Package org.biojava.nbio.structure.symmetry.internal
package org.biojava.nbio.structure.symmetry.internal
-
ClassDescriptionGuesses 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
CeSymm.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.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 method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.Refinement of the self-alignment failed.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 symmetryInterface for all symmetry refinement implementations.Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.