--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_pdbqt_to_sdf.py	Wed Jun 19 06:43:41 2019 -0400
@@ -0,0 +1,40 @@
+import pybel, openbabel
+import sys
+
+
+def main():
+	if len(sys.argv) == 3:
+		process(sys.argv[1], sys.argv[2])
+	else:
+		print("Usage: convert_pdbqt_to_sdf.py <input-pdbqt-file> <output-sdf-file>")
+		exit(1)
+
+def add_property(mol, prop_name, prop_value):
+	newData = openbabel.OBPairData() 
+	newData.SetAttribute(prop_name)
+	newData.SetValue(prop_value) 
+	mol.OBMol.CloneData(newData)
+
+def process(input, output):
+	docked = pybel.readfile('pdbqt', input)
+	sdf = pybel.Outputfile("sdf", output, overwrite=True)
+	for mol in docked:
+		if mol.OBMol.HasData('REMARK'):
+			remark = mol.OBMol.GetData('REMARK').GetValue()
+			lines = remark.splitlines()
+			tokens = lines[0].split()
+		
+			# add the score property
+			add_property(mol, "SCORE", tokens[2]) 
+			# add the first RMSD property
+			add_property(mol, "RMSD_LB", tokens[3])
+			# add the second RMSD property
+			add_property(mol, "RMSD_UB", tokens[4])
+
+		sdf.write(mol)
+
+	sdf.close()
+
+if __name__ == "__main__":
+    main()
+