- automodel-generated PDB or mmCIF files now point to the alignment file
used to generate them.
- Bundled version of HDF5 updated to 1.8.18.
- Bugfix: Whitespace in alignments aligned with gaps is now removed, not
erroneously mapped to the '.' residue type.
- Bugfix: automodel should now output SSBOND and CONECT records for any
disulfide bridges (previously they were present in the initial model but
not the final optimized models).