no fixed bonds

src/process.py

@@ -639,7 +639,7 @@ def do(self):
 
 				elif line.startswith('ENDMDL'):
 					lines.append(line)
-					#mode = convert_pdbqt_to_pdb_by_adt(lines, as_string=True)
+					#mode = convert_pdbqt_to_pdb_by_adt(lfile, lines, as_string=True)
 					mode = convert_pdbqt_to_pdb(''.join(lines))
 					modes[idx] = mode
 
@@ -650,6 +650,7 @@ def do(self):
 					lines.append(line)
 
 		#receptor = convert_pdbqt_to_pdb_by_adt(rpdbqt, as_string=False)
+
 		receptor = convert_pdbqt_to_pdb(rpdbqt, as_string=False)
 
 		for i, row in enumerate(rows):

src/utils.py

@@ -4,6 +4,7 @@
 
 from pymol import cmd
 from rdkit import Chem
+from rdkit.Chem import AllChem
 from MolKit import Read
 from MolKit.pdbWriter import PdbWriter
 from openbabel import openbabel
@@ -26,7 +27,7 @@
 class NewPdbWriter(PdbWriter):
 	def write_string(self, atoms):
 		try:
-			self.write("\\/*&^%$#@!><|", atoms, records=['ATOM', 'HETATM'])
+			self.write("\\/*&^%$#@!><|", atoms, records=['ATOM', 'HETATM', 'CONECT'])
 		except:
 			pass
 
@@ -235,7 +236,34 @@ def generate_complex_pdb(receptor_pdb, ligand_pdb):
 
 	return '\n'.join(complex_lines)
 
-def convert_pdbqt_to_pdb_by_adt(pdbqt, as_string=False):
+"""
+def assign_bond_orders_from_origin(origin_file, pose_string):
+	origin_format = os.path.splitext(origin_file)[1]
+
+	if origin_format == '.pdb':
+		template = Chem.MolFromPDBFile(origin_file)
+
+	elif origin_format == '.mol2':
+		template = Chem.MolFromMol2File(origin_file)
+
+	elif origin_format == '.mol':
+		template = Chem.MolFromMolFile(origin_file)
+
+	elif origin_format == '.sdf':
+		for template in Chem.SDMolSupplier(origin_file):
+			pass
+
+	with open('pose.pdb', 'w') as fw:
+		fw.write(pose_string)
+
+	docked_pose = Chem.MolFromPDBFile('pose.pdb')
+
+	fixed_pose = AllChem.AssignBondOrdersFromTemplate(template, docked_pose)
+
+	return Chem.MolToPDBBlock(fixed_pose)
+"""
+
+def convert_pdbqt_to_pdb_by_adt(origin_file, pdbqt, as_string=False):
 	if as_string:
 		mols = Read(alllines=pdbqt, dataformat='pdbqt')
 	else:
@@ -248,6 +276,8 @@ def convert_pdbqt_to_pdb_by_adt(pdbqt, as_string=False):
 	writer = NewPdbWriter()
 	res = writer.write_string(mol.allAtoms)
 
+	#correct = assign_bond_orders_from_origin(origin_file, res)
+
 	return res
 
 def convert_pdbqt_to_pdb(pdbqt, as_string=True):