We avoid to adapt some code in SWISS-MODEL that way...

HHblits3 starts with the target sequence instead of the sspred/ssconf
sections

- Use new HHblits database in testfiles
- adapt to new file structure (location of cs219.lib)
- generate new files for comparison
  => content of HHblits database changed and some ordering of lines
     is different in HHblits 3 anyways. However, that might be highly
     version specific

logging: All stdout output from the called tools is logged as ost.LogVerbose
and all stderr as ost.LogError
raising: Always raise if something goes wrong as opposed to just log a warning
and potentially return nonsense

functionality if the binding is tested manually, unit tests not yet adapted

This is used in Molck's MapNonStandardResidues which used to fail if there
were missing (or unmappable) backbone atoms in modified residues.