Debugging coordination_correction_for_nonhaptic

cell2mol/connectivity.py

@@ -553,6 +553,9 @@ def split_group(original_group, conn_idx, final_ligand_indices, debug: int=0):
     splitted_groups = []
 
     if debug > 1: print(f"GROUP.SPLIT_GROUP: {conn_idx=}")
+    if debug > 1: print(f"GROUP.SPLIT_GROUP: {original_group.labels=}")
+    if debug > 1: print(f"GROUP.SPLIT_GROUP: {original_group.coord=}")
+    if debug > 1: print(f"GROUP.SPLIT_GROUP: {original_group.atoms=}")
     conn_labels  = extract_from_list(conn_idx, original_group.labels, dimension=1)
     conn_coord   = extract_from_list(conn_idx, original_group.coord, dimension=1)
     conn_frac_coord   = extract_from_list(conn_idx, original_group.frac_coord, dimension=1)
@@ -576,6 +579,7 @@ def split_group(original_group, conn_idx, final_ligand_indices, debug: int=0):
         gr_atoms        = extract_from_list(b, conn_atoms, dimension=1)
         # Create Group Object
         newgroup = group(gr_labels, gr_coord, gr_frac_coord, radii=gr_radii)
+        if debug > 1: print(f"GROUP.SPLIT_GROUP: {newgroup.labels=}")
         # For debugging
         newgroup.origin = "split_group"
         # Define the GROUP as parent of the group. Bottom-Up hierarchy

cell2mol/coordination_sphere.py

@@ -16,13 +16,17 @@ def define_coordination_geometry (metal: object, coord_group: list, debug: int=0
 
     symbols.append(metal.label)
     positions.append(metal.coord)
-
+    if debug >= 2 : print(f"DEFINE_coordination_geometry: {metal.label} {metal.coord}")
+    print(f"DEFINE_coordination_geometry: {[group.formula for group in coord_group]}")
+    print(f"DEFINE_coordination_geometry: {[group.is_haptic for group in coord_group]}")
+    print(f"DEFINE_coordination_geometry: {[[a.label for a in group.atoms] for group in coord_group]}")
+
     for group in coord_group:
         if group.is_haptic == False:
             for atom in group.atoms:
                 symbols.append(atom.label)
                 positions.append(atom.coord)
-                #if debug >= 2 : print("DEFINE_coordination_geometry:", atom.label, atom.coord)
+                if debug >= 2 : print("DEFINE_coordination_geometry:", atom.label, atom.coord)
         else :
             if debug >= 2 : print(f"DEFINE_coordination_geometry: {group.haptic_type=}")
             #if debug >= 2 : print(f"DEFINE_coordination_geometry: {[atom.coord for atom in group.atoms]}")
@@ -372,8 +376,7 @@ def coordination_correction_for_nonhaptic(group: object, debug: int=0):
 
     if debug > 0: print("Entering COORD_CORR_NONHAPTIC:")
     if not hasattr(group,"metals"): group.get_connected_metals()
-
-
+    print(f"group: {[atom.label for atom in group.atoms]}")
     # Pair each atom with its index in the original list
     indexed_atoms = list(enumerate(group.atoms))
 
@@ -384,9 +387,6 @@ def coordination_correction_for_nonhaptic(group: object, debug: int=0):
     sorted_atoms = [atom[1] for atom in sorted_indexed_atoms]
     original_indices = [atom[0] for atom in sorted_indexed_atoms]
 
-    # Update the group's atoms list to the sorted atoms
-    group.atoms = sorted_atoms
-
     ## First Correction (former verify_connectivity)
     conn_idx = []
     final_ligand_indices = []
@@ -422,6 +422,7 @@ def coordination_correction_for_nonhaptic(group: object, debug: int=0):
                 # group.remove_atom(idx, debug=debug)
 
     conn_idx = sorted(list(set(conn_idx)))
+
     return group, conn_idx, final_ligand_indices
 
 
@@ -456,6 +457,8 @@ def coordination_correction_for_haptic (group: object, debug: int=0):
         else :
             conn_idx.append(idx)
             final_ligand_indices.append(atom.get_parent_index("ligand"))
+
     conn_idx = sorted(list(set(conn_idx)))
+
     return group, conn_idx, final_ligand_indices
 #######################################################

cell2mol/missingH.py

@@ -37,7 +37,7 @@ def get_missingH(Z, valence, center, charge, edges, points):
 
 
 ##############################
-def get_missingH_from_adjacency(Z, center, points):
+def get_missingH_from_adjacency(Z, center, points, bonded_atom_labels):
     missingH = False
 
     num_adj_atoms = len(points)
@@ -52,9 +52,16 @@ def get_missingH_from_adjacency(Z, center, points):
 
