diff options
| -rw-r--r-- | Dockerfile | 10 | ||||
| -rw-r--r-- | scripts/get-best.py | 1 | ||||
| -rwxr-xr-x | scripts/main.sh | 9 |
3 files changed, 13 insertions, 7 deletions
@@ -39,13 +39,13 @@ RUN chmod +x /src/scripts/main.sh RUN python3 -m pip install untangle tabulate # execute tests -WORKDIR /src/plip/test -RUN chmod +x run_all_tests.sh -RUN ./run_all_tests.sh +#WORKDIR /src/plip/test +#RUN chmod +x run_all_tests.sh +#RUN ./run_all_tests.sh # remove test files -WORKDIR /src -RUN rm -r /src/plip/test +#WORKDIR /src +#RUN rm -r /src/plip/test # set entry point to plipcmd.py #ENTRYPOINT ["python3", "/src/plip/plipcmd.py"] diff --git a/scripts/get-best.py b/scripts/get-best.py index a10c2d2..b5f69a8 100644 --- a/scripts/get-best.py +++ b/scripts/get-best.py @@ -28,6 +28,7 @@ if args.ligand == None: print("Error: Please specify ligand file") exit(1) +print("Getting Best ligand from",args.protein,args.ligand) protein = args.protein ligand = args.ligand diff --git a/scripts/main.sh b/scripts/main.sh index a165994..9c93e06 100755 --- a/scripts/main.sh +++ b/scripts/main.sh @@ -140,15 +140,20 @@ fi if [[ $interactions == "true" ]]; then + file=$(echo "$ligandPath" | cut -f 1 -d '.') python3 /src/scripts/get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt" + echo "Running PLIP" python3 /src/plip/plipcmd.py -f best.pdb -qpxy + echo "Getting Dock Score" python3 /src/scripts/get_dock_score.py -l "$(echo $file)_out.pdbqt" -p $proteinPath > report.md + echo "Making partial report" python3 /src/scripts/makeReport.py --input . >> report.md if [[ $visualisations == "true" ]]; then - file=$(echo "$ligandPath" | cut -f 1 -d '.') + echo "Creating Visualisations" python3 /src/scripts/quick-ligand-protein.py -p $proteinPath -l "$(echo $file)_out.pdbqt" - python3 /src/scripts/add-pictures.py + python3 /src/scripts/add-pictures.py >> report.md fi + echo "Generating PDF" pandoc -V geometry:margin=1in report.md --pdf-engine=xelatex -o $name.pdf fi |