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authorNavan Chauhan <navanchauhan@gmail.com>2020-09-11 16:17:57 +0530
committerNavan Chauhan <navanchauhan@gmail.com>2020-09-11 16:17:57 +0530
commit004f4513c8cd5cfffbf69484fb39a3d7bc98bd49 (patch)
treede2e1f56a9cca21b6b94f24f6c75409c274ca5de
parentd539597dab80833389797cff73a7b157abd33fe7 (diff)
shifting hardcoded figures to another level
-rw-r--r--scripts/add-pictures.py6
-rwxr-xr-xscripts/main.sh10
-rw-r--r--scripts/makeReport.py5
3 files changed, 12 insertions, 9 deletions
diff --git a/scripts/add-pictures.py b/scripts/add-pictures.py
new file mode 100644
index 0000000..95079f0
--- /dev/null
+++ b/scripts/add-pictures.py
@@ -0,0 +1,6 @@
+print("## Figures", end="\n\n")
+
+print("![Back View](output-back.png){width=100%}", end="\n\n")
+print("![Front View](output-front.png){width=100%}", end="\n\n")
+print("![Close Up View of the Back](closeup-back.png){width=100%}", end="\n\n")
+print("![Close Up View of the Front](closeup-front.png){width=100%}", end="\n\n") \ No newline at end of file
diff --git a/scripts/main.sh b/scripts/main.sh
index 68397fb..a165994 100755
--- a/scripts/main.sh
+++ b/scripts/main.sh
@@ -137,16 +137,18 @@ if [[ $dockingCheck == "true" ]]; then
vina --receptor $proteinPath --ligand $ligandPath --config $config
fi
-if [[ $visualisations == "true" ]]; then
- file=$(echo "$ligandPath" | cut -f 1 -d '.')
- python3 /src/scripts/quick-ligand-protein.py -p $proteinPath -l "$(echo $file)_out.pdbqt"
-fi
+
if [[ $interactions == "true" ]]; then
python3 /src/scripts/get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt"
python3 /src/plip/plipcmd.py -f best.pdb -qpxy
python3 /src/scripts/get_dock_score.py -l "$(echo $file)_out.pdbqt" -p $proteinPath > report.md
python3 /src/scripts/makeReport.py --input . >> report.md
+ if [[ $visualisations == "true" ]]; then
+ file=$(echo "$ligandPath" | cut -f 1 -d '.')
+ python3 /src/scripts/quick-ligand-protein.py -p $proteinPath -l "$(echo $file)_out.pdbqt"
+ python3 /src/scripts/add-pictures.py
+ fi
pandoc -V geometry:margin=1in report.md --pdf-engine=xelatex -o $name.pdf
fi
diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index c83928d..535da9b 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -455,9 +455,4 @@ elif fallback == 1:
tableBody.append(l)
print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
-print("## Figures", end="\n\n")
-print(f"![](output-back.png)", end="\n\n")
-print(f"![](output-front.png)", end="\n\n")
-print(f"![](closeup-back.png)", end="\n\n")
-print(f"![](closeup-front.png)", end="\n\n")