Misc. changes
manually resolving merge
adding new enum to describe symmetry type
update to new SymmetryType class
Adding new demo
adding alternative scoring for significance testing
CEMirrorSymm updates

* Mirror sequence, coordinates, or both.
* Searches for CPs by default
* Display rotation axes (not always meaningful)
CEsymmGUI. Reenable prompt.

This keeps getting accidentally commented out during testing.
Fix CeSymm distanceMatrix

Distance matrices were not being stored. Now
saved and properly post-processed.
CEMirrorSymm improvements

* Inherits from CESymm not CECP, to prevent trivial alignments
* Properly set the distance matrix for reversed alignments
Removing hard-coded path.

Douglas, add it to your VM arguments instead:
    -DPDB_DIR=/Users/dmyerstu/Desktop/the_pdb/
    -DPDB_CACHE_DIR=/Users/dmyerstu/Desktop/the_pdb/
SymmRefiner improvements

* Set a few more properties in the refined AFP
* Superficial changes to main method
Removing hard-coded PDB_DIR settings.

Add them to your default VM arguments instead, a la
    -DPDB_DIR=/tmp/pdb
    -DPDB_CACHE_DIR=/tmp/pdb
Combined runs at different levels of sequence identity
merging peter's latest version
Merge branch 'master' of github.com:rcsb/symmetry
Simplified API for QuatSymmetryDetector.
QuatSymmetryDetector: return results as lists
working on merge
merging Peter's latest commit