rosetta pipeline version v0.2.6

Oligomer/ligands:

• remove several bugs
• allow more options, including ligands and hetero-WT-oligomers

MP-pipeline:

• add some defaults for deepTMHMM
  Postprocessing:
• bugfix postprocessing (with oligomers)

rosetta pipeline version v0.2.5

Change pdb alignment & fix some bugs:

• new default pdb aligner: MMLigner
• bugs for deepTM

rosetta pipeline version v0.2.4

deepTMHMM flags

• remove space in output prism flag
• add retry and sleep mode when server is busy (random time with 5 tries)
• fix-bb before alignment with span (can cause problems otherwise - takes quite long)
• change default chain when using align by span option (Rosetta autosets to A)

general

• change default ddG parsing time to 10h
• update tests

rosetta pipeline version v0.2.3

• bugfixes esp for restart
• add mp pipeline option for using deepTMHMM to define span region
• align protein based on span region

rosetta pipeline version v0.2.2

add prism parser static files:

• software/scripts/FillVariants.py
• software/scripts/PrismData.py
• software/scripts/struc_select_sifts.py

rosetta pipeline version v0.2.1

rosetta-stability-pipeline:

• bugfix ligand=True runs
• bugfix dump pdb flag in soluble pipeline
• correction of consistency check based on processed structure (not initial) for post-relax
• update of unittest + adding of ligand checking to sp-test
• update of test and README/documentation

rosetta pipeline version v0.2

rosetta-stability-pipeline:

• add E_res output prism file
• MPprep alignments on TM region
• bugfix & issues among: HETATOM, closing of loops, restarts, multi-mut parsing, scaling defaults,
• add process feature that checks for present files
• add consistency checking for files after relax
• restart ddG runs if not finished for soluble pipeline (useful for bigger proteins)
• update of test and README/documentation

rosetta pipeline version v0.1.1

rosetta-stability-pipeline:

• MPcartesian ∆∆G run

• restart ddG runs if not finished for soluble pipeline (useful for bigger proteins)

rosetta pipeline version v0.1

rosetta-stability-pipeline:

• MP pipeline
• prism output files (incl git versioning)
• (homo)dimer option
• mut-file handling, including multi-mutations
• sci/unit-test
• dump pdbs
• emission stats
• zipping of folder
• several bugfixes and issues

working release for master

Stability pipeline status from Nov 2020 (last commits from @andershbf)