Checking for empty SCOP files

SCOP files can occationally be empty (eg if the server was down
at time of access). Future calls will now attempt to redownload them.
Cleanup and minor bug fixes
RotationAxis: better handling of translational movements
Removing ScopDatabase from AtomCache

Always fetch the active Scop from the ScopFactory
Test commit
Merge branch 'master' of https://github.com/biojava/biojava.git