use arguments from cli to override config, before

preparator = MoleculePreparation.from_config(config); minor edits to help msg

meeko/cli/mk_prepare_ligand.py

@@ -81,7 +81,7 @@ def cmd_lineparser():
     io_group.add_argument(
         "--charge_from_prop",
         nargs="*",
-        help="set atom partial charges from the input file. The default is PartialCharge for SDF and _TriposPartialCharge for MOL2 unless overriden by a user defined property name. ",
+        help="set atom partial charges from an RDKit atom property based on the input file. The default is 'PartialCharge' for SDF and '_TriposPartialCharge' for MOL2 unless overriden by a user defined property name. ",
     )
     io_group.add_argument(
         "-o",
@@ -555,19 +555,20 @@ def main():
     )
     nr_failures = 0
     is_after_first = False
-    preparator = MoleculePreparation.from_config(config)
 
     if args.charge_from_prop is not None: 
         if args.charge_model != "read": 
             print('--charge_from_prop must be used with --charge_model "read"')
             sys.exit(1)
 
-        preparator.charge_model = "read"
+        config["charge_model"] = "read"
         if args.charge_from_prop: 
-            preparator.charge_atom_prop = args.charge_from_prop[0]
+            config["charge_atom_prop"] = args.charge_from_prop[0]
         else:
             if ext=="mol2": 
-                preparator.charge_atom_prop = "_TriposPartialCharge"
+                config["charge_atom_prop"] = "_TriposPartialCharge"
+
+    preparator = MoleculePreparation.from_config(config)
 
     for mol in mol_supplier:
         if is_after_first and output.is_multimol == False: