CeSymmIterative (biojava 4.2.1 API)

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java.lang.Object
- org.biojava.nbio.structure.symmetry.internal.CeSymmIterative

```
public class CeSymmIterative
extends Object
```
Iterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure.
Works in the following way:
- Run CeSymm on the original structure.
- Calculate the symmetric unit boundaries.
- Run CeSymm on one of the symmetric units to find further symmetries.
- Repeat the last two steps until no more significant results are found.
- Map back all residues in a multiple alignment of the repeats.
- Run a final optimization of all symmetric units correctly superimposed.

Since:: 4.1.1
Author:: Aleix Lafita

Constructor Summary

Constructors
Constructor and Description
`CeSymmIterative(CESymmParameters param)` For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`CeSymmResult`	`execute(Atom[] atoms)` This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CeSymmIterative
```
public CeSymmIterative(CESymmParameters param)
```
    For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
    
    Parameters:
    
    param - CeSymm parameters, make sure they are cloned
- Method Detail
  - execute
```
public CeSymmResult execute(Atom[] atoms)
                     throws StructureException
```
    This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
    
    Parameters:
    
    atoms - atoms
    
    Returns:
    
    CeSymmResult
    
    Throws:
    
    StructureException

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