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Diffstat (limited to 'scripts/report.sh')
| -rw-r--r-- | scripts/report.sh | 67 |
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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