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 of a 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.
SymmetryAxes.Axis	Represents an axis of symmetry
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.