From 2f2cb754e36dd1721775a48578148d98c3f4f11f Mon Sep 17 00:00:00 2001
From: romfas <34626210+RomFas@users.noreply.github.com>
Date: Tue, 3 Oct 2023 20:33:49 -0500
Subject: [PATCH] Delete helper_scripts/Calculate_SASA_and_anchors.sh

---
 helper_scripts/Calculate_SASA_and_anchors.sh | 30 --------------------
 1 file changed, 30 deletions(-)
 delete mode 100644 helper_scripts/Calculate_SASA_and_anchors.sh

diff --git a/helper_scripts/Calculate_SASA_and_anchors.sh b/helper_scripts/Calculate_SASA_and_anchors.sh
deleted file mode 100644
index 569cf3d..0000000
--- a/helper_scripts/Calculate_SASA_and_anchors.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#function pause(){
-#   read -p "$*"
-#}
-
-#mkdir ./new_templates/SASA_csvs
-#for filename in ./new_templates/pMHCI_plus_hydrogens/*.pdb; do
-#	peptide_file=${filename#*/new_templates/pMHCI_plus_hydrogens/}
-#	freesasa --format=rsa --radii=naccess --probe-radius 1.4 --shrake-rupley -n 200 ${filename} | grep "C  " | grep "RES" | awk '{print $4, $7, $8}' > "./new_templates/temp_pMHC.csv"
-#	freesasa --format=rsa --radii=naccess --probe-radius 1.4 --shrake-rupley -n 200 "./new_templates/peptide_only/${peptide_file}" | grep "C  " | grep "RES" | awk '{print $4, $7, $8}' > "./new_templates/temp_peptide.csv"
-#	join -j 1 ./new_templates/temp_pMHC.csv ./new_templates/temp_peptide.csv | tr ' ' ',' | awk -F, -v OFS="," '{$6=$4-$2}1' | awk -F, -v OFS="," '{$7=$5-$3}1' | awk -F, -v pep="$peptide_file", -v OFS="," '{$8=pep}1' | awk -F',' '{print $8, $1, $6, $7}'  > "./new_templates/temp_sidechains.csv"
-#	freesasa --select="carbon_alpha, name CA" --depth=atom --format=xml --radii=naccess --probe-radius 1.4 --shrake-rupley -n 200 "./new_templates/peptide_only/${peptide_file}" | sed -n -e '/chain label="C"/,$p' | grep -Pio 'name="CA".*area="\K[^"]*' > "./new_templates/temp_peptide.csv"
-#	freesasa --select="carbon_alpha, name CA" --depth=atom --format=xml --radii=naccess --probe-radius 1.4 --shrake-rupley -n 200 ${filename} | sed -n -e '/chain label="C"/,$p' | grep -Pio 'name="CA".*area="\K[^"]*' > "./new_templates/temp_pMHC.csv"
-#	paste -d, ./new_templates/temp_pMHC.csv ./new_templates/temp_peptide.csv | awk -F, -v OFS="," '{$3=$2-$1}1' | awk -F',' '{print $3}' > "./new_templates/temp_CA.csv"
-	#pause 'Press [Enter] key to continue...'
-#	paste -d' ' "./new_templates/temp_sidechains.csv" "./new_templates/temp_CA.csv" | tr ' ' ',' | awk -F, -v OFS="," '{$3=$3+$5}1' | awk -F, -v OFS="," '{$4=$4+$5}1' | sort -t, -r -rn -k4,4 | awk -F',' '{print $1, $2, $3, $4}' > "./new_templates/SASA_csvs/${peptide_file}"
-#	rm "./new_templates/temp_pMHC.csv"
-#	rm "./new_templates/temp_peptide.csv"
-#	rm "./new_templates/temp_CA.csv"
-#done
-#cat ./new_templates/SASA_csvs/*.pdb > ./new_templates/SASA_values.csv
-#sed -i 1i"PDB,residue_number,Delta_SASA,Delta_rel_SASA" ./new_templates/SASA_values.csv
-#rm -r ./new_templates/SASA_csvs
-
-naccess ./new_templates/pMHCI_plus_hydrogens/1DUZ.pdb
-#cat .rsa | grep "C  " | grep "RES" | awk '{print $4, $7, $8}' > "./new_templates/temp_pMHC.csv"
-#rm ../Naccess/naccess2.1.1/.rsa
-#naccess ./new_templates/peptide_only/1DUZ.pdb 
-#cat .rsa | grep "C  " | grep "RES" | awk '{print $4, $7, $8}' > "../new_templates/temp_peptide.csv"
-#rm ../Naccess/naccess2.1.1/.rsa
-#join -j 1 ../new_templates/temp_pMHC.csv ../new_templates/temp_peptide.csv | tr ' ' ',' | awk -F, -v OFS="," '{$6=$4-$2}1' | awk -F, -v OFS="," '{$7=$5-$3}1' | awk -F, -v pep="$peptide_file", -v OFS="," '{$8=pep}1' | awk -F',' '{print $8, $1, $6, $7}'  > "../new_templates/temp_sidechains.csv"
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