initial commit

1 files changed, 67 insertions, 0 deletions

diff --git a/scripts/report.sh b/scripts/report.sh
new file mode 100644
index 0000000..98437a3
--- /dev/null
+++ b/scripts/report.sh
@@ -0,0 +1,67 @@
+pwd=$(pwd)
+
+if [ -z "$1" ]
+  then
+    echo "CSV path not provided! 😠"
+	exit
+fi
+input="$1"
+
+ligands=()
+
+while IFS= read -r line
+do
+	mails=$(echo $line | tr "," "\n")
+	i=0
+	code=""
+	for a in $mails; do
+		i=$((i+1))
+		if ((i == 1))
+		then
+			code=$(echo "$a")
+		fi
+		if ((i == 2))
+		then
+			#ligands+=("./ligands/$a.pdbqt")
+            ligands+=("$a")
+		fi
+	done
+done < "$input"
+
+
+proteins=()
+#for file in ./configs/*
+#do
+#	proteins+=("$(basename $file .txt)")
+#done
+
+proteins+=("6VXX")
+
+#ligands=()
+#for file in ./ligands/*
+#do
+#    ligands+=("$(basename $file .pdbqt)")
+#done
+
+for protein in ${proteins[@]}; do
+    for ligand in ${ligands[@]}; do
+        ###cd $pwd/Reports/$protein/$ligand/
+        ###docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f $ligand.pdb  -qpxy
+        echo "Saving Protein-Ligand Complex $ligand"
+        python3.7 ./scripts/get-best.py -p ./targets/$protein.pdbqt -l ./Reports/$protein/$ligand/$ligand.pdbqt
+        fname=$(echo ${protein}_${ligand}.pdb)
+        mv best.pdb ./Reports/$protein/$ligand/$fname
+        cd $pwd/Reports/$protein/$ligand/
+        echo "Processing in PLIP"
+        docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f $fname  -qpxy
+        cd $pwd
+        echo "Generating Images"
+        #python3.7 ./scripts/quick-ligand-protein.py -p ./targets/$protein.pdbqt -l ./Reports/$protein/$ligand/$ligand.pdbqt
+        #mv closeup-front.png closeup-back.png output-back.png output-front.png ./Reports/$protein/$ligand/
+        echo "Generating PDF Report"
+        python3.7 ./scripts/makeReport.py --input ./Reports/$protein/$ligand/ > ./Reports/$protein/$ligand/report.md
+        cd $pwd/Reports/$protein/$ligand/
+        pandoc -V geometry:margin=1in report.md --pdf-engine=xelatex -o $ligand.pdf
+        cd $pwd
+    done
+done
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