Package org.biojava.nbio.structure.symmetry.internal

Class CeSymm

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.CeSymm

public class CeSymm
extends Object

Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.

Iterating over previous results and disabling the diagonal of the previous alignments can also be done with this implementation, which will generate a set of self-alignments (disabled, because none improvements were shown, but can be turn on manually).

Multiple levels of symmetry can be analyzed by finding symmetries in repeats of previous results. This feature allows to find multiple symmetry axes.

The alignment is then refined to obtain a consistent alignment among all residues of the structure and organized into different parts, called symmetric repeats.

After refinement of the initial alignment, an optimization step can be used to improve the overall score of the repeat multiple alignment.

Since:

4.1.1

Author:

Andreas Prlic, Spencer Bliven, Aleix Lafita

Field Summary

Fields

Modifier and Type	Field	Description
static String	algorithmName
static String	version	Version History:

Method Summary

Modifier and Type	Method	Description
protected static CeSymmResult	align(Atom[] atoms, CESymmParameters params)
static CeSymmResult	analyze(Atom[] atoms)	Analyze the symmetries of the input Atom array using the DEFAULT parameters.
static CeSymmResult	analyze(Atom[] atoms, CESymmParameters params)	Analyze the symmetries of the input Atom array using the provided parameters.
static CeSymmResult	analyzeLevel(Atom[] atoms, CESymmParameters params)	Analyze a single level of symmetry.

Methods inherited from class java.lang.Object

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

Field Detail

version

public static final String version

Version History:

• 1.0 - initial implementation of CE-Symm.
• 1.1 - enable multiple CE-Symm runs to calculate all self-alignments.
• 2.0 - refine the alignment for consistency of repeat definition.
• 2.1 - optimize the alignment to improve the score.
• 2.2 - run multiple symmetry levels recursively to find PG and hierarchical symmetries.

See Also:

Constant Field Values

algorithmName

public static final String algorithmName

See Also:

Constant Field Values

Method Detail

align

protected static CeSymmResult align(Atom[] atoms,
                                    CESymmParameters params)
                             throws StructureException

Throws:

StructureException

analyze

public static CeSymmResult analyze(Atom[] atoms)
                            throws StructureException

Analyze the symmetries of the input Atom array using the DEFAULT parameters.

Parameters:

atoms - representative Atom array of the Structure

Returns:

CeSymmResult

Throws:

StructureException

analyze

public static CeSymmResult analyze(Atom[] atoms,
                                   CESymmParameters params)
                            throws StructureException

Analyze the symmetries of the input Atom array using the provided parameters.

Parameters:

atoms - representative Atom array of the Structure

param - CeSymmParameters bean

Returns:

CeSymmResult

Throws:

StructureException

analyzeLevel

public static CeSymmResult analyzeLevel(Atom[] atoms,
                                        CESymmParameters params)
                                 throws StructureException

Analyze a single level of symmetry.

Parameters:

atoms - Atom array of the current level

Returns:

CeSymmResult

Throws:

StructureException