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How to use _get method in robotframework-ioslibrary
Best Python code snippet using robotframework-ioslibrary_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()))...
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