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-rw-r--r--Dockerfile10
-rw-r--r--scripts/get-best.py1
-rwxr-xr-xscripts/main.sh9
3 files changed, 13 insertions, 7 deletions
diff --git a/Dockerfile b/Dockerfile
index 33239ee..ae3143d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -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