diff --git a/src/moffragmentor/sbu/node.py b/src/moffragmentor/sbu/node.py index a4b6718..ce9e947 100644 --- a/src/moffragmentor/sbu/node.py +++ b/src/moffragmentor/sbu/node.py @@ -91,7 +91,7 @@ def _extract_and_wrap(node_indices, all_branching_indices, all_binding_indices, branching_to_binding = set(binding_neighbors).intersection(all_branching_indices) extension_points = [] - + for branching_idx in branching_to_binding | branching_to_node_metal: if branching_idx in node_indices: # find extension point @@ -105,7 +105,7 @@ def _extract_and_wrap(node_indices, all_branching_indices, all_binding_indices, # Now, make a copy of the structure and replace the indices with dummy atoms dummy_structure = Structure.from_sites(mof.structure.sites) - print('binding_to_node_metal', binding_to_node_metal) + print("binding_to_node_metal", binding_to_node_metal) for i in binding_to_node_metal: dummy_structure.replace(i, _BINDING_DUMMY) for i in branching_to_binding | branching_to_node_metal: @@ -125,7 +125,7 @@ def _extract_and_wrap(node_indices, all_branching_indices, all_binding_indices, ) inverse_mapping = {v[0]: k for k, v in mapping_w_dummy.items()} - print('inverse_mapping', inverse_mapping) + print("inverse_mapping", inverse_mapping) # let's replace here now the atoms with the dummys as doing it beforehand might cause issues # (e.g. we do not have the distances for a cutoffdict) @@ -135,7 +135,9 @@ def _extract_and_wrap(node_indices, all_branching_indices, all_binding_indices, mol_w_dummy._sites[inverse_mapping[i]] = Site( _BRANCHING_DUMMY, mol_w_dummy._sites[inverse_mapping[i]].coords, - properties={"original_species": str(original_mol_w_dummy_species[inverse_mapping[i]])}, + properties={ + "original_species": str(original_mol_w_dummy_species[inverse_mapping[i]]) + }, ) for i in binding_to_node_metal: