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How to use _get method in avocado

Best Python code snippet using avocado_python

api_openexplorer_OpenExplorerReporter.py

Source:api_openexplorer_OpenExplorerReporter.py

...78    return get_atom_type_from_atom(item, indices=indices, structure_indices=structure_indices)79def get_atom_index_from_atom(item, indices='all', structure_indices='all'):80    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_index_from_atom as _get81    tmp_item = to_molsysmt_Topology(item)82    return _get(tmp_item, indices=indices, structure_indices=structure_indices)83def get_atom_id_from_atom(item, indices='all', structure_indices='all'):84    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_id_from_atom as _get85    tmp_item = to_molsysmt_Topology(item)86    return _get(tmp_item, indices=indices, structure_indices=structure_indices)87def get_atom_name_from_atom(item, indices='all', structure_indices='all'):88    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_name_from_atom as _get89    tmp_item = to_molsysmt_Topology(item)90    return _get(tmp_item, indices=indices, structure_indices=structure_indices)91def get_atom_type_from_atom(item, indices='all', structure_indices='all'):92    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_type_from_atom as _get93    tmp_item = to_molsysmt_Topology(item)94    return _get(tmp_item, indices=indices, structure_indices=structure_indices)95def get_group_index_from_atom (item, indices='all', structure_indices='all'):96    from molsysmt.api_forms.api_molsysmt_Topology import get_group_index_from_atom as _get97    tmp_item = to_molsysmt_Topology(item)98    return _get(tmp_item, indices=indices, structure_indices=structure_indices)99def get_group_id_from_atom (item, indices='all', structure_indices='all'):100    from molsysmt.api_forms.api_molsysmt_Topology import get_group_id_from_atom as _get101    tmp_item = to_molsysmt_Topology(item)102    return _get(tmp_item, indices=indices, structure_indices=structure_indices)103def get_group_name_from_atom (item, indices='all', structure_indices='all'):104    from molsysmt.api_forms.api_molsysmt_Topology import get_group_name_from_atom as _get105    tmp_item = to_molsysmt_Topology(item)106    return _get(tmp_item, indices=indices, structure_indices=structure_indices)107def get_group_type_from_atom (item, indices='all', structure_indices='all'):108    from molsysmt.api_forms.api_molsysmt_Topology import get_group_type_from_atom as _get109    tmp_item = to_molsysmt_Topology(item)110    return _get(tmp_item, indices=indices, structure_indices=structure_indices)111def get_component_name_from_atom (item, indices='all', structure_indices='all'):112    from molsysmt.api_forms.api_molsysmt_Topology import get_component_name_from_atom as _get113    tmp_item = to_molsysmt_Topology(item)114    return _get(tmp_item, indices=indices, structure_indices=structure_indices)115def get_component_index_from_atom (item, indices='all', structure_indices='all'):116    from molsysmt.api_forms.api_molsysmt_Topology import get_component_index_from_atom as _get117    tmp_item = to_molsysmt_Topology(item)118    return _get(tmp_item, indices=indices, structure_indices=structure_indices)119def get_component_id_from_atom (item, indices='all', structure_indices='all'):120    from molsysmt.api_forms.api_molsysmt_Topology import get_component_id_from_atom as _get121    tmp_item = to_molsysmt_Topology(item)122    return _get(tmp_item, indices=indices, structure_indices=structure_indices)123def get_component_type_from_atom (item, indices='all', structure_indices='all'):124    from molsysmt.api_forms.api_molsysmt_Topology import get_component_type_from_atom as _get125    tmp_item = to_molsysmt_Topology(item)126    return _get(tmp_item, indices=indices, structure_indices=structure_indices)127def get_chain_name_from_atom (item, indices='all', structure_indices='all'):128    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_name_from_atom as _get129    tmp_item = to_molsysmt_Topology(item)130    return _get(tmp_item, indices=indices, structure_indices=structure_indices)131def get_chain_index_from_atom (item, indices='all', structure_indices='all'):132    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_index_from_atom as _get133    tmp_item = to_molsysmt_Topology(item)134    return _get(tmp_item, indices=indices, structure_indices=structure_indices)135def get_chain_id_from_atom (item, indices='all', structure_indices='all'):136    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_id_from_atom as _get137    tmp_item = to_molsysmt_Topology(item)138    return _get(tmp_item, indices=indices, structure_indices=structure_indices)139def get_chain_type_from_atom (item, indices='all', structure_indices='all'):140    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_type_from_atom as _get141    tmp_item = to_molsysmt_Topology(item)142    return _get(tmp_item, indices=indices, structure_indices=structure_indices)143def get_molecule_index_from_atom (item, indices='all', structure_indices='all'):144    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_index_from_atom as _get145    tmp_item = to_molsysmt_Topology(item)146    return _get(tmp_item, indices=indices, structure_indices=structure_indices)147def get_molecule_id_from_atom (item, indices='all', structure_indices='all'):148    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_id_from_atom as _get149    tmp_item = to_molsysmt_Topology(item)150    return _get(tmp_item, indices=indices, structure_indices=structure_indices)151def get_molecule_name_from_atom (item, indices='all', structure_indices='all'):152    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_name_from_atom as _get153    tmp_item = to_molsysmt_Topology(item)154    return _get(tmp_item, indices=indices, structure_indices=structure_indices)155def get_molecule_type_from_atom (item, indices='all', structure_indices='all'):156    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_type_from_atom as _get157    tmp_item = to_molsysmt_Topology(item)158    return _get(tmp_item, indices=indices, structure_indices=structure_indices)159def get_entity_index_from_atom (item, indices='all', structure_indices='all'):160    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_index_from_atom as _get161    tmp_item = to_molsysmt_Topology(item)162    return _get(tmp_item, indices=indices, structure_indices=structure_indices)163def get_entity_id_from_atom (item, indices='all', structure_indices='all'):164    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_id_from_atom as _get165    tmp_item = to_molsysmt_Topology(item)166    return _get(tmp_item, indices=indices, structure_indices=structure_indices)167def get_entity_name_from_atom (item, indices='all', structure_indices='all'):168    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_name_from_atom as _get169    tmp_item = to_molsysmt_Topology(item)170    return _get(tmp_item, indices=indices, structure_indices=structure_indices)171def get_entity_type_from_atom (item, indices='all', structure_indices='all'):172    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_type_from_atom as _get173    tmp_item = to_molsysmt_Topology(item)174    return _get(tmp_item, indices=indices, structure_indices=structure_indices)175def get_n_atoms_from_atom (item, indices='all', structure_indices='all'):176    from molsysmt.api_forms.api_molsysmt_Topology import get_n_atoms_from_atom as _get177    tmp_item = to_molsysmt_Topology(item)178    return _get(tmp_item, indices=indices, structure_indices=structure_indices)179def get_n_groups_from_atom (item, indices='all', structure_indices='all'):180    from molsysmt.api_forms.api_molsysmt_Topology import get_n_groups_from_atom as _get181    tmp_item = to_molsysmt_Topology(item)182    return _get(tmp_item, indices=indices, structure_indices=structure_indices)183def get_n_components_from_atom (item, indices='all', structure_indices='all'):184    from molsysmt.api_forms.api_molsysmt_Topology import get_n_components_from_atom as _get185    tmp_item = to_molsysmt_Topology(item)186    return _get(tmp_item, indices=indices, structure_indices=structure_indices)187def get_n_molecules_from_atom (item, indices='all', structure_indices='all'):188    from molsysmt.api_forms.api_molsysmt_Topology import get_n_molecules_from_atom as _get189    tmp_item = to_molsysmt_Topology(item)190    return _get(tmp_item, indices=indices, structure_indices=structure_indices)191def get_n_chains_from_atom (item, indices='all', structure_indices='all'):192    from molsysmt.api_forms.api_molsysmt_Topology import get_n_chains_from_atom as _get193    tmp_item = to_molsysmt_Topology(item)194    return _get(tmp_item, indices=indices, structure_indices=structure_indices)195def get_n_entities_from_atom (item, indices='all', structure_indices='all'):196    from molsysmt.api_forms.api_molsysmt_Topology import get_n_entities_from_atom as _get197    tmp_item = to_molsysmt_Topology(item)198    return _get(tmp_item, indices=indices, structure_indices=structure_indices)199def get_bonded_atoms_from_atom (item, indices='all', structure_indices='all'):200    from molsysmt.api_forms.api_molsysmt_Topology import get_bonded_atoms_from_atom as _get201    tmp_item = to_molsysmt_Topology(item)202    return _get(tmp_item, indices=indices, structure_indices=structure_indices)203def get_bonded_index_from_atom (item, indices='all', structure_indices='all'):204    from molsysmt.api_forms.api_molsysmt_Topology import get_bonded_index_from_atom as _get205    tmp_item = to_molsysmt_Topology(item)206    return _get(tmp_item, indices=indices, structure_indices=structure_indices)207def get_n_bonds_from_atom (item, indices='all', structure_indices='all'):208    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_atom as _get209    tmp_item = to_molsysmt_Topology(item)210    return _get(tmp_item, indices=indices, structure_indices=structure_indices)211def get_inner_bonded_atoms_from_atom (item, indices='all', structure_indices='all'):212    from molsysmt.api_forms.api_molsysmt_Topology import get_inner_bonded_atoms_from_atom as _get213    tmp_item = to_molsysmt_Topology(item)214    return _get(tmp_item, indices=indices, structure_indices=structure_indices)215def get_n_inner_bonds_from_atom (item, indices='all', structure_indices='all'):216    from molsysmt.api_forms.api_molsysmt_Topology import get_n_inner_bonds_from_atom as _get217    tmp_item = to_molsysmt_Topology(item)218    return _get(tmp_item, indices=indices, structure_indices=structure_indices)219def get_mass_from_atom(item, indices='all', structure_indices='all'):220    from molsysmt.api_forms.api_molsysmt_Topology import get_mass_from_atom as _get221    tmp_item = to_molsysmt_Topology(item)222    return _get(tmp_item, indices=indices, structure_indices=structure_indices)223def get_charge_from_atom(item, indices='all', structure_indices='all'):224    from molsysmt.api_forms.api_molsysmt_Topology import get_charge_from_atom as _get225    tmp_item = to_molsysmt_Topology(item)226    return _get(tmp_item, indices=indices, structure_indices=structure_indices)227def get_coordinates_from_atom(item, indices='all', structure_indices='all'):228    units = item.coordinates.unit229    coordinates = np.array(item.coordinates._value, dtype=float)230    if indices is not 'all':231        coordinates = coordinates[:, indices, :]232    if structure_indices is not 'all':233        coordinates = coordinates[structure_indices, :, :]234    coordinates = coordinates*units235    return coordinates236def get_frame_from_atom(item, indices='all', structure_indices='all'):237    step = get_step_from_system(item, structure_indices=structure_indices)238    time = get_time_from_system(item, structure_indices=structure_indices)239    coordinates = get_coordinates_from_atom(item, indices=indices, structure_indices=structure_indices)240    box = get_box_from_system(item, structure_indices=structure_indices)241    return step, time, coordinates, box242def get_n_structures_from_atom(item, indices='all', structure_indices='all'):243    return get_n_structures_from_system(item, structure_indices=structure_indices)244def get_form_from_atom(item, indices='all', structure_indices='all'):245    return form_name246## group247def get_index_from_group (item, indices='all', structure_indices='all'):248    return get_group_index_from_group (item, indices=indices, structure_indices=structure_indices)249def get_id_from_group (item, indices='all', structure_indices='all'):250    return get_group_id_from_group (item, indices=indices, structure_indices=structure_indices)251def get_name_from_group (item, indices='all', structure_indices='all'):252    return get_group_name_from_group (item, indices=indices, structure_indices=structure_indices)253def get_type_from_group (item, indices='all', structure_indices='all'):254    return get_group_type_from_group (item, indices=indices, structure_indices=structure_indices)255def get_atom_index_from_group(item, indices='all', structure_indices='all'):256    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_index_from_group as _get257    tmp_item = to_molsysmt_Topology(item)258    return _get(tmp_item, indices=indices, structure_indices=structure_indices)259def get_atom_id_from_group(item, indices='all', structure_indices='all'):260    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_id_from_group as _get261    tmp_item = to_molsysmt_Topology(item)262    return _get(tmp_item, indices=indices, structure_indices=structure_indices)263def get_atom_name_from_group(item, indices='all', structure_indices='all'):264    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_name_from_group as _get265    tmp_item = to_molsysmt_Topology(item)266    return _get(tmp_item, indices=indices, structure_indices=structure_indices)267def get_atom_type_from_group(item, indices='all', structure_indices='all'):268    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_type_from_group as _get269    tmp_item = to_molsysmt_Topology(item)270    return _get(tmp_item, indices=indices, structure_indices=structure_indices)271def get_group_index_from_group(item, indices='all', structure_indices='all'):272    from molsysmt.api_forms.api_molsysmt_Topology import get_group_index_from_group as _get273    tmp_item = to_molsysmt_Topology(item)274    return _get(tmp_item, indices=indices, structure_indices=structure_indices)275def get_group_id_from_group(item, indices='all', structure_indices='all'):276    from molsysmt.api_forms.api_molsysmt_Topology import get_group_id_from_group as _get277    tmp_item = to_molsysmt_Topology(item)278    return _get(tmp_item, indices=indices, structure_indices=structure_indices)279def get_group_name_from_group(item, indices='all', structure_indices='all'):280    from molsysmt.api_forms.api_molsysmt_Topology import get_group_name_from_group as _get281    tmp_item = to_molsysmt_Topology(item)282    return _get(tmp_item, indices=indices, structure_indices=structure_indices)283def get_group_type_from_group(item, indices='all', structure_indices='all'):284    from molsysmt.api_forms.api_molsysmt_Topology import get_group_type_from_group as _get285    tmp_item = to_molsysmt_Topology(item)286    return _get(tmp_item, indices=indices, structure_indices=structure_indices)287def get_component_name_from_group (item, indices='all', structure_indices='all'):288    from molsysmt.api_forms.api_molsysmt_Topology import get_component_name_from_group as _get289    tmp_item = to_molsysmt_Topology(item)290    return _get(tmp_item, indices=indices, structure_indices=structure_indices)291def get_component_index_from_group (item, indices='all', structure_indices='all'):292    from molsysmt.api_forms.api_molsysmt_Topology import get_component_index_from_group as _get293    tmp_item = to_molsysmt_Topology(item)294    return _get(tmp_item, indices=indices, structure_indices=structure_indices)295def get_component_id_from_group (item, indices='all', structure_indices='all'):296    from molsysmt.api_forms.api_molsysmt_Topology import get_component_id_from_group as _get297    tmp_item = to_molsysmt_Topology(item)298    return _get(tmp_item, indices=indices, structure_indices=structure_indices)299def get_component_type_from_group (item, indices='all', structure_indices='all'):300    from molsysmt.api_forms.api_molsysmt_Topology import get_component_type_from_group as _get301    tmp_item = to_molsysmt_Topology(item)302    return _get(tmp_item, indices=indices, structure_indices=structure_indices)303def get_chain_name_from_group (item, indices='all', structure_indices='all'):304    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_name_from_group as _get305    tmp_item = to_molsysmt_Topology(item)306    return _get(tmp_item, indices=indices, structure_indices=structure_indices)307def get_chain_index_from_group (item, indices='all', structure_indices='all'):308    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_index_from_group as _get309    tmp_item = to_molsysmt_Topology(item)310    return _get(tmp_item, indices=indices, structure_indices=structure_indices)311def get_chain_id_from_group (item, indices='all', structure_indices='all'):312    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_id_from_group as _get313    tmp_item = to_molsysmt_Topology(item)314    return _get(tmp_item, indices=indices, structure_indices=structure_indices)315def get_chain_type_from_group (item, indices='all', structure_indices='all'):316    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_type_from_group as _get317    tmp_item = to_molsysmt_Topology(item)318    return _get(tmp_item, indices=indices, structure_indices=structure_indices)319def get_molecule_index_from_group (item, indices='all', structure_indices='all'):320    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_index_from_group as _get321    tmp_item = to_molsysmt_Topology(item)322    return _get(tmp_item, indices=indices, structure_indices=structure_indices)323def get_molecule_id_from_group (item, indices='all', structure_indices='all'):324    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_id_from_group as _get325    tmp_item = to_molsysmt_Topology(item)326    return _get(tmp_item, indices=indices, structure_indices=structure_indices)327def get_molecule_name_from_group (item, indices='all', structure_indices='all'):328    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_name_from_group as _get329    tmp_item = to_molsysmt_Topology(item)330    return _get(tmp_item, indices=indices, structure_indices=structure_indices)331def get_molecule_type_from_group (item, indices='all', structure_indices='all'):332    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_type_from_group as _get333    tmp_item = to_molsysmt_Topology(item)334    return _get(tmp_item, indices=indices, structure_indices=structure_indices)335def get_entity_index_from_group (item, indices='all', structure_indices='all'):336    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_index_from_group as _get337    tmp_item = to_molsysmt_Topology(item)338    return _get(tmp_item, indices=indices, structure_indices=structure_indices)339def get_entity_id_from_group (item, indices='all', structure_indices='all'):340    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_id_from_group as _get341    tmp_item = to_molsysmt_Topology(item)342    return _get(tmp_item, indices=indices, structure_indices=structure_indices)343def get_entity_name_from_group (item, indices='all', structure_indices='all'):344    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_name_from_group as _get345    tmp_item = to_molsysmt_Topology(item)346    return _get(tmp_item, indices=indices, structure_indices=structure_indices)347def get_entity_type_from_group (item, indices='all', structure_indices='all'):348    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_type_from_group as _get349    tmp_item = to_molsysmt_Topology(item)350    return _get(tmp_item, indices=indices, structure_indices=structure_indices)351def get_n_atoms_from_group (item, indices='all', structure_indices='all'):352    from molsysmt.api_forms.api_molsysmt_Topology import get_n_atoms_from_group as _get353    tmp_item = to_molsysmt_Topology(item)354    return _get(tmp_item, indices=indices, structure_indices=structure_indices)355def get_n_groups_from_group (item, indices='all', structure_indices='all'):356    from molsysmt.api_forms.api_molsysmt_Topology import get_n_groups_from_group as _get357    tmp_item = to_molsysmt_Topology(item)358    return _get(tmp_item, indices=indices, structure_indices=structure_indices)359def get_n_components_from_group (item, indices='all', structure_indices='all'):360    from molsysmt.api_forms.api_molsysmt_Topology import get_n_components_from_group as _get361    tmp_item = to_molsysmt_Topology(item)362    return _get(tmp_item, indices=indices, structure_indices=structure_indices)363def get_n_molecules_from_group (item, indices='all', structure_indices='all'):364    from molsysmt.api_forms.api_molsysmt_Topology import get_n_molecules_from_group as _get365    tmp_item = to_molsysmt_Topology(item)366    return _get(tmp_item, indices=indices, structure_indices=structure_indices)367def get_n_chains_from_group (item, indices='all', structure_indices='all'):368    from molsysmt.api_forms.api_molsysmt_Topology import get_n_chains_from_group as _get369    tmp_item = to_molsysmt_Topology(item)370    return _get(tmp_item, indices=indices, structure_indices=structure_indices)371def get_n_entities_from_group (item, indices='all', structure_indices='all'):372    from molsysmt.api_forms.api_molsysmt_Topology import get_n_entities_from_group as _get373    tmp_item = to_molsysmt_Topology(item)374    return _get(tmp_item, indices=indices, structure_indices=structure_indices)375def get_n_bonds_from_group (item, indices='all', structure_indices='all'):376    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_group as _get377    tmp_item = to_molsysmt_Topology(item)378    return _get(tmp_item, indices=indices, structure_indices=structure_indices)379def get_mass_from_group(item, indices='all', structure_indices='all'):380    from molsysmt.api_forms.api_molsysmt_Topology import get_mass_from_group as _get381    tmp_item = to_molsysmt_Topology(item)382    return _get(tmp_item, indices=indices, structure_indices=structure_indices)383def get_charge_from_group(item, indices='all', structure_indices='all'):384    from molsysmt.api_forms.api_molsysmt_Topology import get_charge_from_group as _get385    tmp_item = to_molsysmt_Topology(item)386    return _get(tmp_item, indices=indices, structure_indices=structure_indices)387def get_coordinates_from_group(item, indices='all', structure_indices='all'):388    raise NotImplementedError389## component390def get_index_from_component (item, indices='all', structure_indices='all'):391    return get_component_index_from_component (item, indices=indices, structure_indices=structure_indices)392def get_id_from_component (item, indices='all', structure_indices='all'):393    return get_component_id_from_component (item, indices=indices, structure_indices=structure_indices)394def get_name_from_component (item, indices='all', structure_indices='all'):395    return get_component_name_from_component (item, indices=indices, structure_indices=structure_indices)396def get_type_from_component (item, indices='all', structure_indices='all'):397    return get_component_type_from_component (item, indices=indices, structure_indices=structure_indices)398def get_atom_index_from_component(item, indices='all', structure_indices='all'):399    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_index_from_component as _get400    tmp_item = to_molsysmt_Topology(item)401    return _get(tmp_item, indices=indices, structure_indices=structure_indices)402def get_atom_id_from_component(item, indices='all', structure_indices='all'):403    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_id_from_component as _get404    tmp_item = to_molsysmt_Topology(item)405    return _get(tmp_item, indices=indices, structure_indices=structure_indices)406def get_atom_name_from_component(item, indices='all', structure_indices='all'):407    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_name_from_component as _get408    tmp_item = to_molsysmt_Topology(item)409    return _get(tmp_item, indices=indices, structure_indices=structure_indices)410def get_atom_type_from_component(item, indices='all', structure_indices='all'):411    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_type_from_component as _get412    tmp_item = to_molsysmt_Topology(item)413    return _get(tmp_item, indices=indices, structure_indices=structure_indices)414def get_group_index_from_component(item, indices='all', structure_indices='all'):415    from molsysmt.api_forms.api_molsysmt_Topology import get_group_index_from_component as _get416    tmp_item = to_molsysmt_Topology(item)417    return _get(tmp_item, indices=indices, structure_indices=structure_indices)418def get_group_id_from_component(item, indices='all', structure_indices='all'):419    from molsysmt.api_forms.api_molsysmt_Topology import get_group_id_from_component as _get420    tmp_item = to_molsysmt_Topology(item)421    return _get(tmp_item, indices=indices, structure_indices=structure_indices)422def get_group_name_from_component(item, indices='all', structure_indices='all'):423    from molsysmt.api_forms.api_molsysmt_Topology import get_group_name_from_component as _get424    tmp_item = to_molsysmt_Topology(item)425    return _get(tmp_item, indices=indices, structure_indices=structure_indices)426def get_group_type_from_component(item, indices='all', structure_indices='all'):427    from molsysmt.api_forms.api_molsysmt_Topology import get_group_type_from_component as _get428    tmp_item = to_molsysmt_Topology(item)429    return _get(tmp_item, indices=indices, structure_indices=structure_indices)430def get_component_name_from_component (item, indices='all', structure_indices='all'):431    from molsysmt.api_forms.api_molsysmt_Topology import get_component_name_from_component as _get432    tmp_item = to_molsysmt_Topology(item)433    return _get(tmp_item, indices=indices, structure_indices=structure_indices)434def get_component_index_from_component (item, indices='all', structure_indices='all'):435    from molsysmt.api_forms.api_molsysmt_Topology import get_component_index_from_component as _get436    tmp_item = to_molsysmt_Topology(item)437    return _get(tmp_item, indices=indices, structure_indices=structure_indices)438def get_component_id_from_component (item, indices='all', structure_indices='all'):439    from molsysmt.api_forms.api_molsysmt_Topology import get_component_id_from_component as _get440    tmp_item = to_molsysmt_Topology(item)441    return _get(tmp_item, indices=indices, structure_indices=structure_indices)442def get_component_type_from_component (item, indices='all', structure_indices='all'):443    from molsysmt.api_forms.api_molsysmt_Topology import get_component_type_from_component as _get444    tmp_item = to_molsysmt_Topology(item)445    return _get(tmp_item, indices=indices, structure_indices=structure_indices)446def get_chain_name_from_component (item, indices='all', structure_indices='all'):447    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_name_from_component as _get448    tmp_item = to_molsysmt_Topology(item)449    return _get(tmp_item, indices=indices, structure_indices=structure_indices)450def get_chain_index_from_component (item, indices='all', structure_indices='all'):451    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_index_from_component as _get452    tmp_item = to_molsysmt_Topology(item)453    return _get(tmp_item, indices=indices, structure_indices=structure_indices)454def get_chain_id_from_component (item, indices='all', structure_indices='all'):455    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_id_from_component as _get456    tmp_item = to_molsysmt_Topology(item)457    return _get(tmp_item, indices=indices, structure_indices=structure_indices)458def get_chain_type_from_component (item, indices='all', structure_indices='all'):459    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_type_from_component as _get460    tmp_item = to_molsysmt_Topology(item)461    return _get(tmp_item, indices=indices, structure_indices=structure_indices)462def get_molecule_index_from_component (item, indices='all', structure_indices='all'):463    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_index_from_component as _get464    tmp_item = to_molsysmt_Topology(item)465    return _get(tmp_item, indices=indices, structure_indices=structure_indices)466def get_molecule_id_from_component (item, indices='all', structure_indices='all'):467    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_id_from_component as _get468    tmp_item = to_molsysmt_Topology(item)469    return _get(tmp_item, indices=indices, structure_indices=structure_indices)470def get_molecule_name_from_component (item, indices='all', structure_indices='all'):471    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_name_from_component as _get472    tmp_item = to_molsysmt_Topology(item)473    return _get(tmp_item, indices=indices, structure_indices=structure_indices)474def get_molecule_type_from_component (item, indices='all', structure_indices='all'):475    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_type_from_component as _get476    tmp_item = to_molsysmt_Topology(item)477    return _get(tmp_item, indices=indices, structure_indices=structure_indices)478def get_entity_index_from_component (item, indices='all', structure_indices='all'):479    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_index_from_component as _get480    tmp_item = to_molsysmt_Topology(item)481    return _get(tmp_item, indices=indices, structure_indices=structure_indices)482def get_entity_id_from_component (item, indices='all', structure_indices='all'):483    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_id_from_component as _get484    tmp_item = to_molsysmt_Topology(item)485    return _get(tmp_item, indices=indices, structure_indices=structure_indices)486def get_entity_name_from_component (item, indices='all', structure_indices='all'):487    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_name_from_component as _get488    tmp_item = to_molsysmt_Topology(item)489    return _get(tmp_item, indices=indices, structure_indices=structure_indices)490def get_entity_type_from_component (item, indices='all', structure_indices='all'):491    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_type_from_component as _get492    tmp_item = to_molsysmt_Topology(item)493    return _get(tmp_item, indices=indices, structure_indices=structure_indices)494def get_n_atoms_from_component (item, indices='all', structure_indices='all'):495    from molsysmt.api_forms.api_molsysmt_Topology import get_n_atoms_from_component as _get496    tmp_item = to_molsysmt_Topology(item)497    return _get(tmp_item, indices=indices, structure_indices=structure_indices)498def get_n_groups_from_component (item, indices='all', structure_indices='all'):499    from molsysmt.api_forms.api_molsysmt_Topology import get_n_groups_from_component as _get500    tmp_item = to_molsysmt_Topology(item)501    return _get(tmp_item, indices=indices, structure_indices=structure_indices)502def get_n_components_from_component (item, indices='all', structure_indices='all'):503    from molsysmt.api_forms.api_molsysmt_Topology import get_n_components_from_component as _get504    tmp_item = to_molsysmt_Topology(item)505    return _get(tmp_item, indices=indices, structure_indices=structure_indices)506def get_n_molecules_from_component (item, indices='all', structure_indices='all'):507    from molsysmt.api_forms.api_molsysmt_Topology import get_n_molecules_from_component as _get508    tmp_item = to_molsysmt_Topology(item)509    return _get(tmp_item, indices=indices, structure_indices=structure_indices)510def get_n_chains_from_component (item, indices='all', structure_indices='all'):511    from molsysmt.api_forms.api_molsysmt_Topology import get_n_chains_from_component as _get512    tmp_item = to_molsysmt_Topology(item)513    return _get(tmp_item, indices=indices, structure_indices=structure_indices)514def get_n_entities_from_component (item, indices='all', structure_indices='all'):515    from molsysmt.api_forms.api_molsysmt_Topology import get_n_entities_from_component as _get516    tmp_item = to_molsysmt_Topology(item)517    return _get(tmp_item, indices=indices, structure_indices=structure_indices)518def get_n_bonds_from_component (item, indices='all', structure_indices='all'):519    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_component as _get520    tmp_item = to_molsysmt_Topology(item)521    return _get(tmp_item, indices=indices, structure_indices=structure_indices)522def get_mass_from_component(item, indices='all', structure_indices='all'):523    from molsysmt.api_forms.api_molsysmt_Topology import get_mass_from_component as _get524    tmp_item = to_molsysmt_Topology(item)525    return _get(tmp_item, indices=indices, structure_indices=structure_indices)526def get_charge_from_component(item, indices='all', structure_indices='all'):527    from molsysmt.api_forms.api_molsysmt_Topology import get_charge_from_component as _get528    tmp_item = to_molsysmt_Topology(item)529    return _get(tmp_item, indices=indices, structure_indices=structure_indices)530def get_coordinates_from_component(item, indices='all', structure_indices='all'):531    raise NotImplementedError532## molecule533def get_index_from_molecule (item, indices='all', structure_indices='all'):534    return get_molecule_index_from_molecule (item, indices=indices, structure_indices=structure_indices)535def get_id_from_molecule (item, indices='all', structure_indices='all'):536    return get_molecule_id_from_molecule (item, indices=indices, structure_indices=structure_indices)537def get_name_from_molecule (item, indices='all', structure_indices='all'):538    return get_molecule_name_from_molecule (item, indices=indices, structure_indices=structure_indices)539def get_type_from_molecule (item, indices='all', structure_indices='all'):540    return get_molecule_type_from_molecule (item, indices=indices, structure_indices=structure_indices)541def get_atom_index_from_molecule(item, indices='all', structure_indices='all'):542    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_index_from_molecule as _get543    tmp_item = to_molsysmt_Topology(item)544    return _get(tmp_item, indices=indices, structure_indices=structure_indices)545def get_atom_id_from_molecule(item, indices='all', structure_indices='all'):546    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_id_from_molecule as _get547    tmp_item = to_molsysmt_Topology(item)548    return _get(tmp_item, indices=indices, structure_indices=structure_indices)549def get_atom_name_from_molecule(item, indices='all', structure_indices='all'):550    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_name_from_molecule as _get551    tmp_item = to_molsysmt_Topology(item)552    return _get(tmp_item, indices=indices, structure_indices=structure_indices)553def get_atom_type_from_molecule(item, indices='all', structure_indices='all'):554    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_type_from_molecule as _get555    tmp_item = to_molsysmt_Topology(item)556    return _get(tmp_item, indices=indices, structure_indices=structure_indices)557def get_group_index_from_molecule(item, indices='all', structure_indices='all'):558    from molsysmt.api_forms.api_molsysmt_Topology import get_group_index_from_molecule as _get559    tmp_item = to_molsysmt_Topology(item)560    return _get(tmp_item, indices=indices, structure_indices=structure_indices)561def get_group_id_from_molecule(item, indices='all', structure_indices='all'):562    from molsysmt.api_forms.api_molsysmt_Topology import get_group_id_from_molecule as _get563    tmp_item = to_molsysmt_Topology(item)564    return _get(tmp_item, indices=indices, structure_indices=structure_indices)565def get_group_name_from_molecule(item, indices='all', structure_indices='all'):566    from molsysmt.api_forms.api_molsysmt_Topology import get_group_name_from_molecule as _get567    tmp_item = to_molsysmt_Topology(item)568    return _get(tmp_item, indices=indices, structure_indices=structure_indices)569def get_group_type_from_molecule(item, indices='all', structure_indices='all'):570    from molsysmt.api_forms.api_molsysmt_Topology import get_group_type_from_molecule as _get571    tmp_item = to_molsysmt_Topology(item)572    return _get(tmp_item, indices=indices, structure_indices=structure_indices)573def get_component_name_from_molecule (item, indices='all', structure_indices='all'):574    from molsysmt.api_forms.api_molsysmt_Topology import get_component_name_from_molecule as _get575    tmp_item = to_molsysmt_Topology(item)576    return _get(tmp_item, indices=indices, structure_indices=structure_indices)577def get_component_index_from_molecule (item, indices='all', structure_indices='all'):578    from molsysmt.api_forms.api_molsysmt_Topology import get_component_index_from_molecule as _get579    tmp_item = to_molsysmt_Topology(item)580    return _get(tmp_item, indices=indices, structure_indices=structure_indices)581def get_component_id_from_molecule (item, indices='all', structure_indices='all'):582    from molsysmt.api_forms.api_molsysmt_Topology import get_component_id_from_molecule as _get583    tmp_item = to_molsysmt_Topology(item)584    return _get(tmp_item, indices=indices, structure_indices=structure_indices)585def get_component_type_from_molecule (item, indices='all', structure_indices='all'):586    from molsysmt.api_forms.api_molsysmt_Topology import get_component_type_from_molecule as _get587    tmp_item = to_molsysmt_Topology(item)588    return _get(tmp_item, indices=indices, structure_indices=structure_indices)589def get_chain_name_from_molecule (item, indices='all', structure_indices='all'):590    