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

Interface Summary

Interface	Description
OrderDetector	A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.
SymmetryRefiner	Interface for all symmetry refinement implementations.

Class Summary

Class	Description
AngleOrderDetectorPlus	Guesses an order of rotational symmetry from the angle.
CeSymm	Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.
CeSymmIterative	Iterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure.
CESymmParameters	Provides parameters to CeSymm.
CeSymmResult	This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.
GraphComponentOrderDetector	The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.
GraphComponentRefiner	The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.
ResidueGroup	A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.
SequenceFunctionOrderDetector	Calls Spencer's method for determining order.
SequenceFunctionRefiner	Creates a refined alignment with the CE-Symm alternative self-alignment.
SymmetryAxes	Data Structure that stores all the symmetry axis that describe the symmetry of a structure.
SymmOptimizer	Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.

Enum Summary

Enum	Description
CESymmParameters.OrderDetectorMethod
CESymmParameters.RefineMethod
CESymmParameters.SymmetryType	The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.

Exception Summary

Exception	Description
RefinerFailedException	Refinement of the self-alignment failed.