Add maximum RMSD for alignment threshold

[andreasprlic]

CE has a parameter for the maximum RMSD at which to stop optimizing the alignment. Can we expose this parameter also for CE-Symm?

[andreasprlic]

This parameter makes a big difference for detection of the local symmetry that is in 1e9q.B. The global alignment also find symmetry, but the exact symmetric motif does not get detected precisely.

   CeSymm ceSymm = new CeSymm();

    CeParameters params =  (CeParameters) ceSymm.getParameters();

    if ( params == null) {
        params = new CeParameters();
        ceSymm.setParameters(params);
    }
   params.setMaxOptRMSD(3.0);

[andreasprlic]

also 1hiv.A gets much better with max RMSD of 3.0

[sbliven]

It should be easy to add an option to CESymmMain in symmetry-tools. Any other parameters we should expose?

[lafita]

Now we have all the CE parameters exposed, because CeSymmParameters implements CEParameters.