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_name_from_molecule as _get591    tmp_item = to_molsysmt_Topology(item)592    return _get(tmp_item, indices=indices, structure_indices=structure_indices)593def get_chain_index_from_molecule (item, indices='all', structure_indices='all'):594    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_index_from_molecule as _get595    tmp_item = to_molsysmt_Topology(item)596    return _get(tmp_item, indices=indices, structure_indices=structure_indices)597def get_chain_id_from_molecule (item, indices='all', structure_indices='all'):598    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_id_from_molecule as _get599    tmp_item = to_molsysmt_Topology(item)600    return _get(tmp_item, indices=indices, structure_indices=structure_indices)601def get_chain_type_from_molecule (item, indices='all', structure_indices='all'):602    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_type_from_molecule as _get603    tmp_item = to_molsysmt_Topology(item)604    return _get(tmp_item, indices=indices, structure_indices=structure_indices)605def get_molecule_index_from_molecule (item, indices='all', structure_indices='all'):606    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_index_from_molecule as _get607    tmp_item = to_molsysmt_Topology(item)608    return _get(tmp_item, indices=indices, structure_indices=structure_indices)609def get_molecule_id_from_molecule (item, indices='all', structure_indices='all'):610    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_id_from_molecule as _get611    tmp_item = to_molsysmt_Topology(item)612    return _get(tmp_item, indices=indices, structure_indices=structure_indices)613def get_molecule_name_from_molecule (item, indices='all', structure_indices='all'):614    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_name_from_molecule as _get615    tmp_item = to_molsysmt_Topology(item)616    return _get(tmp_item, indices=indices, structure_indices=structure_indices)617def get_molecule_type_from_molecule (item, indices='all', structure_indices='all'):618    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_type_from_molecule as _get619    tmp_item = to_molsysmt_Topology(item)620    return _get(tmp_item, indices=indices, structure_indices=structure_indices)621def get_entity_index_from_molecule (item, indices='all', structure_indices='all'):622    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_index_from_molecule as _get623    tmp_item = to_molsysmt_Topology(item)624    return _get(tmp_item, indices=indices, structure_indices=structure_indices)625def get_entity_id_from_molecule (item, indices='all', structure_indices='all'):626    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_id_from_molecule as _get627    tmp_item = to_molsysmt_Topology(item)628    return _get(tmp_item, indices=indices, structure_indices=structure_indices)629def get_entity_name_from_molecule (item, indices='all', structure_indices='all'):630    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_name_from_molecule as _get631    tmp_item = to_molsysmt_Topology(item)632    return _get(tmp_item, indices=indices, structure_indices=structure_indices)633def get_entity_type_from_molecule (item, indices='all', structure_indices='all'):634    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_type_from_molecule as _get635    tmp_item = to_molsysmt_Topology(item)636    return _get(tmp_item, indices=indices, structure_indices=structure_indices)637def get_n_atoms_from_molecule (item, indices='all', structure_indices='all'):638    from molsysmt.api_forms.api_molsysmt_Topology import get_n_atoms_from_molecule as _get639    tmp_item = to_molsysmt_Topology(item)640    return _get(tmp_item, indices=indices, structure_indices=structure_indices)641def get_n_groups_from_molecule (item, indices='all', structure_indices='all'):642    from molsysmt.api_forms.api_molsysmt_Topology import get_n_groups_from_molecule as _get643    tmp_item = to_molsysmt_Topology(item)644    return _get(tmp_item, indices=indices, structure_indices=structure_indices)645def get_n_components_from_molecule (item, indices='all', structure_indices='all'):646    from molsysmt.api_forms.api_molsysmt_Topology import get_n_components_from_molecule as _get647    tmp_item = to_molsysmt_Topology(item)648    return _get(tmp_item, indices=indices, structure_indices=structure_indices)649def get_n_molecules_from_molecule (item, indices='all', structure_indices='all'):650    from molsysmt.api_forms.api_molsysmt_Topology import get_n_molecules_from_molecule as _get651    tmp_item = to_molsysmt_Topology(item)652    return _get(tmp_item, indices=indices, structure_indices=structure_indices)653def get_n_chains_from_molecule (item, indices='all', structure_indices='all'):654    from molsysmt.api_forms.api_molsysmt_Topology import get_n_chains_from_molecule as _get655    tmp_item = to_molsysmt_Topology(item)656    return _get(tmp_item, indices=indices, structure_indices=structure_indices)657def get_n_entities_from_molecule (item, indices='all', structure_indices='all'):658    from molsysmt.api_forms.api_molsysmt_Topology import get_n_entities_from_molecule as _get659    tmp_item = to_molsysmt_Topology(item)660    return _get(tmp_item, indices=indices, structure_indices=structure_indices)661def get_n_bonds_from_molecule (item, indices='all', structure_indices='all'):662    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_molecule as _get663    tmp_item = to_molsysmt_Topology(item)664    return _get(tmp_item, indices=indices, structure_indices=structure_indices)665def get_mass_from_molecule(item, indices='all', structure_indices='all'):666    from molsysmt.api_forms.api_molsysmt_Topology import get_mass_from_molecule as _get667    tmp_item = to_molsysmt_Topology(item)668    return _get(tmp_item, indices=indices, structure_indices=structure_indices)669def get_charge_from_molecule(item, indices='all', structure_indices='all'):670    from molsysmt.api_forms.api_molsysmt_Topology import get_charge_from_molecule as _get671    tmp_item = to_molsysmt_Topology(item)672    return _get(tmp_item, indices=indices, structure_indices=structure_indices)673def get_coordinates_from_molecule(item, indices='all', structure_indices='all'):674    raise NotImplementedError675## chain676def get_index_from_chain (item, indices='all', structure_indices='all'):677    return get_chain_index_from_chain (item, indices=indices, structure_indices=structure_indices)678def get_id_from_chain (item, indices='all', structure_indices='all'):679    return get_chain_id_from_chain (item, indices=indices, structure_indices=structure_indices)680def get_name_from_chain (item, indices='all', structure_indices='all'):681    return get_chain_name_from_chain (item, indices=indices, structure_indices=structure_indices)682def get_type_from_chain (item, indices='all', structure_indices='all'):683    return get_chain_type_from_chain (item, indices=indices, structure_indices=structure_indices)684def get_atom_index_from_chain(item, indices='all', structure_indices='all'):685    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_index_from_chain as _get686    tmp_item = to_molsysmt_Topology(item)687    return _get(tmp_item, indices=indices, structure_indices=structure_indices)688def get_atom_id_from_chain(item, indices='all', structure_indices='all'):689    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_id_from_chain as _get690    tmp_item = to_molsysmt_Topology(item)691    return _get(tmp_item, indices=indices, structure_indices=structure_indices)692def get_atom_name_from_chain(item, indices='all', structure_indices='all'):693    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_name_from_chain as _get694    tmp_item = to_molsysmt_Topology(item)695    return _get(tmp_item, indices=indices, structure_indices=structure_indices)696def get_atom_type_from_chain(item, indices='all', structure_indices='all'):697    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_type_from_chain as _get698    tmp_item = to_molsysmt_Topology(item)699    return _get(tmp_item, indices=indices, structure_indices=structure_indices)700def get_group_index_from_chain(item, indices='all', structure_indices='all'):701    from molsysmt.api_forms.api_molsysmt_Topology import get_group_index_from_chain as _get702    tmp_item = to_molsysmt_Topology(item)703    return _get(tmp_item, indices=indices, structure_indices=structure_indices)704def get_group_id_from_chain(item, indices='all', structure_indices='all'):705    from molsysmt.api_forms.api_molsysmt_Topology import get_group_id_from_chain as _get706    tmp_item = to_molsysmt_Topology(item)707    return _get(tmp_item, indices=indices, structure_indices=structure_indices)708def get_group_name_from_chain(item, indices='all', structure_indices='all'):709    from molsysmt.api_forms.api_molsysmt_Topology import get_group_name_from_chain as _get710    tmp_item = to_molsysmt_Topology(item)711    return _get(tmp_item, indices=indices, structure_indices=structure_indices)712def get_group_type_from_chain(item, indices='all', structure_indices='all'):713    from molsysmt.api_forms.api_molsysmt_Topology import get_group_type_from_chain as _get714    tmp_item = to_molsysmt_Topology(item)715    return _get(tmp_item, indices=indices, structure_indices=structure_indices)716def get_component_name_from_chain (item, indices='all', structure_indices='all'):717    from molsysmt.api_forms.api_molsysmt_Topology import get_component_name_from_chain as _get718    tmp_item = to_molsysmt_Topology(item)719    return _get(tmp_item, indices=indices, structure_indices=structure_indices)720def get_component_index_from_chain (item, indices='all', structure_indices='all'):721    from molsysmt.api_forms.api_molsysmt_Topology import get_component_index_from_chain as _get722    tmp_item = to_molsysmt_Topology(item)723    return _get(tmp_item, indices=indices, structure_indices=structure_indices)724def get_component_id_from_chain (item, indices='all', structure_indices='all'):725    from molsysmt.api_forms.api_molsysmt_Topology import get_component_id_from_chain as _get726    tmp_item = to_molsysmt_Topology(item)727    return _get(tmp_item, indices=indices, structure_indices=structure_indices)728def get_component_type_from_chain (item, indices='all', structure_indices='all'):729    from molsysmt.api_forms.api_molsysmt_Topology import get_component_type_from_chain as _get730    tmp_item = to_molsysmt_Topology(item)731    return _get(tmp_item, indices=indices, structure_indices=structure_indices)732def get_chain_name_from_chain (item, indices='all', structure_indices='all'):733    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_name_from_chain as _get734    tmp_item = to_molsysmt_Topology(item)735    return _get(tmp_item, indices=indices, structure_indices=structure_indices)736def get_chain_index_from_chain (item, indices='all', structure_indices='all'):737    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_index_from_chain as _get738    tmp_item = to_molsysmt_Topology(item)739    return _get(tmp_item, indices=indices, structure_indices=structure_indices)740def get_chain_id_from_chain (item, indices='all', structure_indices='all'):741    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_id_from_chain as _get742    tmp_item = to_molsysmt_Topology(item)743    return _get(tmp_item, indices=indices, structure_indices=structure_indices)744def get_chain_type_from_chain (item, indices='all', structure_indices='all'):745    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_type_from_chain as _get746    tmp_item = to_molsysmt_Topology(item)747    return _get(tmp_item, indices=indices, structure_indices=structure_indices)748def get_molecule_index_from_chain (item, indices='all', structure_indices='all'):749    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_index_from_chain as _get750    tmp_item = to_molsysmt_Topology(item)751    return _get(tmp_item, indices=indices, structure_indices=structure_indices)752def get_molecule_id_from_chain (item, indices='all', structure_indices='all'):753    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_id_from_chain as _get754    tmp_item = to_molsysmt_Topology(item)755    return _get(tmp_item, indices=indices, structure_indices=structure_indices)756def get_molecule_name_from_chain (item, indices='all', structure_indices='all'):757    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_name_from_chain as _get758    tmp_item = to_molsysmt_Topology(item)759    return _get(tmp_item, indices=indices, structure_indices=structure_indices)760def get_molecule_type_from_chain (item, indices='all', structure_indices='all'):761    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_type_from_chain as _get762    tmp_item = to_molsysmt_Topology(item)763    return _get(tmp_item, indices=indices, structure_indices=structure_indices)764def get_entity_index_from_chain (item, indices='all', structure_indices='all'):765    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_index_from_chain as _get766    tmp_item = to_molsysmt_Topology(item)767    return _get(tmp_item, indices=indices, structure_indices=structure_indices)768def get_entity_id_from_chain (item, indices='all', structure_indices='all'):769    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_id_from_chain as _get770    tmp_item = to_molsysmt_Topology(item)771    return _get(tmp_item, indices=indices, structure_indices=structure_indices)772def get_entity_name_from_chain (item, indices='all', structure_indices='all'):773    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_name_from_chain as _get774    tmp_item = to_molsysmt_Topology(item)775    return _get(tmp_item, indices=indices, structure_indices=structure_indices)776def get_entity_type_from_chain (item, indices='all', structure_indices='all'):777    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_type_from_chain as _get778    tmp_item = to_molsysmt_Topology(item)779    return _get(tmp_item, indices=indices, structure_indices=structure_indices)780def get_n_atoms_from_chain (item, indices='all', structure_indices='all'):781    from molsysmt.api_forms.api_molsysmt_Topology import get_n_atoms_from_chain as _get782    tmp_item = to_molsysmt_Topology(item)783    return _get(tmp_item, indices=indices, structure_indices=structure_indices)784def get_n_groups_from_chain (item, indices='all', structure_indices='all'):785    from molsysmt.api_forms.api_molsysmt_Topology import get_n_groups_from_chain as _get786    tmp_item = to_molsysmt_Topology(item)787    return _get(tmp_item, indices=indices, structure_indices=structure_indices)788def get_n_components_from_chain (item, indices='all', structure_indices='all'):789    from molsysmt.api_forms.api_molsysmt_Topology import get_n_components_from_chain as _get790    tmp_item = to_molsysmt_Topology(item)791    return _get(tmp_item, indices=indices, structure_indices=structure_indices)792def get_n_molecules_from_chain (item, indices='all', structure_indices='all'):793    from molsysmt.api_forms.api_molsysmt_Topology import get_n_molecules_from_chain as _get794    tmp_item = to_molsysmt_Topology(item)795    return _get(tmp_item, indices=indices, structure_indices=structure_indices)796def get_n_chains_from_chain (item, indices='all', structure_indices='all'):797    from molsysmt.api_forms.api_molsysmt_Topology import get_n_chains_from_chain as _get798    tmp_item = to_molsysmt_Topology(item)799    return _get(tmp_item, indices=indices, structure_indices=structure_indices)800def get_n_entities_from_chain (item, indices='all', structure_indices='all'):801    from molsysmt.api_forms.api_molsysmt_Topology import get_n_entities_from_chain as _get802    tmp_item = to_molsysmt_Topology(item)803    return _get(tmp_item, indices=indices, structure_indices=structure_indices)804def get_n_bonds_from_chain (item, indices='all', structure_indices='all'):805    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_chain as _get806    tmp_item = to_molsysmt_Topology(item)807    return _get(tmp_item, indices=indices, structure_indices=structure_indices)808def get_mass_from_chain(item, indices='all', structure_indices='all'):809    from molsysmt.api_forms.api_molsysmt_Topology import get_mass_from_chain as _get810    tmp_item = to_molsysmt_Topology(item)811    return _get(tmp_item, indices=indices, structure_indices=structure_indices)812def get_charge_from_chain(item, indices='all', structure_indices='all'):813    from molsysmt.api_forms.api_molsysmt_Topology import get_charge_from_chain as _get814    tmp_item = to_molsysmt_Topology(item)815    return _get(tmp_item, indices=indices, structure_indices=structure_indices)816def get_coordinates_from_chain(item, indices='all', structure_indices='all'):817    raise NotImplementedError818## entity819def get_index_from_entity (item, indices='all', structure_indices='all'):820    return get_entity_index_from_entity (item, indices=indices, structure_indices=structure_indices)821def get_id_from_entity (item, indices='all', structure_indices='all'):822    return get_entity_id_from_entity (item, indices=indices, structure_indices=structure_indices)823def get_name_from_entity (item, indices='all', structure_indices='all'):824    return get_entity_name_from_entity (item, indices=indices, structure_indices=structure_indices)825def get_type_from_entity (item, indices='all', structure_indices='all'):826    return get_entity_type_from_entity (item, indices=indices, structure_indices=structure_indices)827def get_atom_index_from_entity(item, indices='all', structure_indices='all'):828    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_index_from_entity as _get829    tmp_item = to_molsysmt_Topology(item)830    return _get(tmp_item, indices=indices, structure_indices=structure_indices)831def get_atom_id_from_entity(item, indices='all', structure_indices='all'):832    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_id_from_entity as _get833    tmp_item = to_molsysmt_Topology(item)834    return _get(tmp_item, indices=indices, structure_indices=structure_indices)835def get_atom_name_from_entity(item, indices='all', structure_indices='all'):836    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_name_from_entity as _get837    tmp_item = to_molsysmt_Topology(item)838    return _get(tmp_item, indices=indices, structure_indices=structure_indices)839def get_atom_type_from_entity(item, indices='all', structure_indices='all'):840    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_type_from_entity as _get841    tmp_item = to_molsysmt_Topology(item)842    return _get(tmp_item, indices=indices, structure_indices=structure_indices)843def get_group_index_from_entity(item, indices='all', structure_indices='all'):844    from molsysmt.api_forms.api_molsysmt_Topology import get_group_index_from_entity as _get845    tmp_item = to_molsysmt_Topology(item)846    return _get(tmp_item, indices=indices, structure_indices=structure_indices)847def get_group_id_from_entity(item, indices='all', structure_indices='all'):848    from