Debugging

cell2mol/classes.py

@@ -1972,6 +1972,7 @@ def create_bonds(self, debug: int=0):
                 mol.smiles_with_H = [lig.smiles for lig in mol.ligands]
                 mol.smiles = []
                 for lig in mol.ligands:
+                    print(f"CELL.CREATE_BONDS: Correcting Smiles for ligand {lig.formula}")
                     result = correct_smiles_ligand(lig, debug=debug)
                     if result == False:
                         if debug >= 1: print(f"CELL.CREATE_BONDS: error correcting smiles for ligand {lig.formula}")

cell2mol/new_charge_assignment.py

@@ -176,6 +176,10 @@ def prepare_mol (mol):
     tmp_smiles = []
 
     for lig in mol.ligands: 
+        if hasattr(lig, "smiles"):
+            print(f"prepare_mol: {lig.formula=} {lig.smiles=}")
+        else:
+            print(f"prepare_mol: {lig.formula=}")
         tmp_smiles.append(lig.smiles)
         parent_indices = lig.get_parent_indices("molecule")
         for kdx, a in enumerate(parent_indices):

cell2mol/refcell.py

@@ -38,9 +38,10 @@ def process_refcell(input_path, name, current_dir, debug=0):
             # Finalize and save the reference cell object if no errors
             if refcell.error_case == 0:
                 get_unique_species_in_reference(refcell, debug) 
+                print_refmoleclist(refcell)
             else:
                 print(f"Error occurred in processing reference cell: error case {refcell.error_case}")
-            print_refmoleclist(refcell)
+
             if hasattr(refcell, "unique_species"):
                 print_unique_species(refcell)
             refcell.save(ref_cell_fname)