Made InterfaceLigandFinder work with chains and whole PDB Ids.
Wrote a test for InterfaceLigandFinder, which currently doesn't work.
Merge branch 'master' of https://github.com/rcsb/symmetry
Added buildAfpChain method to AlignmentMapping.
Fix bug using replaceOptAln
Implemented createSubstructure(order, index); needs testing.
Fixing geometry bugs

Replacing broken methods with RotationAxis.getProjectedDistance()
Check that SymmRefiner's hard-coded path exists

Its the next best thing to actual arguments
Improving robustness of NamesCensus input file

Allow comments and trailing tokens in the domain list, allowing the
benchmark.tsv file from the supplementals to be used.

Also stores the mapping in the results file
Fix logging configuration

remove duplicate console appenders & separate test and main
configurations
Use predictable scop version
Fix bug with calculating order of translational repeats
Fixed 2 bugs in Protodomain.createSubstructure using index > 0; wrote at
test for the case. Wrote a copy-constructor for Protodomain, and a
method to append Protodomains.
Started writing ConservedSequenceFinder.
Adding test for RotationOrderDetector
Adding second detection method within RotationOrderDetector
Adding some additional RotationOrderDetector methods
Adding cusp code
Wrote some code for querying from MESPEUS and relating that data to
symmetry.
Created PeakCountingOrderDetector.