molsysmt.api_forms.api_molsysmt_Topology import get_group_id_from_entity as _get849    tmp_item = to_molsysmt_Topology(item)850    return _get(tmp_item, indices=indices, structure_indices=structure_indices)851def get_group_name_from_entity(item, indices='all', structure_indices='all'):852    from molsysmt.api_forms.api_molsysmt_Topology import get_group_name_from_entity as _get853    tmp_item = to_molsysmt_Topology(item)854    return _get(tmp_item, indices=indices, structure_indices=structure_indices)855def get_group_type_from_entity(item, indices='all', structure_indices='all'):856    from molsysmt.api_forms.api_molsysmt_Topology import get_group_type_from_entity as _get857    tmp_item = to_molsysmt_Topology(item)858    return _get(tmp_item, indices=indices, structure_indices=structure_indices)859def get_component_name_from_entity (item, indices='all', structure_indices='all'):860    from molsysmt.api_forms.api_molsysmt_Topology import get_component_name_from_entity as _get861    tmp_item = to_molsysmt_Topology(item)862    return _get(tmp_item, indices=indices, structure_indices=structure_indices)863def get_component_index_from_entity (item, indices='all', structure_indices='all'):864    from molsysmt.api_forms.api_molsysmt_Topology import get_component_index_from_entity as _get865    tmp_item = to_molsysmt_Topology(item)866    return _get(tmp_item, indices=indices, structure_indices=structure_indices)867def get_component_id_from_entity (item, indices='all', structure_indices='all'):868    from molsysmt.api_forms.api_molsysmt_Topology import get_component_id_from_entity as _get869    tmp_item = to_molsysmt_Topology(item)870    return _get(tmp_item, indices=indices, structure_indices=structure_indices)871def get_component_type_from_entity (item, indices='all', structure_indices='all'):872    from molsysmt.api_forms.api_molsysmt_Topology import get_component_type_from_entity as _get873    tmp_item = to_molsysmt_Topology(item)874    return _get(tmp_item, indices=indices, structure_indices=structure_indices)875def get_chain_name_from_entity (item, indices='all', structure_indices='all'):876    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_name_from_entity as _get877    tmp_item = to_molsysmt_Topology(item)878    return _get(tmp_item, indices=indices, structure_indices=structure_indices)879def get_chain_index_from_entity (item, indices='all', structure_indices='all'):880    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_index_from_entity as _get881    tmp_item = to_molsysmt_Topology(item)882    return _get(tmp_item, indices=indices, structure_indices=structure_indices)883def get_chain_id_from_entity (item, indices='all', structure_indices='all'):884    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_id_from_entity as _get885    tmp_item = to_molsysmt_Topology(item)886    return _get(tmp_item, indices=indices, structure_indices=structure_indices)887def get_chain_type_from_entity (item, indices='all', structure_indices='all'):888    from molsysmt.api_forms.api_molsysmt_Topology import get_chain_type_from_entity as _get889    tmp_item = to_molsysmt_Topology(item)890    return _get(tmp_item, indices=indices, structure_indices=structure_indices)891def get_molecule_index_from_entity (item, indices='all', structure_indices='all'):892    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_index_from_entity as _get893    tmp_item = to_molsysmt_Topology(item)894    return _get(tmp_item, indices=indices, structure_indices=structure_indices)895def get_molecule_id_from_entity (item, indices='all', structure_indices='all'):896    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_id_from_entity as _get897    tmp_item = to_molsysmt_Topology(item)898    return _get(tmp_item, indices=indices, structure_indices=structure_indices)899def get_molecule_name_from_entity (item, indices='all', structure_indices='all'):900    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_name_from_entity as _get901    tmp_item = to_molsysmt_Topology(item)902    return _get(tmp_item, indices=indices, structure_indices=structure_indices)903def get_molecule_type_from_entity (item, indices='all', structure_indices='all'):904    from molsysmt.api_forms.api_molsysmt_Topology import get_molecule_type_from_entity as _get905    tmp_item = to_molsysmt_Topology(item)906    return _get(tmp_item, indices=indices, structure_indices=structure_indices)907def get_entity_index_from_entity (item, indices='all', structure_indices='all'):908    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_index_from_entity as _get909    tmp_item = to_molsysmt_Topology(item)910    return _get(tmp_item, indices=indices, structure_indices=structure_indices)911def get_entity_id_from_entity (item, indices='all', structure_indices='all'):912    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_id_from_entity as _get913    tmp_item = to_molsysmt_Topology(item)914    return _get(tmp_item, indices=indices, structure_indices=structure_indices)915def get_entity_name_from_entity (item, indices='all', structure_indices='all'):916    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_name_from_entity as _get917    tmp_item = to_molsysmt_Topology(item)918    return _get(tmp_item, indices=indices, structure_indices=structure_indices)919def get_entity_type_from_entity (item, indices='all', structure_indices='all'):920    from molsysmt.api_forms.api_molsysmt_Topology import get_entity_type_from_entity as _get921    tmp_item = to_molsysmt_Topology(item)922    return _get(tmp_item, indices=indices, structure_indices=structure_indices)923def get_n_atoms_from_entity (item, indices='all', structure_indices='all'):924    from molsysmt.api_forms.api_molsysmt_Topology import get_n_atoms_from_entity as _get925    tmp_item = to_molsysmt_Topology(item)926    return _get(tmp_item, indices=indices, structure_indices=structure_indices)927def get_n_groups_from_entity (item, indices='all', structure_indices='all'):928    from molsysmt.api_forms.api_molsysmt_Topology import get_n_groups_from_entity as _get929    tmp_item = to_molsysmt_Topology(item)930    return _get(tmp_item, indices=indices, structure_indices=structure_indices)931def get_n_components_from_entity (item, indices='all', structure_indices='all'):932    from molsysmt.api_forms.api_molsysmt_Topology import get_n_components_from_entity as _get933    tmp_item = to_molsysmt_Topology(item)934    return _get(tmp_item, indices=indices, structure_indices=structure_indices)935def get_n_molecules_from_entity (item, indices='all', structure_indices='all'):936    from molsysmt.api_forms.api_molsysmt_Topology import get_n_molecules_from_entity as _get937    tmp_item = to_molsysmt_Topology(item)938    return _get(tmp_item, indices=indices, structure_indices=structure_indices)939def get_n_chains_from_entity (item, indices='all', structure_indices='all'):940    from molsysmt.api_forms.api_molsysmt_Topology import get_n_chains_from_entity as _get941    tmp_item = to_molsysmt_Topology(item)942    return _get(tmp_item, indices=indices, structure_indices=structure_indices)943def get_n_entities_from_entity (item, indices='all', structure_indices='all'):944    from molsysmt.api_forms.api_molsysmt_Topology import get_n_entities_from_entity as _get945    tmp_item = to_molsysmt_Topology(item)946    return _get(tmp_item, indices=indices, structure_indices=structure_indices)947def get_n_bonds_from_entity (item, indices='all', structure_indices='all'):948    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_entity as _get949    tmp_item = to_molsysmt_Topology(item)950    return _get(tmp_item, indices=indices, structure_indices=structure_indices)951def get_mass_from_entity(item, indices='all', structure_indices='all'):952    from molsysmt.api_forms.api_molsysmt_Topology import get_mass_from_entity as _get953    tmp_item = to_molsysmt_Topology(item)954    return _get(tmp_item, indices=indices, structure_indices=structure_indices)955def get_charge_from_entity(item, indices='all', structure_indices='all'):956    from molsysmt.api_forms.api_molsysmt_Topology import get_charge_from_entity as _get957    tmp_item = to_molsysmt_Topology(item)958    return _get(tmp_item, indices=indices, structure_indices=structure_indices)959def get_coordinates_from_entity(item, indices='all', structure_indices='all'):960    raise NotImplementedError961## system962def get_bonded_atoms_from_system(item, indices='all', structure_indices='all'):963    from molsysmt.api_forms.api_molsysmt_Topology import get_bonded_atoms_from_system as _get964    tmp_item = to_molsysmt_Topology(item)965    return _get(tmp_item, indices=indices, structure_indices=structure_indices)966def get_n_atoms_from_system(item, indices='all', structure_indices='all'):967    from molsysmt.api_forms.api_molsysmt_Topology import get_n_atoms_from_system as _get968    tmp_item = to_molsysmt_Topology(item)969    return _get(tmp_item, indices=indices, structure_indices=structure_indices)970def get_n_groups_from_system(item, indices='all', structure_indices='all'):971    from molsysmt.api_forms.api_molsysmt_Topology import get_n_groups_from_system as _get972    tmp_item = to_molsysmt_Topology(item)973    return _get(tmp_item, indices=indices, structure_indices=structure_indices)974def get_n_components_from_system(item, indices='all', structure_indices='all'):975    from molsysmt.api_forms.api_molsysmt_Topology import get_n_components_from_system as _get976    tmp_item = to_molsysmt_Topology(item)977    return _get(tmp_item, indices=indices, structure_indices=structure_indices)978def get_n_chains_from_system(item, indices='all', structure_indices='all'):979    from molsysmt.api_forms.api_molsysmt_Topology import get_n_chains_from_system as _get980    tmp_item = to_molsysmt_Topology(item)981    return _get(tmp_item, indices=indices, structure_indices=structure_indices)982def get_n_molecules_from_system(item, indices='all', structure_indices='all'):983    from molsysmt.api_forms.api_molsysmt_Topology import get_n_molecules_from_system as _get984    tmp_item = to_molsysmt_Topology(item)985    return _get(tmp_item, indices=indices, structure_indices=structure_indices)986def get_n_entities_from_system(item, indices='all', structure_indices='all'):987    from molsysmt.api_forms.api_molsysmt_Topology import get_n_entities_from_system as _get988    tmp_item = to_molsysmt_Topology(item)989    return _get(tmp_item, indices=indices, structure_indices=structure_indices)990def get_n_bonds_from_system(item, indices='all', structure_indices='all'):991    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_system as _get992    tmp_item = to_molsysmt_Topology(item)993    return _get(tmp_item, indices=indices, structure_indices=structure_indices)994def get_n_aminoacids_from_system (item, indices='all', structure_indices='all'):995    from molsysmt.api_forms.api_molsysmt_Topology import get_n_aminoacids_from_system as _get996    tmp_item = to_molsysmt_Topology(item)997    return _get(tmp_item, indices=indices, structure_indices=structure_indices)998def get_n_nucleotides_from_system (item, indices='all', structure_indices='all'):999    from molsysmt.api_forms.api_molsysmt_Topology import get_n_nucleotides_from_system as _get1000    tmp_item = to_molsysmt_Topology(item)1001    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1002def get_n_ions_from_system (item, indices='all', structure_indices='all'):1003    from molsysmt.api_forms.api_molsysmt_Topology import get_n_ions_from_system as _get1004    tmp_item = to_molsysmt_Topology(item)1005    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1006def get_n_waters_from_system (item, indices='all', structure_indices='all'):1007    from molsysmt.api_forms.api_molsysmt_Topology import get_n_waters_from_system as _get1008    tmp_item = to_molsysmt_Topology(item)1009    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1010def get_n_cosolutes_from_system (item, indices='all', structure_indices='all'):1011    from molsysmt.api_forms.api_molsysmt_Topology import get_n_cosolutes_from_system as _get1012    tmp_item = to_molsysmt_Topology(item)1013    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1014def get_n_small_molecules_from_system (item, indices='all', structure_indices='all'):1015    from molsysmt.api_forms.api_molsysmt_Topology import get_n_small_molecules_from_system as _get1016    tmp_item = to_molsysmt_Topology(item)1017    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1018def get_n_peptides_from_system (item, indices='all', structure_indices='all'):1019    from molsysmt.api_forms.api_molsysmt_Topology import get_n_peptides_from_system as _get1020    tmp_item = to_molsysmt_Topology(item)1021    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1022def get_n_proteins_from_system (item, indices='all', structure_indices='all'):1023    from molsysmt.api_forms.api_molsysmt_Topology import get_n_proteins_from_system as _get1024    tmp_item = to_molsysmt_Topology(item)1025    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1026def get_n_dnas_from_system (item, indices='all', structure_indices='all'):1027    from molsysmt.api_forms.api_molsysmt_Topology import get_n_dnas_from_system as _get1028    tmp_item = to_molsysmt_Topology(item)1029    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1030def get_n_rnas_from_system (item, indices='all', structure_indices='all'):1031    from molsysmt.api_forms.api_molsysmt_Topology import get_n_rnas_from_system as _get1032    tmp_item = to_molsysmt_Topology(item)1033    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1034def get_mass_from_system(item, indices='all', structure_indices='all'):1035    from molsysmt.api_forms.api_molsysmt_Topology import get_mass_from_system as _get1036    tmp_item = to_molsysmt_Topology(item)1037    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1038def get_charge_from_system(item, indices='all', structure_indices='all'):1039    from molsysmt.api_forms.api_molsysmt_Topology import get_charge_from_system as _get1040    tmp_item = to_molsysmt_Topology(item)1041    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1042def get_coordinates_from_system(item, indices='all', structure_indices='all'):1043    return get_coordinates_from_atom(item, indices='all', structure_indices=structure_indices)1044def get_box_from_system(item, indices='all', structure_indices='all'):1045    output = None1046    if item.box is not None:1047        units = item.box.unit1048        output = np.array(item.box._value, dtype=float)1049        if structure_indices is not 'all':1050            output = output[structure_indices, :, :]1051        output = output*units1052    return output1053def get_box_shape_from_system(item, indices='all', structure_indices='all'):1054    from molsysmt import box_shape_from_box_vectors1055    tmp_box = get_box_from_system(item, structure_indices=structure_indices)1056    output = box_shape_from_box_vectors(tmp_box)1057    return output1058def get_box_lengths_from_system(item, indices='all', structure_indices='all'):1059    from molsysmt import box_lengths_from_box_vectors1060    tmp_box = get_box_from_system(item, structure_indices=structure_indices)1061    output = box_lengths_from_box_vectors(tmp_box)1062    return output1063def get_box_angles_from_system(item, indices='all', structure_indices='all'):1064    from molsysmt import box_angles_from_box_vectors1065    tmp_box = get_box_from_system(item, structure_indices=structure_indices)1066    output = box_angles_from_box_vectors(tmp_box)1067    return output1068def get_time_from_system(item, indices='all', structure_indices='all'):1069    output = None1070    if item.time is not None:1071        units = item.time.unit1072        output = np.array(item.time._value, dtype=float)1073        if structure_indices is not 'all':1074            output = output[structure_indices]1075        output = output*units1076    return output1077def get_step_from_system(item, indices='all', structure_indices='all'):1078    output = None1079    if item.step is not None:1080        output = np.array(item.step, dtype=int)1081        if structure_indices is not 'all':1082            output = output[structure_indices]1083    return time1084def get_frame_from_system(item, indices='all', structure_indices='all'):1085    coordinates = get_coordinates_from_system(item, structure_indices=structure_indices)1086    box = get_box_from_system(item, structure_indices=structure_indices)1087    step = get_step_from_system(item, structure_indices=structure_indices)1088    time = get_time_from_system(item, structure_indices=structure_indices)1089    return step, time, coordinates, box1090def get_n_structures_from_system(item, indices='all', structure_indices='all'):1091    if structure_indices is 'all':1092        output=len(item.coordinates)1093    else:1094        output = structure_indices.shape[0]1095    return output1096def get_form_from_system(item, indices='all', structure_indices='all'):1097    return form_name1098## bond1099def get_index_from_bond(item, indices='all', structure_indices='all'):1100    return get_bond_index_from_bond(item, indices=indices)1101def get_order_from_bond(item, indices='all', structure_indices='all'):1102    return get_bond_order_from_bond(item, indices=indices)1103def get_type_from_bond(item, indices='all', structure_indices='all'):1104    return get_bond_type_from_bond(item, indices=indices)1105def get_bond_index_from_bond(item, indices='all', structure_indices='all'):1106    from molsysmt.api_forms.api_molsysmt_Topology import get_bond_index_from_bond as _get1107    tmp_item = to_molsysmt_Topology(item)1108    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1109def get_bond_order_from_bond(item, indices='all', structure_indices='all'):1110    from molsysmt.api_forms.api_molsysmt_Topology import get_bond_order_from_bond as _get1111    tmp_item = to_molsysmt_Topology(item)1112    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1113def get_bond_type_from_bond(item, indices='all', structure_indices='all'):1114    from molsysmt.api_forms.api_molsysmt_Topology import get_bond_type_from_bond as _get1115    tmp_item = to_molsysmt_Topology(item)1116    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1117def get_atom_index_from_bond(item, indices='all', structure_indices='all'):1118    from molsysmt.api_forms.api_molsysmt_Topology import get_atom_index_from_bond as _get1119    tmp_item = to_molsysmt_Topology(item)1120    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1121def get_n_bonds_from_bond(item, indices='all', structure_indices='all'):1122    from molsysmt.api_forms.api_molsysmt_Topology import get_n_bonds_from_bond as _get1123    tmp_item = to_molsysmt_Topology(item)1124    return _get(tmp_item, indices=indices, structure_indices=structure_indices)1125##### Set1126def set_box_to_system(item, indices='all', structure_indices='all', value=None):1127    raise NotImplementedError1128def set_coordinates_to_system(item, indices='all', structure_indices='all', value=None):...

