Implemented createSubstructure(order, index); needs testing.
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.
Wrote some code for querying from MESPEUS and relating that data to
symmetry.
Created PeakCountingOrderDetector.
Working to remove ava_core as a dependency (issue #30). Replaced all
uses of PdbChainKey with StructureName, and deprecated some classes.
Reverted some of the previous conversions of StructureName to
PdbChainKey, so that the symmetry project can at least build for now.
Resolve conflicts. Added sampleRotations().
Added -storemapping to CLI.
Improved LigandFinder, adding functionality from InterfaceLigandFinder
to it. Deprecated InterfaceLigandFinder and its test.
Moved some code to ScopSupport.
Made ScopSupport.getAllDomainUnder take a boolean indicating whether to
include all proteins.
Just extracted the minimum score into an argument.
Fixed a compilation error.
Some improvements to CLI.
Improvements to CLI and Census.
Set system property PDB_DIR.
Fixed the basic stats in Census.
Set time taken in Results and census XML.
Removed a debugging statement in Protodomain.