From 004f4513c8cd5cfffbf69484fb39a3d7bc98bd49 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Fri, 11 Sep 2020 16:17:57 +0530
Subject: shifting hardcoded figures to another level

---
 scripts/add-pictures.py |  6 ++++++
 scripts/main.sh         | 10 ++++++----
 scripts/makeReport.py   |  5 -----
 3 files changed, 12 insertions(+), 9 deletions(-)
 create mode 100644 scripts/add-pictures.py

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")
-- 
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