api_molsysmt_Topology.py

Source:api_molsysmt_Topology.py

...60def get_type_from_atom (item, indices='all', structure_indices='all'):61    return get_atom_type_from_atom(item, indices=indices, structure_indices=structure_indices)62def get_atom_index_from_atom (item, indices='all', structure_indices='all'):63    from .api_molsysmt_DataFrame import get_atom_index_from_atom as _get64    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)65def get_atom_id_from_atom (item, indices='all', structure_indices='all'):66    from .api_molsysmt_DataFrame import get_atom_id_from_atom as _get67    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)68def get_atom_name_from_atom (item, indices='all', structure_indices='all'):69    from .api_molsysmt_DataFrame import get_atom_name_from_atom as _get70    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)71def get_atom_type_from_atom (item, indices='all', structure_indices='all'):72    from .api_molsysmt_DataFrame import get_atom_type_from_atom as _get73    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)74def get_group_index_from_atom (item, indices='all', structure_indices='all'):75    from .api_molsysmt_DataFrame import get_group_index_from_atom as _get76    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)77def get_group_id_from_atom (item, indices='all', structure_indices='all'):78    from .api_molsysmt_DataFrame import get_group_id_from_atom as _get79    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)80def get_group_name_from_atom (item, indices='all', structure_indices='all'):81    from .api_molsysmt_DataFrame import get_group_name_from_atom as _get82    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)83def get_group_type_from_atom (item, indices='all', structure_indices='all'):84    from .api_molsysmt_DataFrame import get_group_type_from_atom as _get85    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)86def get_component_index_from_atom (item, indices='all', structure_indices='all'):87    from .api_molsysmt_DataFrame import get_component_index_from_atom as _get88    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)89def get_component_id_from_atom (item, indices='all', structure_indices='all'):90    from .api_molsysmt_DataFrame import get_component_id_from_atom as _get91    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)92def get_component_name_from_atom (item, indices='all', structure_indices='all'):93    from .api_molsysmt_DataFrame import get_component_name_from_atom as _get94    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)95def get_component_type_from_atom (item, indices='all', structure_indices='all'):96    from .api_molsysmt_DataFrame import get_component_type_from_atom as _get97    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)98def get_chain_index_from_atom (item, indices='all', structure_indices='all'):99    from .api_molsysmt_DataFrame import get_chain_index_from_atom as _get100    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)101def get_chain_id_from_atom (item, indices='all', structure_indices='all'):102    from .api_molsysmt_DataFrame import get_chain_id_from_atom as _get103    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)104def get_chain_name_from_atom (item, indices='all', structure_indices='all'):105    from .api_molsysmt_DataFrame import get_chain_name_from_atom as _get106    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)107def get_chain_type_from_atom (item, indices='all', structure_indices='all'):108    from .api_molsysmt_DataFrame import get_chain_type_from_atom as _get109    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)110def get_molecule_index_from_atom (item, indices='all', structure_indices='all'):111    from .api_molsysmt_DataFrame import get_molecule_index_from_atom as _get112    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)113def get_molecule_id_from_atom (item, indices='all', structure_indices='all'):114    from .api_molsysmt_DataFrame import get_molecule_id_from_atom as _get115    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)116def get_molecule_name_from_atom (item, indices='all', structure_indices='all'):117    from .api_molsysmt_DataFrame import get_molecule_name_from_atom as _get118    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)119def get_molecule_type_from_atom (item, indices='all', structure_indices='all'):120    from .api_molsysmt_DataFrame import get_molecule_type_from_atom as _get121    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)122def get_entity_index_from_atom (item, indices='all', structure_indices='all'):123    from .api_molsysmt_DataFrame import get_entity_index_from_atom as _get124    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)125def get_entity_id_from_atom (item, indices='all', structure_indices='all'):126    from .api_molsysmt_DataFrame import get_entity_id_from_atom as _get127    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)128def get_entity_name_from_atom (item, indices='all', structure_indices='all'):129    from .api_molsysmt_DataFrame import get_entity_name_from_atom as _get130    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)131def get_entity_type_from_atom (item, indices='all', structure_indices='all'):132    from .api_molsysmt_DataFrame import get_entity_type_from_atom as _get133    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)134def get_bonded_atoms_from_atom (item, indices='all', structure_indices='all'):135    from .api_molsysmt_DataFrame import get_bonded_atoms_from_atom as _get136    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)137def get_n_atoms_from_atom (item, indices='all', structure_indices='all'):138    from .api_molsysmt_DataFrame import get_n_atoms_from_atom as _get139    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)140def get_n_groups_from_atom (item, indices='all', structure_indices='all'):141    from .api_molsysmt_DataFrame import get_n_groups_from_atom as _get142    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)143def get_n_components_from_atom (item, indices='all', structure_indices='all'):144    from .api_molsysmt_DataFrame import get_n_components_from_atom as _get145    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)146def get_n_molecules_from_atom (item, indices='all', structure_indices='all'):147    from .api_molsysmt_DataFrame import get_n_molecules_from_atom as _get148    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)149def get_n_chains_from_atom (item, indices='all', structure_indices='all'):150    from .api_molsysmt_DataFrame import get_n_chains_from_atom as _get151    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)152def get_n_entities_from_atom (item, indices='all', structure_indices='all'):153    from .api_molsysmt_DataFrame import get_n_entities_from_atom as _get154    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)155def get_n_bonds_from_atom (item, indices='all', structure_indices='all'):156    from .api_molsysmt_DataFrame import get_n_bonds_from_atom as _get157    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)158def get_mass_from_atom(item, indices='all', structure_indices='all'):159    from .api_molsysmt_DataFrame import get_mass_from_atom as _get160    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)161def get_charge_from_atom(item, indices='all', structure_indices='all'):162    from .api_molsysmt_DataFrame import get_charge_from_atom as _get163    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)164def get_form_from_atom(item, indices='all', structure_indices='all'):165    return form_name166## group167def get_index_from_group (item, indices='all', structure_indices='all'):168    get_group_index_from_group (item, indices=indices, structure_indices=structure_indices)169def get_id_from_group (item, indices='all', structure_indices='all'):170    get_group_id_from_group (item, indices=indices, structure_indices=structure_indices)171def get_name_from_group (item, indices='all', structure_indices='all'):172    get_group_name_from_group (item, indices=indices, structure_indices=structure_indices)173def get_type_from_group (item, indices='all', structure_indices='all'):174    get_group_type_from_group (item, indices=indices, structure_indices=structure_indices)175def get_atom_index_from_group (item, indices='all', structure_indices='all'):176    from .api_molsysmt_DataFrame import get_atom_index_from_group as _get177    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)178def get_atom_id_from_group (item, indices='all', structure_indices='all'):179    from .api_molsysmt_DataFrame import get_atom_id_from_group as _get180    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)181def get_atom_name_from_group (item, indices='all', structure_indices='all'):182    from .api_molsysmt_DataFrame import get_atom_name_from_group as _get183    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)184def get_atom_type_from_group (item, indices='all', structure_indices='all'):185    from .api_molsysmt_DataFrame import get_atom_type_from_group as _get186    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)187def get_group_index_from_group (item, indices='all', structure_indices='all'):188    from .api_molsysmt_DataFrame import get_group_index_from_group as _get189    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)190def get_group_id_from_group (item, indices='all', structure_indices='all'):191    from .api_molsysmt_DataFrame import get_group_id_from_group as _get192    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)193def get_group_name_from_group (item, indices='all', structure_indices='all'):194    from .api_molsysmt_DataFrame import get_group_name_from_group as _get195    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)196def get_group_type_from_group (item, indices='all', structure_indices='all'):197    from .api_molsysmt_DataFrame import get_group_type_from_group as _get198    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)199def get_component_index_from_group (item, indices='all', structure_indices='all'):200    from .api_molsysmt_DataFrame import get_component_index_from_group as _get201    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)202def get_component_id_from_group (item, indices='all', structure_indices='all'):203    from .api_molsysmt_DataFrame import get_component_id_from_group as _get204    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)205def get_component_name_from_group (item, indices='all', structure_indices='all'):206    from .api_molsysmt_DataFrame import get_component_name_from_group as _get207    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)208def get_component_type_from_group (item, indices='all', structure_indices='all'):209    from .api_molsysmt_DataFrame import get_component_type_from_group as _get210    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)211def get_chain_index_from_group (item, indices='all', structure_indices='all'):212    from .api_molsysmt_DataFrame import get_chain_index_from_group as _get213    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)214def get_chain_id_from_group (item, indices='all', structure_indices='all'):215    from .api_molsysmt_DataFrame import get_chain_id_from_group as _get216    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)217def get_chain_name_from_group (item, indices='all', structure_indices='all'):218    from .api_molsysmt_DataFrame import get_chain_name_from_group as _get219    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)220def get_chain_type_from_group (item, indices='all', structure_indices='all'):221    from .api_molsysmt_DataFrame import get_chain_type_from_group as _get222    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)223def get_molecule_index_from_group (item, indices='all', structure_indices='all'):224    from .api_molsysmt_DataFrame import get_molecule_index_from_group as _get225    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)226def get_molecule_id_from_group (item, indices='all', structure_indices='all'):227    from .api_molsysmt_DataFrame import get_molecule_id_from_group as _get228    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)229def get_molecule_name_from_group (item, indices='all', structure_indices='all'):230    from .api_molsysmt_DataFrame import get_molecule_name_from_group as _get231    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)232def get_molecule_type_from_group (item, indices='all', structure_indices='all'):233    from .api_molsysmt_DataFrame import get_molecule_type_from_group as _get234    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)235def get_entity_index_from_group (item, indices='all', structure_indices='all'):236    from .api_molsysmt_DataFrame import get_entity_index_from_group as _get237    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)238def get_entity_id_from_group (item, indices='all', structure_indices='all'):239    from .api_molsysmt_DataFrame import get_entity_id_from_group as _get240    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)241def get_entity_name_from_group (item, indices='all', structure_indices='all'):242    from .api_molsysmt_DataFrame import get_entity_name_from_group as _get243    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)244def get_entity_type_from_group (item, indices='all', structure_indices='all'):245    from .api_molsysmt_DataFrame import get_entity_type_from_group as _get246    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)247def get_n_atoms_from_group (item, indices='all', structure_indices='all'):248    from .api_molsysmt_DataFrame import get_n_atoms_from_group as _get249    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)250def get_n_groups_from_group (item, indices='all', structure_indices='all'):251    from .api_molsysmt_DataFrame import get_n_groups_from_group as _get252    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)253def get_n_components_from_group (item, indices='all', structure_indices='all'):254    from .api_molsysmt_DataFrame import get_n_components_from_group as _get255    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)256def get_n_molecules_from_group (item, indices='all', structure_indices='all'):257    from .api_molsysmt_DataFrame import get_n_molecules_from_group as _get258    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)259def get_n_chains_from_group (item, indices='all', structure_indices='all'):260    from .api_molsysmt_DataFrame import get_n_chains_from_group as _get261    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)262def get_n_entities_from_group (item, indices='all', structure_indices='all'):263    from .api_molsysmt_DataFrame import get_n_entities_from_group as _get264    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)265def get_n_bonds_from_group (item, indices='all', structure_indices='all'):266    from .api_molsysmt_DataFrame import get_n_bonds_from_group as _get267    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)268def get_mass_from_group(item, indices='all', structure_indices='all'):269    from .api_molsysmt_DataFrame import get_mass_from_group as _get270    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)271def get_charge_from_group(item, indices='all', structure_indices='all'):272    from .api_molsysmt_DataFrame import get_charge_from_group as _get273    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)274## component275def get_index_from_component (item, indices='all', structure_indices='all'):276    return get_component_index_from_component (item, indices=indices, structure_indices=structure_indices)277def get_id_from_component (item, indices='all', structure_indices='all'):278    return get_component_id_from_component (item, indices=indices, structure_indices=structure_indices)279def get_name_from_component (item, indices='all', structure_indices='all'):280    return get_component_name_from_component (item, indices=indices, structure_indices=structure_indices)281def get_type_from_component (item, indices='all', structure_indices='all'):282    return get_component_type_from_component (item, indices=indices, structure_indices=structure_indices)283def get_atom_index_from_component(item, indices='all', structure_indices='all'):284    from .api_molsysmt_DataFrame import get_atom_index_from_component as _get285    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)286def get_atom_id_from_component(item, indices='all', structure_indices='all'):287    from .api_molsysmt_DataFrame import get_atom_id_from_component as _get288    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)289def get_atom_name_from_component(item, indices='all', structure_indices='all'):290    from .api_molsysmt_DataFrame import get_atom_name_from_component as _get291    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)292def get_atom_type_from_component(item, indices='all', structure_indices='all'):293    from .api_molsysmt_DataFrame import get_atom_type_from_component as _get294    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)295def get_group_index_from_component(item, indices='all', structure_indices='all'):296    from .api_molsysmt_DataFrame import get_group_index_from_component as _get297    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)298def