Class CeSymm
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.internal.CeSymm
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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
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Field Summary
Fields Modifier and Type Field Description static String
algorithmName
static String
version
Version History:
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Method Summary
All Methods Static Methods Concrete Methods 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.
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Field Detail
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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
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algorithmName
public static final String algorithmName
- See Also:
- Constant Field Values
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Method Detail
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align
protected static CeSymmResult align(Atom[] atoms, CESymmParameters params) throws StructureException
- Throws:
StructureException
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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
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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 Structureparam
- CeSymmParameters bean- Returns:
- CeSymmResult
- Throws:
StructureException
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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
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