Debugging extract_from_list

lcmd-epfl · Apr 23, 2024 · 452318e · 452318e
1 parent b79234f
commit 452318e
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diff --git a/cell2mol/cell_reconstruction.py b/cell2mol/cell_reconstruction.py
@@ -506,6 +506,7 @@ def combine(tobemerged: list, references: list, cellvec: list, threshold_tmat: f
                     reordered_newmolec.cell_indices = reordered_cell_indices
                     reordered_newmolec.set_fractional_coord(reordered_frac_cood)
                     reordered_newmolec.set_atoms(create_adjacencies=True, debug=2)
+
                     if reordered_newmolec.iscomplex: 
                         reordered_newmolec.split_complex()
                         reordered_newmolec.get_hapticity(debug=debug)
@@ -515,6 +516,7 @@ def combine(tobemerged: list, references: list, cellvec: list, threshold_tmat: f
                             met.get_coordination_geometry(debug=debug) 
                     if debug >= 1: print(f"COMBINE: {reordered_newmolec.fomula=}")
                     if debug >= 1: print(f"COMBINE: {reordered_newmolec=}")
+
                     issame = compare_species(reordered_newmolec, ref, debug=debug)
                     if issame:    ## Then is a molecule that appears in the reference list 
                         found = True 

diff --git a/cell2mol/charge_assignment.py b/cell2mol/charge_assignment.py
@@ -869,6 +869,8 @@ def prepare_unresolved(unique_indices: list, unique_species: list, distributions
                 list_indices.append(spec.get_parent_index("molecule"))
                 list_options.append(options)
 
+    # TODO: we use metal OS predicted by ML to select the best charge distribution
+
     return list_molecules, list_indices, list_options
 
 #######################################################    

diff --git a/cell2mol/other.py b/cell2mol/other.py
@@ -12,8 +12,11 @@ def extract_from_list(entrylist: list, old_array: list, dimension: int=2, debug:
                 new_array[idx, jdx] = old_array[row][col]
     elif dimension == 1:
         new_array = np.empty((length), dtype=object)
+        print("EXTRACT_FROM_LIST. received:", entrylist, old_array)
         for idx, val in enumerate(entrylist):
+            print("EXTRACT_FROM_LIST. received:", idx, val, old_array[val])
             new_array[idx] = old_array[val]
+        print(f"EXTRACT_FROM_LIST. {new_array=}")
     return list(new_array)
     #return list([np.stack(list(new_array), axis=0)])