get_group_id_from_component(item, indices='all', structure_indices='all'):299    from .api_molsysmt_DataFrame import get_group_id_from_component as _get300    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)301def get_group_name_from_component(item, indices='all', structure_indices='all'):302    from .api_molsysmt_DataFrame import get_group_name_from_component as _get303    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)304def get_group_type_from_component(item, indices='all', structure_indices='all'):305    from .api_molsysmt_DataFrame import get_group_type_from_component as _get306    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)307def get_component_name_from_component (item, indices='all', structure_indices='all'):308    from .api_molsysmt_DataFrame import get_component_name_from_component as _get309    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)310def get_component_index_from_component (item, indices='all', structure_indices='all'):311    from .api_molsysmt_DataFrame import get_component_index_from_component as _get312    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)313def get_component_id_from_component (item, indices='all', structure_indices='all'):314    from .api_molsysmt_DataFrame import get_component_id_from_component as _get315    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)316def get_component_type_from_component (item, indices='all', structure_indices='all'):317    from .api_molsysmt_DataFrame import get_component_type_from_component as _get318    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)319def get_chain_name_from_component (item, indices='all', structure_indices='all'):320    from .api_molsysmt_DataFrame import get_chain_name_from_component as _get321    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)322def get_chain_index_from_component (item, indices='all', structure_indices='all'):323    from .api_molsysmt_DataFrame import get_chain_index_from_component as _get324    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)325def get_chain_id_from_component (item, indices='all', structure_indices='all'):326    from .api_molsysmt_DataFrame import get_chain_id_from_component as _get327    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)328def get_chain_type_from_component (item, indices='all', structure_indices='all'):329    from .api_molsysmt_DataFrame import get_chain_type_from_component as _get330    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)331def get_molecule_index_from_component (item, indices='all', structure_indices='all'):332    from .api_molsysmt_DataFrame import get_molecule_index_from_component as _get333    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)334def get_molecule_id_from_component (item, indices='all', structure_indices='all'):335    from .api_molsysmt_DataFrame import get_molecule_id_from_component as _get336    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)337def get_molecule_name_from_component (item, indices='all', structure_indices='all'):338    from .api_molsysmt_DataFrame import get_molecule_name_from_component as _get339    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)340def get_molecule_type_from_component (item, indices='all', structure_indices='all'):341    from .api_molsysmt_DataFrame import get_molecule_type_from_component as _get342    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)343def get_entity_index_from_component (item, indices='all', structure_indices='all'):344    from .api_molsysmt_DataFrame import get_entity_index_from_component as _get345    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)346def get_entity_id_from_component (item, indices='all', structure_indices='all'):347    from .api_molsysmt_DataFrame import get_entity_id_from_component as _get348    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)349def get_entity_name_from_component (item, indices='all', structure_indices='all'):350    from .api_molsysmt_DataFrame import get_entity_name_from_component as _get351    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)352def get_entity_type_from_component (item, indices='all', structure_indices='all'):353    from .api_molsysmt_DataFrame import get_entity_type_from_component as _get354    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)355def get_n_atoms_from_component (item, indices='all', structure_indices='all'):356    from .api_molsysmt_DataFrame import get_n_atoms_from_component as _get357    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)358def get_n_groups_from_component (item, indices='all', structure_indices='all'):359    from .api_molsysmt_DataFrame import get_n_groups_from_component as _get360    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)361def get_n_components_from_component (item, indices='all', structure_indices='all'):362    from .api_molsysmt_DataFrame import get_n_components_from_component as _get363    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)364def get_n_molecules_from_component (item, indices='all', structure_indices='all'):365    from .api_molsysmt_DataFrame import get_n_molecules_from_component as _get366    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)367def get_n_chains_from_component (item, indices='all', structure_indices='all'):368    from .api_molsysmt_DataFrame import get_n_chains_from_component as _get369    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)370def get_n_entities_from_component (item, indices='all', structure_indices='all'):371    from .api_molsysmt_DataFrame import get_n_entities_from_component as _get372    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)373def get_n_bonds_from_component (item, indices='all', structure_indices='all'):374    from .api_molsysmt_DataFrame import get_n_bonds_from_component as _get375    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)376def get_mass_from_component(item, indices='all', structure_indices='all'):377    from .api_molsysmt_DataFrame import get_mass_from_component as _get378    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)379def get_charge_from_component(item, indices='all', structure_indices='all'):380    from .api_molsysmt_DataFrame import get_charge_from_component as _get381    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)382## molecule383def get_index_from_molecule (item, indices='all', structure_indices='all'):384    return get_molecule_index_from_molecule (item, indices=indices, structure_indices=structure_indices)385def get_id_from_molecule (item, indices='all', structure_indices='all'):386    return get_molecule_id_from_molecule (item, indices=indices, structure_indices=structure_indices)387def get_name_from_molecule (item, indices='all', structure_indices='all'):388    return get_molecule_name_from_molecule (item, indices=indices, structure_indices=structure_indices)389def get_type_from_molecule (item, indices='all', structure_indices='all'):390    return get_molecule_type_from_molecule (item, indices=indices, structure_indices=structure_indices)391def get_atom_index_from_molecule(item, indices='all', structure_indices='all'):392    from .api_molsysmt_DataFrame import get_atom_index_from_molecule as _get393    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)394def get_atom_id_from_molecule(item, indices='all', structure_indices='all'):395    from .api_molsysmt_DataFrame import get_atom_id_from_molecule as _get396    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)397def get_atom_name_from_molecule(item, indices='all', structure_indices='all'):398    from .api_molsysmt_DataFrame import get_atom_name_from_molecule as _get399    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)400def get_atom_type_from_molecule(item, indices='all', structure_indices='all'):401    from .api_molsysmt_DataFrame import get_atom_type_from_molecule as _get402    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)403def get_group_index_from_molecule(item, indices='all', structure_indices='all'):404    from .api_molsysmt_DataFrame import get_group_index_from_molecule as _get405    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)406def get_group_id_from_molecule(item, indices='all', structure_indices='all'):407    from .api_molsysmt_DataFrame import get_group_id_from_molecule as _get408    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)409def get_group_name_from_molecule(item, indices='all', structure_indices='all'):410    from .api_molsysmt_DataFrame import get_group_name_from_molecule as _get411    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)412def get_group_type_from_molecule(item, indices='all', structure_indices='all'):413    from .api_molsysmt_DataFrame import get_group_type_from_molecule as _get414    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)415def get_component_name_from_molecule (item, indices='all', structure_indices='all'):416    from .api_molsysmt_DataFrame import get_component_name_from_molecule as _get417    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)418def get_component_index_from_molecule (item, indices='all', structure_indices='all'):419    from .api_molsysmt_DataFrame import get_component_index_from_molecule as _get420    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)421def get_component_id_from_molecule (item, indices='all', structure_indices='all'):422    from .api_molsysmt_DataFrame import get_component_id_from_molecule as _get423    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)424def get_component_type_from_molecule (item, indices='all', structure_indices='all'):425    from .api_molsysmt_DataFrame import get_component_type_from_molecule as _get426    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)427def get_chain_name_from_molecule (item, indices='all', structure_indices='all'):428    from .api_molsysmt_DataFrame import get_chain_name_from_molecule as _get429    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)430def get_chain_index_from_molecule (item, indices='all', structure_indices='all'):431    from .api_molsysmt_DataFrame import get_chain_index_from_molecule as _get432    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)433def get_chain_id_from_molecule (item, indices='all', structure_indices='all'):434    from .api_molsysmt_DataFrame import get_chain_id_from_molecule as _get435    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)436def get_chain_type_from_molecule (item, indices='all', structure_indices='all'):437    from .api_molsysmt_DataFrame import get_chain_type_from_molecule as _get438    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)439def get_molecule_index_from_molecule (item, indices='all', structure_indices='all'):440    from .api_molsysmt_DataFrame import get_molecule_index_from_molecule as _get441    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)442def get_molecule_id_from_molecule (item, indices='all', structure_indices='all'):443    from .api_molsysmt_DataFrame import get_molecule_id_from_molecule as _get444    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)445def get_molecule_name_from_molecule (item, indices='all', structure_indices='all'):446    from .api_molsysmt_DataFrame import get_molecule_name_from_molecule as _get447    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)448def get_molecule_type_from_molecule (item, indices='all', structure_indices='all'):449    from .api_molsysmt_DataFrame import get_molecule_type_from_molecule as _get450    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)451def get_entity_index_from_molecule (item, indices='all', structure_indices='all'):452    from .api_molsysmt_DataFrame import get_entity_index_from_molecule as _get453    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)454def get_entity_id_from_molecule (item, indices='all', structure_indices='all'):455    from .api_molsysmt_DataFrame import get_entity_id_from_molecule as _get456    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)457def get_entity_name_from_molecule (item, indices='all', structure_indices='all'):458    from .api_molsysmt_DataFrame import get_entity_name_from_molecule as _get459    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)460def get_entity_type_from_molecule (item, indices='all', structure_indices='all'):461    from .api_molsysmt_DataFrame import get_entity_type_from_molecule as _get462    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)463def get_n_atoms_from_molecule (item, indices='all', structure_indices='all'):464    from .api_molsysmt_DataFrame import get_n_atoms_from_molecule as _get465    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)466def get_n_groups_from_molecule (item, indices='all', structure_indices='all'):467    from .api_molsysmt_DataFrame import get_n_groups_from_molecule as _get468    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)469def get_n_components_from_molecule (item, indices='all', structure_indices='all'):470    from .api_molsysmt_DataFrame import get_n_components_from_molecule as _get471    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)472def get_n_molecules_from_molecule (item, indices='all', structure_indices='all'):473    from .api_molsysmt_DataFrame import get_n_molecules_from_molecule as _get474    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)475def get_n_chains_from_molecule (item, indices='all', structure_indices='all'):476    from .api_molsysmt_DataFrame import get_n_chains_from_molecule as _get477    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)478def get_n_entities_from_molecule (item, indices='all', structure_indices='all'):479    from .api_molsysmt_DataFrame import get_n_entities_from_molecule as _get480    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)481def get_n_bonds_from_molecule (item, indices='all', structure_indices='all'):482    from .api_molsysmt_DataFrame import get_n_bonds_from_molecule as _get483    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)484def get_mass_from_molecule(item, indices='all', structure_indices='all'):485    from .api_molsysmt_DataFrame import get_mass_from_molecule as _get486    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)487def get_charge_from_molecule(item, indices='all', structure_indices='all'):488    from .api_molsysmt_DataFrame import get_charge_from_molecule as _get489    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)490## chain491def get_index_from_chain (item, indices='all', structure_indices='all'):492    return get_chain_index_from_chain (item, indices=indices, structure_indices=structure_indices)493def get_id_from_chain (item, indices='all', structure_indices='all'):494    return get_chain_id_from_chain (item, indices=indices, structure_indices=structure_indices)495def get_name_from_chain (item, indices='all', structure_indices='all'):496    return get_chain_name_from_chain (item, indices=indices, structure_indices=structure_indices)497def get_type_from_chain (item, indices='all', structure_indices='all'):498    return get_chain_type_from_chain (item, indices=indices, structure_indices=structure_indices)499def get_atom_index_from_chain(item, indices='all', structure_indices='all'):500    from .api_molsysmt_DataFrame import get_atom_index_from_chain as _get501    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)502def get_atom_id_from_chain(item, indices='all', structure_indices='all'):503    from .api_molsysmt_DataFrame import get_atom_id_from_chain as _get504    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)505def get_atom_name_from_chain(item, indices='all', structure_indices='all'):506    from .api_molsysmt_DataFrame import get_atom_name_from_chain as _get507    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)508def get_atom_type_from_chain(item, indices='all', structure_indices='all'):509    from .api_molsysmt_DataFrame import get_atom_type_from_chain as _get510    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)511def get_group_index_from_chain(item, indices='all', structure_indices='all'):512    from .api_molsysmt_DataFrame import get_group_index_from_chain as _get513    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)514def get_group_id_from_chain(item, indices='all', structure_indices='all'):515    from .api_molsysmt_DataFrame import get_group_id_from_chain as _get516    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)517def get_group_name_from_chain(item, indices='all', structure_indices='all'):518    from .api_molsysmt_DataFrame import get_group_name_from_chain as _get519    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)520def get_group_type_from_chain(item, indices='all', structure_indices='all'):521    from .api_molsysmt_DataFrame import get_group_type_from_chain as _get522    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)523def get_component_name_from_chain (item, indices='all', structure_indices='all'):524    from .api_molsysmt_DataFrame import get_component_name_from_chain as _get525    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)526def get_component_index_from_chain (item, indices='all', structure_indices='all'):527    from .api_molsysmt_DataFrame import get_component_index_from_chain as _get528    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)529def get_component_id_from_chain (item, indices='all', structure_indices='all'):530    