From f4d3f99b944c78ec305ffdaa8a606b80a7d9dcdc Mon Sep 17 00:00:00 2001
From: my-name <yuri.cho@epfl.ch>
Date: Thu, 25 Apr 2024 18:10:49 +0200
Subject: [PATCH] Debugging

---
 cell2mol/c2m_module.py        |  9 +++++++--
 cell2mol/charge_assignment.py | 10 +++++-----
 cell2mol/classes.py           |  2 +-
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/cell2mol/c2m_module.py b/cell2mol/c2m_module.py
index 0dd29a67..a19aaf2d 100644
--- a/cell2mol/c2m_module.py
+++ b/cell2mol/c2m_module.py
@@ -20,7 +20,9 @@ def cell2mol(newcell: object, reconstruction: bool=True, charge_assignment: bool
             else:
                 tend = time.time()
                 if debug >= 1: print(f"\nCell Reconstruction Finished Normally. Total execution time: {tend - tini:.2f} seconds")
-
+        else:
+            return newcell
+        
     if charge_assignment:
         tini = time.time()
 
@@ -36,6 +38,8 @@ def cell2mol(newcell: object, reconstruction: bool=True, charge_assignment: bool
                 tend = time.time()
                 if debug >= 1: print(f"Charge Assignment Finished Normally. Total execution time: {tend - tini:.2f} seconds")
                 # newcell.predict_metal_ox(debug=debug) # predict metal oxidation state using Random Forest model
+        else:
+            return newcell  
         
     if spin_assignment:
         if not newcell.error_prepare_mols:
@@ -43,5 +47,6 @@ def cell2mol(newcell: object, reconstruction: bool=True, charge_assignment: bool
             newcell.assign_spin(debug=debug)
             tend = time.time()
             if debug >= 1: print(f"\nTotal execution time for Spin Assignment: {tend - tini:.2f} seconds")
-
+        else:
+            return newcell
     return newcell
diff --git a/cell2mol/charge_assignment.py b/cell2mol/charge_assignment.py
index 15569061..34324f10 100644
--- a/cell2mol/charge_assignment.py
+++ b/cell2mol/charge_assignment.py
@@ -417,7 +417,7 @@ def get_protonation_states_specie(specie: object, debug: int=0) -> list:
                         addedlist[idx] = 1
                     else:
                         mol = ligand.get_parent("molecule")
-                        iscarbene, tmp_element, tmp_added, tmp_metal = check_carbenes(a, ligand, mol)
+                        iscarbene, tmp_element, tmp_added, tmp_metal = check_carbenes(a, ligand)
                         if debug >= 2: print(f"        GET_PROTONATION_STATES: Evaluating as carbene and {iscarbene}")
                         if iscarbene:
                             # Carbene identified
@@ -698,7 +698,7 @@ def eval_chargelist(atom_charges: list, debug: int=0) -> Tuple[np.ndarray, np.nd
     return abstotal, abs_atcharge, zwitt
 
 #######################################################
-def check_carbenes(atom: object, ligand: object, molecule: object, debug: int=0) -> Tuple[bool, str, int, int]:
+def check_carbenes(atom: object, ligand: object, debug: int=0) -> Tuple[bool, str, int, int]:
     # Function that determines whether a given connected "atom" of a "ligand" of a "molecule" is a carbene
     # This function is in progress. Ideally, should be able to identify Fischer, Schrock and N-Heterocyclic Carbenes
     # The former two cases probably require rules that involve other ligands in the molecule, hence why the "molecule" is provided
@@ -709,7 +709,7 @@ def check_carbenes(atom: object, ligand: object, molecule: object, debug: int=0)
 
     # about Metal electrons: This variable is a way to contemplate cases in which the metal atom is actually contributing with electrons to the metal-ligand bond.
     # about Metal electrons: In reality, I'm not sure about how to use it correctly, and now is used without much chemical sense
-
+    
     iscarbene = False
     element = "H"
     addedlist = 0
@@ -718,8 +718,8 @@ def check_carbenes(atom: object, ligand: object, molecule: object, debug: int=0)
     # Initial attempt with Carbenes, but they are much more complex
     # Looks for Neighbouring N atoms
     list_of_coord_atoms = []
-    for i in atom.adjacency:
-        list_of_coord_atoms.append(ligand.labels[i])
+    for adj in atom.adjacency:
+        list_of_coord_atoms.append(ligand.get_parent("molecule").labels[adj])
     numN = list_of_coord_atoms.count("N")
 
     if numN == 2:  # it is an N-Heterocyclic carbenes
diff --git a/cell2mol/classes.py b/cell2mol/classes.py
index b0531efd..2ac91437 100644
--- a/cell2mol/classes.py
+++ b/cell2mol/classes.py
@@ -1303,9 +1303,9 @@ def get_moleclist(self, blocklist=None, debug: int=0):
         cov_factor = 1.3
 
         if blocklist is None: blocklist = split_species(self.labels, self.coord, cov_factor=cov_factor, debug=debug)
+        if blocklist is None: return None
         if debug > 0: print(f"CELL.MOLECLIST: found {len(blocklist)} blocks")
         if debug > 0: print(f"CELL.MOLECLIST: {blocklist=}")
-        if blocklist is None: return None
         
         self.moleclist = []
         for b in blocklist: