[stability pipeline] have alignment of PRISM input file with pdb

[j0kaso]

currently a prism file can be read as input and uses it ( if this option was selected) by generating a mut_file out of it. But it only works if the pdb numbering matches the prism-file numbering. So it would be great, if we could include an alignment there.

if they do not match - we currently (likely) get an error due to missmatch of WT-resid-type (if they all would still match, but would be miss-aligned, we would not find out currently - same for mut-file btw - but I guess this would be very unlikely and only if we have very few variants in the exp-prism-file/mut-file)

How to do:

• make alignment of prims-file with pdb-sequence
• shift the mutations accordingly

Code to change

• main: prism_rosetta_parser.py: prism_to_mut
• minor: structure_input.py: make_mutfiles

[j0kaso]

not applicable anymore as prism files are not anymore allowed in the rosetta-stability-pipeline. generate a mutfile using https://github.com/KULL-Centre/PRISM/blob/dev_v0.1/software/scripts/prism2mutfile.py. this works also with putting in a pdb to align it according to that (including renumbering to rosetta numbering, output this pdb too)