RCSB has removed rcsb.org/pdb/rest api calls. This PR removes references to old api calls and calls the new API calls to give the same data. This also removes some references to the BioJava package
Checklist
[x] Code compiles correctly
[x] Created tests which fail without the change (if possible)
[x] All tests passing
[x] Extended the README / documentation, if necessary
Description
RCSB has removed rcsb.org/pdb/rest api calls. This PR removes references to old api calls and calls the new API calls to give the same data. This also removes some references to the BioJava package
Checklist