use all atoms; to be consistent with the paper

src/DiffAtomComp.py

@@ -452,26 +452,18 @@ def read_file_and_get_coordinates(file_path):
 
     # Initialize a list to hold all atom coordinates
     all_atom_coordinates = []
-    backbone_coords = []
-    backbone_chains = []
-
-    backbone_atoms = ['N', 'CA', 'C', 'O']
 
     # Iterate through each model, chain, and residue in the structure to get atoms
     for model in structure:
         for chain in model:
             chain_id = chain.get_id()
             for residue in chain:
                 for atom in residue:
-                    if atom.get_name() in backbone_atoms:
-                        # Append the atom's coordinates to the list
-                        backbone_coords.append(atom.get_coord())
-                        # backbone_chains.append(chain_id)
-
-    # interp_backbone_coords = interp_backbone(backbone_coords, backbone_chains)
+                    # Append the atom's coordinates to the list
+                    all_atom_coordinates.append(atom.get_coord())
 
     # Return the numpy array of coordinates
-    return np.array(backbone_coords)
+    return np.array(all_atom_coordinates)
 
 
 def pad_and_convert_to_tensor(atom_coords_list, device):

src/tool.py

@@ -1206,11 +1206,7 @@ def single_fit_button_clicked(self):
         from chimerax.map.molmap import molecule_map
         mol_vol = molecule_map(self.session, mol.atoms, self._single_fit_res.value(), grid_spacing=self.fit_vol.data.step[0])
 
-        backbone_atoms = ['N', 'CA', 'C', 'O']
-        is_backbone = np.isin(mol.atoms.names, backbone_atoms)
-
-        input_coords = mol.atoms.scene_coords[is_backbone]
-        # input_coords = mol.atoms.scene_coords
+        input_coords = mol.atoms.scene_coords
 
         # Fit
         timer_start = datetime.now()