Phenylketonuria/Task6 Scripts

CN_dist2.R

CN_dist2.R is a R script that makes histograms for the CN-Score distribution (for all and extracted pairs). Furthermore it calculates the top L-Score (L = protein length) for each residue i that belongs to the top L CN_dist2.R script-call:
R CMD BATCH --slave '--args infile1=<FILE1> infile2=<FILE2> png_file=<OUTFILE1> output=<OUTFILE>' contact_map.R /dev/tty

-infile1         The evfold file with path.
-infile2         The extracted evfold file with path.
-png_file        PNG-file (.png) and the path, where the image of the multiple histogram with the CN-score frequencies 
                 for all and extracted residues should be saved.
-output          File-name and path, where the L-Scores should be stored.

contact_map.R

contact_map.R is a R script that creates a contact map with the output-files of the two perl scripts above (pdb = reference structure, extracted = predicted).
contact_map.R script-call:
R CMD BATCH '--args infile1=<FILE1> infile2=<FILE2> tophits=<#pairs> output=<OUTFILE>' contact_map.R

-infile1         The sorted and extracted evfold file with path.
-infile2         The pdb-contact file (output of contact_map.pl) with path.
-tophits         number, how many of the best residue pairs should be represented in the contact map.
-output          File-name of the map and the path, where it should be stored. File must be a PNG-File (.png).