RMSD for 1000 Mutants about smlde

[LaneYahtzee]

Task re-assigned to Jason Li. Marking as complete.

[pvalle6]

Preprocess.sub here below

# Define variables
ipath=/ddnA/project/jjung1/pvalle6/workspace/
        # Path to folder that contains all results from AlphaFold (Default: input)
opath=/ddnA/project/jjung1/pvalle6/Protein_peptide_complex/
        # Path to folder that put all output files  (Default: output)
ppn=20
        # Number of processes per node  (Default: 20)
        
# Activate pymol environment
module load python/3.8.5-anaconda
source activate pymol

# Load GNU Parallel
module load gnuparallel/20190222/intel-19.0.5

# Change work directory
cd $PBS_O_WORKDIR

# Create a list of input files
ifiles=(`cd $ipath; find . -name 'ranked_0.pdb' | sed -e 's|^./||g' -e  's|/ranked_0.pdb||g'`)

# Process AlphaFold results
parallel --workdir $PBS_O_WORKDIR -j$ppn \
         "sed -e 's|INPUT|$ipath/{}/ranked_0.pdb|g' -e 's|OUTPUT|$opath/{}.pdb|g' script.pml | pymol -cpq" ::: ${ifiles[@]}
         
# Deactivate pymol environment
conda deactivate

[pvalle6]

added new folder in test branch called RMSD

[pvalle6]

PML script and sub script created for

[pvalle6]

Thank you @LaneYahtzee