From the symmetry project to biojava.structure.symmetry.

Only the finished and stable functionalities for the internal symmetry detection have been ported, leaving some experimental and in development methods in the symmetry project.

What is included?

• Calculate optimal self-alignment of a structure (by disallowing identity diagonal).
• Calculate internal symmetric subunits of a structure.
• Calculate the symmetry axes that relate all the internal subunits.
• Calculate the highest point group symmetry combining internal and quaternary symmetries.
• SymmetryGUI to trigger symmetry analysis choosing the parameters and visualizing the results in Jmol.

What is left in symmetry project for development?

• MULTIPLE Refiner: needs a graph representation and graph algorithms (future biojava jgraph library import).
• Order Detector Methods: some of them still in development/benchmarking.