Error handling

[mittinatten]

• Should error verbosity be global?
• Make sure there is consistent practice for when to warn/fail and asserts.
• Make error messages GNU-compliant http://www.gnu.org/prep/standards/html_node/Errors.html#Errors

[mittinatten]

Only use errors for input validation (i.e. valid parameters and PDB-files, residue codes, etc.) Use asserts to check for null pointers, invalid orders of calls (i.e. requesting value before calculation is performed, etc.)

[mittinatten]

CLI now does some basic consistency checking of parameters, instead of relying on return values from API. 47bba15718d83d3391cefe5214167d01f498d0ff