Fix a NullPointer in createAFPChain

Ignore errors when trying to set the structure names
Fix ScopFactory bug

The current version was being returned sometimes,
even when an older version was requested.
updating example to latest API
some cleanup
Merge pull request #73 from andreasprlic/master

some cleanup
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.