from .api_molsysmt_DataFrame import get_component_id_from_chain as _get531    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)532def get_component_type_from_chain (item, indices='all', structure_indices='all'):533    from .api_molsysmt_DataFrame import get_component_type_from_chain as _get534    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)535def get_chain_name_from_chain (item, indices='all', structure_indices='all'):536    from .api_molsysmt_DataFrame import get_chain_name_from_chain as _get537    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)538def get_chain_index_from_chain (item, indices='all', structure_indices='all'):539    from .api_molsysmt_DataFrame import get_chain_index_from_chain as _get540    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)541def get_chain_id_from_chain (item, indices='all', structure_indices='all'):542    from .api_molsysmt_DataFrame import get_chain_id_from_chain as _get543    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)544def get_chain_type_from_chain (item, indices='all', structure_indices='all'):545    from .api_molsysmt_DataFrame import get_chain_type_from_chain as _get546    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)547def get_molecule_index_from_chain (item, indices='all', structure_indices='all'):548    from .api_molsysmt_DataFrame import get_molecule_index_from_chain as _get549    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)550def get_molecule_id_from_chain (item, indices='all', structure_indices='all'):551    from .api_molsysmt_DataFrame import get_molecule_id_from_chain as _get552    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)553def get_molecule_name_from_chain (item, indices='all', structure_indices='all'):554    from .api_molsysmt_DataFrame import get_molecule_name_from_chain as _get555    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)556def get_molecule_type_from_chain (item, indices='all', structure_indices='all'):557    from .api_molsysmt_DataFrame import get_molecule_type_from_chain as _get558    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)559def get_entity_index_from_chain (item, indices='all', structure_indices='all'):560    from .api_molsysmt_DataFrame import get_entity_index_from_chain as _get561    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)562def get_entity_id_from_chain (item, indices='all', structure_indices='all'):563    from .api_molsysmt_DataFrame import get_entity_id_from_chain as _get564    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)565def get_entity_name_from_chain (item, indices='all', structure_indices='all'):566    from .api_molsysmt_DataFrame import get_entity_name_from_chain as _get567    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)568def get_entity_type_from_chain (item, indices='all', structure_indices='all'):569    from .api_molsysmt_DataFrame import get_entity_type_from_chain as _get570    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)571def get_n_atoms_from_chain (item, indices='all', structure_indices='all'):572    from .api_molsysmt_DataFrame import get_n_atoms_from_chain as _get573    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)574def get_n_groups_from_chain (item, indices='all', structure_indices='all'):575    from .api_molsysmt_DataFrame import get_n_groups_from_chain as _get576    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)577def get_n_components_from_chain (item, indices='all', structure_indices='all'):578    from .api_molsysmt_DataFrame import get_n_components_from_chain as _get579    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)580def get_n_molecules_from_chain (item, indices='all', structure_indices='all'):581    from .api_molsysmt_DataFrame import get_n_molecules_from_chain as _get582    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)583def get_n_chains_from_chain (item, indices='all', structure_indices='all'):584    from .api_molsysmt_DataFrame import get_n_chains_from_chain as _get585    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)586def get_n_entities_from_chain (item, indices='all', structure_indices='all'):587    from .api_molsysmt_DataFrame import get_n_entities_from_chain as _get588    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)589def get_n_bonds_from_chain (item, indices='all', structure_indices='all'):590    from .api_molsysmt_DataFrame import get_n_bonds_from_chain as _get591    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)592def get_mass_from_chain(item, indices='all', structure_indices='all'):593    from .api_molsysmt_DataFrame import get_mass_from_chain as _get594    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)595def get_charge_from_chain(item, indices='all', structure_indices='all'):596    from .api_molsysmt_DataFrame import get_charge_from_chain as _get597    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)598## entity599def get_index_from_entity (item, indices='all', structure_indices='all'):600    return get_entity_index_from_entity (item, indices=indices, structure_indices=structure_indices)601def get_id_from_entity (item, indices='all', structure_indices='all'):602    return get_entity_id_from_entity (item, indices=indices, structure_indices=structure_indices)603def get_name_from_entity (item, indices='all', structure_indices='all'):604    return get_entity_name_from_entity (item, indices=indices, structure_indices=structure_indices)605def get_type_from_entity (item, indices='all', structure_indices='all'):606    return get_entity_type_from_entity (item, indices=indices, structure_indices=structure_indices)607def get_atom_index_from_entity(item, indices='all', structure_indices='all'):608    from .api_molsysmt_DataFrame import get_atom_index_from_entity as _get609    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)610def get_atom_id_from_entity(item, indices='all', structure_indices='all'):611    from .api_molsysmt_DataFrame import get_atom_id_from_entity as _get612    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)613def get_atom_name_from_entity(item, indices='all', structure_indices='all'):614    from .api_molsysmt_DataFrame import get_atom_name_from_entity as _get615    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)616def get_atom_type_from_entity(item, indices='all', structure_indices='all'):617    from .api_molsysmt_DataFrame import get_atom_type_from_entity as _get618    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)619def get_group_index_from_entity(item, indices='all', structure_indices='all'):620    from .api_molsysmt_DataFrame import get_group_index_from_entity as _get621    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)622def get_group_id_from_entity(item, indices='all', structure_indices='all'):623    from .api_molsysmt_DataFrame import get_group_id_from_entity as _get624    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)625def get_group_name_from_entity(item, indices='all', structure_indices='all'):626    from .api_molsysmt_DataFrame import get_group_name_from_entity as _get627    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)628def get_group_type_from_entity(item, indices='all', structure_indices='all'):629    from .api_molsysmt_DataFrame import get_group_type_from_entity as _get630    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)631def get_component_name_from_entity (item, indices='all', structure_indices='all'):632    from .api_molsysmt_DataFrame import get_component_name_from_entity as _get633    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)634def get_component_index_from_entity (item, indices='all', structure_indices='all'):635    from .api_molsysmt_DataFrame import get_component_index_from_entity as _get636    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)637def get_component_id_from_entity (item, indices='all', structure_indices='all'):638    from .api_molsysmt_DataFrame import get_component_id_from_entity as _get639    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)640def get_component_type_from_entity (item, indices='all', structure_indices='all'):641    from .api_molsysmt_DataFrame import get_component_type_from_entity as _get642    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)643def get_chain_name_from_entity (item, indices='all', structure_indices='all'):644    from .api_molsysmt_DataFrame import get_chain_name_from_entity as _get645    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)646def get_chain_index_from_entity (item, indices='all', structure_indices='all'):647    from .api_molsysmt_DataFrame import get_chain_index_from_entity as _get648    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)649def get_chain_id_from_entity (item, indices='all', structure_indices='all'):650    from .api_molsysmt_DataFrame import get_chain_id_from_entity as _get651    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)652def get_chain_type_from_entity (item, indices='all', structure_indices='all'):653    from .api_molsysmt_DataFrame import get_chain_type_from_entity as _get654    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)655def get_molecule_index_from_entity (item, indices='all', structure_indices='all'):656    from .api_molsysmt_DataFrame import get_molecule_index_from_entity as _get657    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)658def get_molecule_id_from_entity (item, indices='all', structure_indices='all'):659    from .api_molsysmt_DataFrame import get_molecule_id_from_entity as _get660    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)661def get_molecule_name_from_entity (item, indices='all', structure_indices='all'):662    from .api_molsysmt_DataFrame import get_molecule_name_from_entity as _get663    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)664def get_molecule_type_from_entity (item, indices='all', structure_indices='all'):665    from .api_molsysmt_DataFrame import get_molecule_type_from_entity as _get666    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)667def get_entity_index_from_entity (item, indices='all', structure_indices='all'):668    from .api_molsysmt_DataFrame import get_entity_index_from_entity as _get669    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)670def get_entity_id_from_entity (item, indices='all', structure_indices='all'):671    from .api_molsysmt_DataFrame import get_entity_id_from_entity as _get672    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)673def get_entity_name_from_entity (item, indices='all', structure_indices='all'):674    from .api_molsysmt_DataFrame import get_entity_name_from_entity as _get675    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)676def get_entity_type_from_entity (item, indices='all', structure_indices='all'):677    from .api_molsysmt_DataFrame import get_entity_type_from_entity as _get678    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)679def get_n_atoms_from_entity (item, indices='all', structure_indices='all'):680    from .api_molsysmt_DataFrame import get_n_atoms_from_entity as _get681    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)682def get_n_groups_from_entity (item, indices='all', structure_indices='all'):683    from .api_molsysmt_DataFrame import get_n_groups_from_entity as _get684    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)685def get_n_components_from_entity (item, indices='all', structure_indices='all'):686    from .api_molsysmt_DataFrame import get_n_components_from_entity as _get687    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)688def get_n_molecules_from_entity (item, indices='all', structure_indices='all'):689    from .api_molsysmt_DataFrame import get_n_molecules_from_entity as _get690    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)691def get_n_chains_from_entity (item, indices='all', structure_indices='all'):692    from .api_molsysmt_DataFrame import get_n_chains_from_entity as _get693    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)694def get_n_entities_from_entity (item, indices='all', structure_indices='all'):695    from .api_molsysmt_DataFrame import get_n_entities_from_entity as _get696    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)697def get_n_bonds_from_entity (item, indices='all', structure_indices='all'):698    from .api_molsysmt_DataFrame import get_n_bonds_from_entity as _get699    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)700def get_mass_from_entity(item, indices='all', structure_indices='all'):701    from .api_molsysmt_DataFrame import get_mass_from_entity as _get702    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)703def get_charge_from_entity(item, indices='all', structure_indices='all'):704    from .api_molsysmt_DataFrame import get_charge_from_entity as _get705    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)706## system707def get_bonded_atoms_from_system(item, indices='all', structure_indices='all'):708    from .api_molsysmt_DataFrame import get_bonded_atoms_from_system as _get709    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)710def get_n_atoms_from_system(item, indices='all', structure_indices='all'):711    from .api_molsysmt_DataFrame import get_n_atoms_from_system as _get712    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)713def get_n_groups_from_system(item, indices='all', structure_indices='all'):714    from .api_molsysmt_DataFrame import get_n_groups_from_system as _get715    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)716def get_n_components_from_system(item, indices='all', structure_indices='all'):717    from .api_molsysmt_DataFrame import get_n_components_from_system as _get718    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)719def get_n_chains_from_system(item, indices='all', structure_indices='all'):720    from .api_molsysmt_DataFrame import get_n_chains_from_system as _get721    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)722def get_n_molecules_from_system(item, indices='all', structure_indices='all'):723    from .api_molsysmt_DataFrame import get_n_molecules_from_system as _get724    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)725def get_n_entities_from_system(item, indices='all', structure_indices='all'):726    from .api_molsysmt_DataFrame import get_n_entities_from_system as _get727    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)728def get_n_bonds_from_system(item, indices='all', structure_indices='all'):729    from .api_molsysmt_DataFrame import get_n_bonds_from_system as _get730    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)731def get_n_aminoacids_from_system (item, indices='all', structure_indices='all'):732    from .api_molsysmt_DataFrame import get_n_aminoacids_from_system as _get733    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)734def get_n_nucleotides_from_system (item, indices='all', structure_indices='all'):735    from .api_molsysmt_DataFrame import get_n_nucleotides_from_system as _get736    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)737def get_n_ions_from_system (item, indices='all', structure_indices='all'):738    from .api_molsysmt_DataFrame import get_n_ions_from_system as _get739    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)740def get_n_waters_from_system (item, indices='all', structure_indices='all'):741    from .api_molsysmt_DataFrame import get_n_waters_from_system as _get742    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)743def get_n_cosolutes_from_system (item, indices='all', structure_indices='all'):744    from .api_molsysmt_DataFrame import get_n_cosolutes_from_system as _get745    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)746def get_n_small_molecules_from_system (item, indices='all', structure_indices='all'):747    from .api_molsysmt_DataFrame import get_n_small_molecules_from_system as _get748    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)749def get_n_peptides_from_system (item, indices='all', structure_indices='all'):750    from .api_molsysmt_DataFrame import get_n_peptides_from_system as _get751    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)752def get_n_proteins_from_system (item, indices='all', structure_indices='all'):753    from .api_molsysmt_DataFrame import get_n_proteins_from_system as _get754    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)755def get_n_dnas_from_system (item, indices='all', structure_indices='all'):756    from .api_molsysmt_DataFrame import get_n_dnas_from_system as _get757    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)758def get_n_rnas_from_system (item, indices='all', structure_indices='all'):759    from .api_molsysmt_DataFrame import get_n_dnas_from_system as _get760    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)761def get_mass_from_system(item, indices='all', structure_indices='all'):762    from .api_molsysmt_DataFrame import get_mass_from_system as _get763    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)764def get_charge_from_system(item, indices='all', structure_indices='all'):765    return _get(item.dataframe, indices=indices, structure_indices=structure_indices)766def get_n_structures_from_system(item, indices='all', structure_indices='all'):767    return 0768def get_form_from_system(item, indices='all', structure_indices='all'):...

