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-rw-r--r--scripts/report.sh67
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 \ No newline at end of file