[stability_pipeline] prism-to-mut mapping error when having pdb file with several chains

[j0kaso]

wrong resdata_reverse counting if e.g. chain C should be used (starting with chain A for counting). error rises in prism-to-mut.

example call for testing:

python /groups/sbinlab/tiemann/repos/PRISM/PRISM/software/rosetta_ddG_pipeline/run_pipeline.py \
    --structure /groups/sbinlab/tiemann/projects/PRISM/2020_09-parameter_tuning/input_final/OmpLA/1qd6.pdb \
    --mutate_mode prism \
    --prism /groups/sbinlab/tiemann/projects/PRISM/2020_09-parameter_tuning/input_final/OmpLA/prism_mave_102-106_OmpLA_ecoli.txt \
    --outputpath /groups/sbinlab/tiemann/projects/PRISM/2020_09-parameter_tuning/output-benchmark_relax_test/OmpLA/relaxrep1_relaxstruc20_repeat5_repack8.0 \
    --mode fullrun --chainid C --is_membrane True --mp_calc_span_mode DSSP --mp_align_ref 1qd6_C \
    --mp_prep_align_mode OPM --benchmark_mp_repack 8.0 --benchmark_mp_repeat 5 --benchmark_mp_relax_repeat 1 \
    --benchmark_mp_relax_strucs 1 --slurm_partition sbinlab --overwrite_path True

[j0kaso]

prism option not available anymore use mutfiles