api_openexplorer_Explorer.py

Source:api_openexplorer_Explorer.py

...76##### Get77def get_atom_id_from_atom(item, indices='all', structure_indices='all'):78    from molsysmt.api_forms.api_openmm_Topology import get_atom_id_from_atom as _get79    tmp_item = to_openmm_Topology(item)80    return _get(tmp_item, indices=indices, structure_indices=structure_indices)81def get_atom_name_from_atom(item, indices='all', structure_indices='all'):82    from molsysmt.api_forms.api_openmm_Topology import get_atom_name_from_atom as _get83    tmp_item = to_openmm_Topology(item)84    return _get(tmp_item, indices=indices, structure_indices=structure_indices)85def get_atom_type_from_atom(item, indices='all', structure_indices='all'):86    from molsysmt.api_forms.api_openmm_Topology import get_atom_type_from_atom as _get87    tmp_item = to_openmm_Topology(item)88    return _get(tmp_item, indices=indices, structure_indices=structure_indices)89def get_group_index_from_atom (item, indices='all', structure_indices='all'):90    from molsysmt.api_forms.api_openmm_Topology import get_group_index_from_atom as _get91    tmp_item = to_openmm_Topology(item)92    return _get(tmp_item, indices=indices, structure_indices=structure_indices)93def get_component_index_from_atom (item, indices='all', structure_indices='all'):94    from molsysmt.api_forms.api_openmm_Topology import get_component_index_from_atom as _get95    tmp_item = to_openmm_Topology(item)96    return _get(tmp_item, indices=indices, structure_indices=structure_indices)97def get_chain_index_from_atom (item, indices='all', structure_indices='all'):98    from molsysmt.api_forms.api_openmm_Topology import get_chain_index_from_atom as _get99    tmp_item = to_openmm_Topology(item)100    return _get(tmp_item, indices=indices, structure_indices=structure_indices)101def get_molecule_index_from_atom (item, indices='all', structure_indices='all'):102    from molsysmt.api_forms.api_openmm_Topology import get_molecule_index_from_atom as _get103    tmp_item = to_openmm_Topology(item)104    return _get(tmp_item, indices=indices, structure_indices=structure_indices)105def get_entity_index_from_atom (item, indices='all', structure_indices='all'):106    from molsysmt.api_forms.api_openmm_Topology import get_entity_index_from_atom as _get107    tmp_item = to_openmm_Topology(item)108    return _get(tmp_item, indices=indices, structure_indices=structure_indices)109def get_inner_bonded_atoms_from_atom (item, indices='all', structure_indices='all'):110    from molsysmt.api_forms.api_openmm_Topology import get_inner_bonded_atoms_from_atom as _get111    tmp_item = to_openmm_Topology(item)112    return _get(tmp_item, indices=indices, structure_indices=structure_indices)113def get_n_inner_bonds_from_atom (item, indices='all', structure_indices='all'):114    from molsysmt.api_forms.api_openmm_Topology import get_n_inner_bonds_from_atom as _get115    tmp_item = to_openmm_Topology(item)116    return _get(tmp_item, indices=indices, structure_indices=structure_indices)117def get_coordinates_from_atom(item, indices='all', structure_indices='all'):118    from molsysmt.api_forms.api_openmm_Context import get_coordinates_from_atom as _get119    tmp_item = to_openmm_Context(item)120    return _get(tmp_item, indices=indices, structure_indices=structure_indices)121## group122def get_group_id_from_group(item, indices='all', structure_indices='all'):123    from molsysmt.api_forms.api_openmm_Topology import get_group_id_from_group as _get124    tmp_item = to_openmm_Topology(item)125    return _get(tmp_item, indices=indices, structure_indices=structure_indices)126def get_group_name_from_group(item, indices='all', structure_indices='all'):127    from molsysmt.api_forms.api_openmm_Topology import get_group_name_from_group as _get128    tmp_item = to_openmm_Topology(item)129    return _get(tmp_item, indices=indices, structure_indices=structure_indices)130def get_group_type_from_group(item, indices='all', structure_indices='all'):131    from molsysmt.api_forms.api_openmm_Topology import get_group_type_from_group as _get132    tmp_item = to_openmm_Topology(item)133    return _get(tmp_item, indices=indices, structure_indices=structure_indices)134## component135def get_component_name_from_component (item, indices='all', structure_indices='all'):136    from molsysmt.api_forms.api_openmm_Topology import get_component_name_from_component as _get137    tmp_item = to_openmm_Topology(item)138    return _get(tmp_item, indices=indices, structure_indices=structure_indices)139def get_component_id_from_component (item, indices='all', structure_indices='all'):140    from molsysmt.api_forms.api_openmm_Topology import get_component_id_from_component as _get141    tmp_item = to_openmm_Topology(item)142    return _get(tmp_item, indices=indices, structure_indices=structure_indices)143def get_component_type_from_component (item, indices='all', structure_indices='all'):144    from molsysmt.api_forms.api_openmm_Topology import get_component_type_from_component as _get145    tmp_item = to_openmm_Topology(item)146    return _get(tmp_item, indices=indices, structure_indices=structure_indices)147## molecule148def get_molecule_id_from_molecule (item, indices='all', structure_indices='all'):149    from molsysmt.api_forms.api_openmm_Topology import get_molecule_id_from_molecule as _get150    tmp_item = to_openmm_Topology(item)151    return _get(tmp_item, indices=indices, structure_indices=structure_indices)152def get_molecule_name_from_molecule (item, indices='all', structure_indices='all'):153    from molsysmt.api_forms.api_openmm_Topology import get_molecule_name_from_molecule as _get154    tmp_item = to_openmm_Topology(item)155    return _get(tmp_item, indices=indices, structure_indices=structure_indices)156def get_molecule_type_from_molecule (item, indices='all', structure_indices='all'):157    from molsysmt.api_forms.api_openmm_Topology import get_molecule_type_from_molecule as _get158    tmp_item = to_openmm_Topology(item)159    return _get(tmp_item, indices=indices, structure_indices=structure_indices)160## chain161def get_chain_name_from_chain (item, indices='all', structure_indices='all'):162    from molsysmt.api_forms.api_openmm_Topology import get_chain_name_from_chain as _get163    tmp_item = to_openmm_Topology(item)164    return _get(tmp_item, indices=indices, structure_indices=structure_indices)165def get_chain_id_from_chain (item, indices='all', structure_indices='all'):166    from molsysmt.api_forms.api_openmm_Topology import get_chain_id_from_chain as _get167    tmp_item = to_openmm_Topology(item)168    return _get(tmp_item, indices=indices, structure_indices=structure_indices)169def get_chain_type_from_chain (item, indices='all', structure_indices='all'):170    from molsysmt.api_forms.api_openmm_Topology import get_chain_type_from_chain as _get171    tmp_item = to_openmm_Topology(item)172    return _get(tmp_item, indices=indices, structure_indices=structure_indices)173## entity174def get_entity_id_from_entity (item, indices='all', structure_indices='all'):175    from molsysmt.api_forms.api_openmm_Topology import get_entity_id_from_entity as _get176    tmp_item = to_openmm_Topology(item)177    return _get(tmp_item, indices=indices, structure_indices=structure_indices)178def get_entity_name_from_entity (item, indices='all', structure_indices='all'):179    from molsysmt.api_forms.api_openmm_Topology import get_entity_name_from_entity as _get180    tmp_item = to_openmm_Topology(item)181    return _get(tmp_item, indices=indices, structure_indices=structure_indices)182def get_entity_type_from_entity (item, indices='all', structure_indices='all'):183    from molsysmt.api_forms.api_openmm_Topology import get_entity_type_from_entity as _get184    tmp_item = to_openmm_Topology(item)185    return _get(tmp_item, indices=indices, structure_indices=structure_indices)186## system187def get_n_atoms_from_system(item, indices='all', structure_indices='all'):188    from molsysmt.api_forms.api_openmm_Topology import get_n_atoms_from_system as _get189    tmp_item = to_openmm_Topology(item)190    return _get(tmp_item, indices=indices, structure_indices=structure_indices)191def get_n_groups_from_system(item, indices='all', structure_indices='all'):192    from molsysmt.api_forms.api_openmm_Topology import get_n_groups_from_system as _get193    tmp_item = to_openmm_Topology(item)194    return _get(tmp_item, indices=indices, structure_indices=structure_indices)195def get_n_components_from_system(item, indices='all', structure_indices='all'):196    from molsysmt.api_forms.api_openmm_Topology import get_n_components_from_system as _get197    tmp_item = to_openmm_Topology(item)198    return _get(tmp_item, indices=indices, structure_indices=structure_indices)199def get_n_chains_from_system(item, indices='all', structure_indices='all'):200    from molsysmt.api_forms.api_openmm_Topology import get_n_chains_from_system as _get201    tmp_item = to_openmm_Topology(item)202    return _get(tmp_item, indices=indices, structure_indices=structure_indices)203def get_n_molecules_from_system(item, indices='all', structure_indices='all'):204    from molsysmt.api_forms.api_openmm_Topology import get_n_molecules_from_system as _get205    tmp_item = to_openmm_Topology(item)206    return _get(tmp_item, indices=indices, structure_indices=structure_indices)207def get_n_entities_from_system(item, indices='all', structure_indices='all'):208    from molsysmt.api_forms.api_openmm_Topology import get_n_entities_from_system as _get209    tmp_item = to_openmm_Topology(item)210    return _get(tmp_item, indices=indices, structure_indices=structure_indices)211def get_n_bonds_from_system(item, indices='all', structure_indices='all'):212    from molsysmt.api_forms.api_openmm_Topology import get_n_bonds_from_system as _get213    tmp_item = to_openmm_Topology(item)214    return _get(tmp_item, indices=indices, structure_indices=structure_indices)215def get_coordinates_from_system(item, indices='all', structure_indices='all'):216    from molsysmt.api_forms.api_openmm_Context import get_coordinates_from_system as _get217    tmp_item = to_openmm_Context(item)218    return _get(tmp_item, indices=indices, structure_indices=structure_indices)219def get_box_from_system(item, indices='all', structure_indices='all'):220    from molsysmt.api_forms.api_openmm_Context import get_box_from_system as _get221    tmp_item = to_openmm_Context(item)222    return _get(tmp_item, indices=indices, structure_indices=structure_indices)223def get_box_shape_from_system(item, indices='all', structure_indices='all'):224    from molsysmt.api_forms.api_openmm_Context import get_box_shape_from_system as _get225    tmp_item = to_openmm_Context(item)226    return _get(tmp_item, indices=indices, structure_indices=structure_indices)227def get_box_lengths_from_system(item, indices='all', structure_indices='all'):228    from molsysmt.api_forms.api_openmm_Context import get_box_lengths_from_system as _get229    tmp_item = to_openmm_Context(item)230    return _get(tmp_item, indices=indices, structure_indices=structure_indices)231def get_box_angles_from_system(item, indices='all', structure_indices='all'):232    from molsysmt.api_forms.api_openmm_Context import get_box_angles_from_system as _get233    tmp_item = to_openmm_Context(item)234    return _get(tmp_item, indices=indices, structure_indices=structure_indices)235def get_time_from_system(item, indices='all', structure_indices='all'):236    from molsysmt.api_forms.api_openmm_Context import get_time_from_system as _get237    tmp_item = to_openmm_Context(item)238    return _get(tmp_item, indices=indices, structure_indices=structure_indices)239def get_step_from_system(item, indices='all', structure_indices='all'):240    from molsysmt.api_forms.api_openmm_Context import get_step_from_system as _get241    tmp_item = to_openmm_Context(item)242    return _get(tmp_item, indices=indices, structure_indices=structure_indices)243def get_n_structures_from_system(item, indices='all', structure_indices='all'):244    if structure_indices is 'all':245        return 1246    else:247        output = structure_indices.shape[0]248        if output>1:249            raise ValueError('The molecular system has a single frame')250        return output251def get_bonded_atoms_from_system(item, indices='all', structure_indices='all'):252    from molsysmt.api_forms.api_openmm_Topology import get_bonded_atoms_from_system as _get253    tmp_item = to_openmm_Topology(item)254    return _get(tmp_item, indices=indices, structure_indices=structure_indices)255def get_form_from_system(item, indices='all', structure_indices='all'):256    return form_name257def get_has_topology_from_system(item, indices='all', structure_indices='all'):258    return with_topology259def get_has_parameters_from_system(item, indices='all', structure_indices='all'):260    return with_parameters261def get_has_coordinates_from_system(item, indices='all', structure_indices='all'):262    return with_coordinates263def get_has_box_from_system(item, indices='all', structure_indices='all'):264    output = False265    if with_box:266        tmp_box = get_box_from_system(item, indices=indices, structure_indices=structure_indices)267        if tmp_box[0] is not None:268            output = True269    return output270def get_has_bonds_from_system(item, indices='all', structure_indices='all'):271    output = False272    if with_topology:273        if get_n_bonds_from_system(item, indices=indices, structure_indices=structure_indices):274            output = True275    return output276## bond277def get_bond_order_from_bond(item, indices='all', structure_indices='all'):278    from molsysmt.api_forms.api_openmm_Topology import get_bond_order_from_bond as _get279    tmp_item = to_openmm_Topology(item)280    return _get(tmp_item, indices=indices, structure_indices=structure_indices)281def get_bond_type_from_bond(item, indices='all', structure_indices='all'):282    from molsysmt.api_forms.api_openmm_Topology import get_bond_type_from_bond as _get283    tmp_item = to_openmm_Topology(item)284    return _get(tmp_item, indices=indices, structure_indices=structure_indices)285def get_atom_index_from_bond(item, indices='all', structure_indices='all'):286    from molsysmt.api_forms.api_openmm_Topology import get_atom_index_from_bond as _get287    tmp_item = to_openmm_Topology(item)288    return _get(tmp_item, indices=indices, structure_indices=structure_indices)289##### Set290def set_box_to_system(item, indices='all', structure_indices='all', value=None):291    from molsysmt.api_forms.api_openmm_Context import set_box_to_system as _set292    return _set(item.context, indices=indices, structure_indices=structure_indices, value=value)293def set_coordinates_to_system(item, indices='all', structure_indices='all', value=None):294    from molsysmt.api_forms.api_openmm_Context import set_coordinates_to_system as _set...

test_themes.py

Source:test_themes.py

...123        self.assertEqual(t2.cursor_color, (255, 255, 255, 255))124        self.assertEqual(t2.selection_color, (255, 255, 255, 255))125        self.assertEqual(t2.surface_clear_color, (0, 0, 0, 0))126        self.assertEqual(t2.title_font_color, (205, 102, 29, 255))127    def test_get(self) -> None:128        """129        Test custom types get.130        """131        t = pygame_menu.themes.THEME_DEFAULT132        img = pygame_menu.BaseImage(pygame_menu.baseimage.IMAGE_EXAMPLE_GRAY_LINES)133        class Test(object):134            """135            Class to test.136            """137            pass138        def dummy() -> bool:139            """140            Callable.141            """142            return True143        # Test correct144        t._get({}, '', 'alignment', pygame_menu.locals.ALIGN_LEFT)145        t._get({}, '', 'callable', dummy)146        t._get({}, '', 'callable', dummy)147        t._get({}, '', 'color', (1, 1, 1))148        t._get({}, '', 'color', [11, 1, 0, 55])149        t._get({}, '', 'color', [11, 1, 0])150        t._get({}, '', 'color_image', (1, 1, 1))151        t._get({}, '', 'color_image', [11, 1, 0, 55])152        t._get({}, '', 'color_image', [11, 1, 0])153        t._get({}, '', 'color_image', img)154        t._get({}, '', 'color_image_none', [11, 1, 0, 55])155        t._get({}, '', 'color_image_none', img)156        t._get({}, '', 'color_image_none', None)157        t._get({}, '', 'color_none', (1, 1, 1))158        t._get({}, '', 'color_none', [11, 1, 0, 55])159        t._get({}, '', 'color_none', [11, 1, 0])160        t._get({}, '', 'color_none', None)161        t._get({}, '', 'cursor', 1)162        t._get({}, '', 'cursor', None)163        t._get({}, '', 'font', 'font')164        t._get({}, '', 'font', Path('.'))165        t._get({}, '', 'image', img)166        t._get({}, '', 'none', None)167        t._get({}, '', 'position', pygame_menu.locals.POSITION_SOUTHWEST)168        t._get({}, '', 'position_vector', [pygame_menu.locals.POSITION_WEST, pygame_menu.locals.POSITION_NORTH])169        t._get({}, '', 'tuple2', (1, -1))170        t._get({}, '', 'tuple2', (1, 1))171        t._get({}, '', 'tuple2', [1, -1])172        t._get({}, '', 'tuple2int', (0.000000000, 0.0))173        t._get({}, '', 'tuple2int', (1.0, -1))174        t._get({}, '', 'tuple2int', [1, -1])175        t._get({}, '', 'tuple3', [1, -1, 1])176        t._get({}, '', 'tuple3int', [1, -1.0, 1])177        t._get({}, '', 'type', bool)178        t._get({}, '', bool, True)179        t._get({}, '', callable, dummy)180        t._get({}, '', int, 4)181        t._get({}, '', str, 'hi')182        t._get({}, '', Test, Test())183        self.assertTrue(t._get({}, '', 'callable', dummy)())184        # Test raises185        invalid_pos_vector = [186            [pygame_menu.locals.POSITION_WEST, pygame_menu.locals.POSITION_WEST],187            [pygame_menu.locals.POSITION_WEST, 2],188            [pygame_menu.locals.POSITION_WEST, bool]189        ]190        self.assertRaises(AssertionError, lambda: t._get({}, '', 'callable', bool))191        self.assertRaises(AssertionError, lambda: t._get({}, '', 'color', [1, 1, 1, 256]))192        self.assertRaises(AssertionError, lambda: t._get({}, '', 'color', [11, 1, -1]))193        self.assertRaises(AssertionError, lambda: t._get({}, '', 'color', [11, 1, -1]))194        self.assertRaises(AssertionError, lambda: t._get({}, '', 'color', [11, 1]))195        self.assertRaises(AssertionError, lambda: t._get({}, '', 'color', None))196        self.assertRaises(AssertionError, lambda: t._get({}, '', 'cursor', 'hi'))197        self.assertRaises(AssertionError, lambda: t._get({}, '', 'font', 1))198        self.assertRaises(AssertionError, lambda: t._get({}, '', 'image', bool))199        self.assertRaises(AssertionError, lambda: t._get({}, '', 'none', 1))200        self.assertRaises(AssertionError, lambda: t._get({}, '', 'none', bool))201        self.assertRaises(AssertionError, lambda: t._get({}, '', 'position', 'position-invalid'))202        self.assertRaises(AssertionError, lambda: t._get({}, '', 'position_vector', invalid_pos_vector))203        self.assertRaises(AssertionError, lambda: t._get({}, '', 'position_vector', invalid_pos_vector[0]))204        self.assertRaises(AssertionError, lambda: t._get({}, '', 'position_vector', invalid_pos_vector[1]))205        self.assertRaises(AssertionError, lambda: t._get({}, '', 'position_vector', invalid_pos_vector[2]))206        self.assertRaises(AssertionError, lambda: t._get({}, '', 'tuple2', (1, 1, 1)))207        self.assertRaises(AssertionError, lambda: t._get({}, '', 'tuple2.1', (1, 1)))208        self.assertRaises(AssertionError, lambda: t._get({}, '', 'tuple2int', (1.5, 1)))209        self.assertRaises(AssertionError, lambda: t._get({}, '', 'tuple3', (1, 1, 1, 1)))210        self.assertRaises(AssertionError, lambda: t._get({}, '', 'tuple3int', (1, 1, 1.000001)))211        self.assertRaises(AssertionError, lambda: t._get({}, '', 'type', 'bool'))212        self.assertRaises(AssertionError, lambda: t._get({}, '', 'unknown', Test()))213        self.assertRaises(AssertionError, lambda: t._get({}, '', bool, 4.4))214        self.assertRaises(AssertionError, lambda: t._get({}, '', callable, Test()))...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.