the tree.
Each node of the tree specifies an alignment between those repeats below each of its children. It is also associated with a symmetry axis, which is calculated based on the associated operator as well as any parent operators. 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

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SymmetryAxes.Axis
Represents an axis of symmetry

Nested Classes
Modifier and Type	Class and Description
`static class`	`SymmetryAxes.Axis` Represents an axis of symmetry

Constructor Summary

Constructors
Constructor and Description

SymmetryAxes()
Constructor.

Constructors
Constructor and Description
`SymmetryAxes()` Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAxis(javax.vecmath.Matrix4d axis, int order, CESymmParameters.SymmetryType type)` Adds a new axis of symmetry to the bottom level of the tree
`List<javax.vecmath.Matrix4d>`	`getElementaryAxes()` Return the operator for 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<SymmetryAxes.Axis>`	`getElementaryAxesObjects()` 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.
`SymmetryAxes.Axis`	`getElementaryAxis(int level)`
`List<Integer>`	`getFirstRepeats(int level)` Get the first repeat index of each axis of a specified level.
`int`	`getNumLevels()`
`int`	`getNumRepeats()` Get the number of repeats.
`List<List<Integer>>`	`getRepeatRelation(int level)` Get the indices of participating repeats in Cauchy two-line form.
`List<List<Integer>>`	`getRepeatRelation(int level, int firstRepeat)`
`List<List<Integer>>`	`getRepeatRelation(SymmetryAxes.Axis axis)`
`List<List<Integer>>`	`getRepeatsCyclicForm(int level)`
`List<List<Integer>>`	`getRepeatsCyclicForm(int level, int firstRepeat)` Get the indices of participating repeats in cyclic form.
`static String`	`getRepeatsCyclicForm(List<List<Integer>> cycleForm, List<?> repeats)`
`List<List<Integer>>`	`getRepeatsCyclicForm(SymmetryAxes.Axis axis)`
`String`	`getRepeatsCyclicForm(SymmetryAxes.Axis axis, List<?> repeats)`
`javax.vecmath.Matrix4d`	`getRepeatTransform(int repeat)` Return the transformation that needs to be applied to a repeat in order to superimpose onto repeat 0.
`javax.vecmath.Matrix4d`	`getRepeatTransform(int x, int y)` Return the transformation that needs to be applied to repeat x in order to superimpose onto repeat y.
`List<SymmetryAxes.Axis>`	`getSymmetryAxes()` Return all symmetry axes of of the structure: the set of axes that describe all parts of the structure.
`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,
                    int order,
                    CESymmParameters.SymmetryType type)
```
    Adds a new axis of symmetry to the bottom level of the tree
    
    Parameters:
    
    axis - the new axis of symmetry found
    
    order - number of parts that this axis divides the structure in
    
    type - indicates whether the axis has OPEN or CLOSED symmetry
  - 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 the operator for 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.
  - getElementaryAxesObjects
```
public List<SymmetryAxes.Axis> getElementaryAxesObjects()
```
    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(int level)
```
    Get the indices of participating repeats in Cauchy two-line form.
    Returns two lists of the same length. The first gives a list of all repeat indices which are aligned at the specified level of symmetry (e.g. 0 through the degree of this level). The second list gives the corresponding repeats after applying the operator once.
    
    Parameters:
    
    level - the axis index
    
    Returns:
    
    the double List of repeat relations, or null if the level is invalid
    
    See Also:
    
    for an equivalent specification with half the memory
  - getRepeatRelation
```
public List<List<Integer>> getRepeatRelation(SymmetryAxes.Axis axis)
```
  - getRepeatRelation
```
public List<List<Integer>> getRepeatRelation(int level,
                                             int firstRepeat)
```
  - getRepeatsCyclicForm
```
public List<List<Integer>> getRepeatsCyclicForm(int level,
                                                int firstRepeat)
```
    Get the indices of participating repeats in cyclic form.
    Each inner list gives a set of equivalent repeats and should have length equal to the order of the axis' operator.
    
    Parameters:
    
    level -
    
    firstRepeat -
    
    Returns:
  - getRepeatsCyclicForm
```
public List<List<Integer>> getRepeatsCyclicForm(SymmetryAxes.Axis axis)
```
  - getRepeatsCyclicForm
```
public List<List<Integer>> getRepeatsCyclicForm(int level)
```
  - getRepeatsCyclicForm
```
public String getRepeatsCyclicForm(SymmetryAxes.Axis axis,
                                   List<?> repeats)
```
  - getRepeatsCyclicForm
```
public static String getRepeatsCyclicForm(List<List<Integer>> cycleForm,
                                          List<?> repeats)
```
  - getRepeatTransform
```
public javax.vecmath.Matrix4d getRepeatTransform(int repeat)
```
    Return the transformation that needs to be applied to a repeat in order to superimpose onto repeat 0.
    
    Parameters:
    
    repeat - the repeat index
    
    Returns:
    
    transformation matrix for the repeat
  - getRepeatTransform
```
public javax.vecmath.Matrix4d getRepeatTransform(int x,
                                                 int y)
```
    Return the transformation that needs to be applied to repeat x in order to superimpose onto repeat y.
    
    Parameters:
    
    x - the first repeat index (transformed)
    
    y - the second repeat index (fixed)
    
    Returns:
    
    transformation matrix for the repeat x
  - getSymmetryAxes
```
public List<SymmetryAxes.Axis> getSymmetryAxes()
```
    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 degrees.
    
    Returns:
    
    axes all symmetry axes of the structure.
  - getNumRepeats
```
public int getNumRepeats()
```
    Get the number of repeats. This is equal to the product of all degrees.
    
    Returns:
    
    Number of repeats (leaves of the tree).
  - getFirstRepeats
```
public List<Integer> getFirstRepeats(int level)
```
    Get the first repeat index of each axis of a specified level.
    
    Parameters:
    
    level - level of the tree to cut at
    
    Returns:
    
    List of first Repeats of each index, sorted in ascending order
  - getElementaryAxis
```
public SymmetryAxes.Axis getElementaryAxis(int level)
```
  - getNumLevels
```
public int getNumLevels()
```

Class SymmetryAxes

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SymmetryAxes

Method Detail

addAxis

updateAxis

getElementaryAxes

getElementaryAxesObjects

getRepeatRelation

getRepeatRelation

getRepeatRelation

getRepeatsCyclicForm

getRepeatsCyclicForm

getRepeatsCyclicForm

getRepeatsCyclicForm

getRepeatsCyclicForm

getRepeatTransform

getRepeatTransform

getSymmetryAxes

getNumRepeats

getFirstRepeats

getElementaryAxis

getNumLevels