added docking score feeature to main.sh and report generation

3 files changed, 49 insertions, 2 deletions

diff --git a/scripts/get_dock_score.py b/scripts/get_dock_score.py
new file mode 100644
index 0000000..a47312b
--- /dev/null
+++ b/scripts/get_dock_score.py
@@ -0,0 +1,46 @@
+#!/usr/bin/python3
+
+import argparse
+
+parser = argparse.ArgumentParser(description=desc_text)
+parser.add_argument("-p","--protein",help="Path to protein file")
+parser.add_argument("-l","--ligand",help="Path to ligand_out file")
+
+args = parser.parse_args()
+
+if args.protein == None:
+    print("Error: Please specify protein file")
+    exit(1)
+if args.ligand == None:
+    print("Error: Please specify ligand file")
+    exit(1)
+
+
+protein = args.protein
+ligand = args.ligand
+
+from os.path import basename
+
+print("# " + str(basename(protein)).replace(".pdbqt","") + "-" + str(basename(ligand)).replace("_out.pdbqt",""), end="\n\n")
+
+from tabulate import tabulate
+
+file = open(ligand, "r")
+lines = file.readlines()
+results = []
+i = 1
+for line in lines:
+    ta = []
+    if line.find('REMARK VINA') == 0 and line.split()[3] != "":
+        l = line.split()
+        ta.append(i)
+        ta.append(l[3])
+        ta.append(l[4])
+        ta.append(l[5])
+        i += 1
+    if ta != []:
+        results.append(ta)
+
+print("## Docking Scores",end="\n\n")
+print(tabulate(results,headers=["No.","Affinity","rmsd l.b","rmsd u.b"]))
+print("",end="\n\n")
diff --git a/scripts/main.sh b/scripts/main.sh
index 90d128b..68397fb 100755
--- a/scripts/main.sh
+++ b/scripts/main.sh
@@ -145,7 +145,8 @@ fi
 if [[ $interactions == "true" ]]; then
     python3 /src/scripts/get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt"
     python3 /src/plip/plipcmd.py -f best.pdb -qpxy
-    python3 /src/scripts/makeReport.py --input . > report.md
+    python3 /src/scripts/get_dock_score.py -l "$(echo $file)_out.pdbqt" -p $proteinPath > report.md
+    python3 /src/scripts/makeReport.py --input . >> report.md
     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 b905cf0..79d9c70 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -44,7 +44,7 @@ for x in doc.report.bindingsite:
 
 
 name = doc.report.pdbid.cdata
-print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
+#print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
 
 print("## Visualisation", end="\n\n")    
 print(f'![]({image})', end="\n\n")