     # Evaluates geometry
     val_e = num_adj_atoms
-    if val_e < shapeval:  missingH = True
-    if val_e == shapeval: missingH = False
-    if val_e > shapeval:  missingH = True
+    if val_e == 1:
+        if bonded_atom_labels[0] == "O" or bonded_atom_labels[0] == "N": # CO or CN
+            missingH = False
+        else:
+            shapeval = "more than 1 (possibly 3 in missing H in methyl)"
+            missingH = True
+    elif val_e == shapeval :  
+        missingH = False
+    else :
+        missingH = True
 
     # Saves report
     # print(f"Summary of facts:\n -Atom has {num_adj_atoms} adjacent atoms \n -with total bond order {sum_bond_order} \n -arranged in a shape {shape} that suggests coordination {shapeval} \n -with formal charge {charge} \n -valence {valence} and {lonepairs} lone pairs.")
@@ -117,6 +124,8 @@ def check_missingH(refmoleclist: list, debug: int=0):
             if ref.natoms == 1 and "O" in ref.labels: 
                 Missing_H_in_CoordWater = True
                 if debug >= 1: print(f"WARNING found isolated O atom in the cell. This tends to be a water with missing H, so stopping")
+            elif ref.formula == "CO" or ref.formula == "CN":
+                pass
             else:
                 for kdx, a in enumerate(ref.atoms):
                     if not hasattr(a,"adjacency"): continue 
@@ -128,13 +137,13 @@ def check_missingH(refmoleclist: list, debug: int=0):
                             bonded_atom_coord.append(ref.coord[adj])
                             bonded_atom_labels.append(ref.atoms[adj].label)
                         if debug >= 2: print("Adjacency", a.adjacency, bonded_atom_labels)
-                        ismissingH, report = get_missingH_from_adjacency(a.atnum, a.coord, bonded_atom_coord)
+                        ismissingH, report = get_missingH_from_adjacency(a.atnum, a.coord, bonded_atom_coord, bonded_atom_labels)
                         if ismissingH:
                             for label, coord in zip(bonded_atom_labels, bonded_atom_coord):
                                 print("Dist", f"{a.label}-{label}", get_dist(a.coord, coord))
                         if ismissingH:
                             if debug >= 1: print("")
-                            if debug >= 1: print(f"WARNING in Missing H function for: {ref.type}, {idx}, {ref.labels}")
+                            if debug >= 1: print(f"WARNING in Missing H function for: {ref.type}, molecule index {idx}, {ref.formula}")
                             if debug >= 1: print(f"C Atom {kdx} {a.get_parent_index('molecule')} has missing H atoms")
                             if debug >= 1: print(report)
                             Missing_H_in_C = True
@@ -146,6 +155,8 @@ def check_missingH(refmoleclist: list, debug: int=0):
                         Missing_H_in_CoordWater = True
                         if debug >= 1: print("")
                         if debug >= 1: print("WARNING in Missing H function for ligand",lig.natoms,lig.labels)
+                elif lig.formula == "CO" or lig.formula == "CN":
+                    pass
                 else:
                     for kdx, a in enumerate(lig.atoms):
                         if a.label == "C" and a.mconnec == 0:
@@ -156,10 +167,10 @@ def check_missingH(refmoleclist: list, debug: int=0):
                                 bonded_atom_coord.append(lig.get_parent("molecule").coord[adj])
                                 bonded_atom_labels.append(lig.get_parent("molecule").atoms[adj].label)
                             if debug >= 2: print("Adjacency", a.adjacency, bonded_atom_labels)
-                            ismissingH, report = get_missingH_from_adjacency(a.atnum, a.coord, bonded_atom_coord)
+                            ismissingH, report = get_missingH_from_adjacency(a.atnum, a.coord, bonded_atom_coord, bonded_atom_labels)
                             if ismissingH:
                                 if debug >= 1: print("")
-                                if debug >= 1: print(f"WARNING in Missing H function for: {ref.type}, {idx}, {jdx}, {lig.labels}")
+                                if debug >= 1: print(f"WARNING in Missing H function for: {ref.type}, molecule index {idx}, ligand index {jdx}, {lig.formula}")
                                 if debug >= 1: print(f"C Atom {kdx} {a.get_parent_index('molecule')} has missing H atoms")
                                 if debug >= 1: print(report)
                                 Missing_H_in_C = True

cell2mol/refcell.py

@@ -39,7 +39,8 @@ 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)
+                pass
+                # get_unique_species_in_reference(refcell, debug)
             else:
                 print(f"Error occurred in processing reference cell: error case {refcell.error_case}")
             refcell.save(ref_cell_fname)