A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.
Interface for all symmetry refinement implementations.
Guesses an order of rotational symmetry from the angle.
Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.
Iterative version of CeSymm that aims at identifying all symmetry axis of a structure.
Provides parameters to
This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.
The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.
The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.
A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.
Calls Spencer's method for determining order.
Creates a refined alignment with the CE-Symm alternative self-alignment.
Data Structure that stores all the symmetry axis that describe the symmetry of a structure.
Represents an axis of symmetry
Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.
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.
Refinement of the self-alignment failed.
Copyright © 2000–2017 BioJava. All rights reserved.