Debugging

lcmd-epfl · Apr 23, 2024 · 6b6395a · 6b6395a
1 parent 3a371b6
commit 6b6395a
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/cell2mol/charge_assignment.py b/cell2mol/charge_assignment.py
@@ -202,7 +202,7 @@ def get_protonation_states_specie(specie: object, debug: int=0) -> list:
     # Program runs sequentially for each group of the ligand
     for g in ligand.groups:
         parent_indices = g.get_parent_indices("ligand")
-
+        if debug >= 2: print(f"    GET_PROTONATION_STATES: Evaluating group {g.formula} with parent_indices {parent_indices}")
         ########################
         # Cases with Hapticity #
         ########################

diff --git a/cell2mol/classes.py b/cell2mol/classes.py
@@ -1321,9 +1321,10 @@ def get_moleclist(self, blocklist=None, debug: int=0):
                 mol_frac_coord  = extract_from_list(b, self.frac_coord, dimension=1)
                 newmolec.set_fractional_coord(mol_frac_coord, debug=debug)
             # The split_complex must be below the frac_coord, so they are carried on to the ligands
-            if newmolec.iscomplex: 
-                if debug > 0: print(f"CELL.MOLECLIST: splitting complex")
-                newmolec.split_complex(debug=debug)
+            # if newmolec.iscomplex: 
+            #     if debug > 0: print(f"CELL.MOLECLIST: splitting complex")
+            #     newmolec.split_complex(debug=debug)
+            # Not needed here, as the reconstruction will take care of it
             self.moleclist.append(newmolec)
 
         return self.moleclist