molsysmt.form.bcifreader_PdbxContainers_DataContainer package

Submodules

molsysmt.form.bcifreader_PdbxContainers_DataContainer.add module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.add.add(to_item, item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.append_structures module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.append_structures.append_structures(item, structure_id=None, time=None, coordinates=None, box=None, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.attributes module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.copy module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.copy.copy(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.extract module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.extract.extract(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_alternate_location_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_alternate_location_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_b_factor_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_bioassembly_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_box_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_coordinates_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_formal_charge_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_n_bioassemblies_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_n_structures_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_occupancy_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_partial_charge_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_structure_id_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_structural_attributes.get_time_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_atom_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_index_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_order_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_order_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_order_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_order_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_order_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_order_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_order_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_type_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bond_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atom_pairs_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atom_pairs_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atom_pairs_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atom_pairs_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atom_pairs_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atom_pairs_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atom_pairs_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_bonded_atoms_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_chain_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_component_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_entity_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_group_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bond_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bond_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bond_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bond_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bond_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bond_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bond_index_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atom_pairs_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atom_pairs_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atom_pairs_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atom_pairs_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atom_pairs_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atom_pairs_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atom_pairs_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atoms_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atoms_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atoms_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atoms_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atoms_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_inner_bonded_atoms_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_molecule_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_amino_acids_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_amino_acids_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_amino_acids_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_amino_acids_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_amino_acids_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_amino_acids_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_aminoacids_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_atoms_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_atoms_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_atoms_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_atoms_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_atoms_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_atoms_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_bonds_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_chains_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_chains_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_chains_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_chains_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_chains_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_chains_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_chains_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_components_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_components_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_components_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_components_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_components_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_components_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_components_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_dnas_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_dnas_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_dnas_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_dnas_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_dnas_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_dnas_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_dnas_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_entities_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_entities_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_entities_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_entities_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_entities_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_entities_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_entities_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_groups_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_groups_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_groups_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_groups_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_groups_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_groups_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_groups_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_inner_bonds_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_inner_bonds_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_inner_bonds_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_inner_bonds_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_inner_bonds_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_inner_bonds_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_ions_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_ions_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_ions_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_ions_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_ions_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_ions_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_ions_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_lipids_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_lipids_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_lipids_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_lipids_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_lipids_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_lipids_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_lipids_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_molecules_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_molecules_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_molecules_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_molecules_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_molecules_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_molecules_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_molecules_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_nucleotides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_nucleotides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_nucleotides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_nucleotides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_nucleotides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_nucleotides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_nucleotides_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_peptides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_peptides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_peptides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_peptides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_peptides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_peptides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_peptides_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_polysaccharides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_polysaccharides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_polysaccharides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_polysaccharides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_polysaccharides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_polysaccharides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_polysaccharides_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_proteins_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_proteins_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_proteins_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_proteins_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_proteins_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_proteins_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_proteins_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_rnas_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_rnas_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_rnas_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_rnas_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_rnas_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_rnas_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_rnas_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_saccharides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_saccharides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_saccharides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_saccharides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_saccharides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_saccharides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_saccharides_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_small_molecules_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_small_molecules_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_small_molecules_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_small_molecules_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_small_molecules_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_small_molecules_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_small_molecules_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_waters_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_waters_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_waters_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_waters_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_waters_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_waters_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.get_topological_attributes.get_n_waters_from_system(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.has_attribute module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.is_form module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.is_form.is_form(item)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.iterators module

class molsysmt.form.bcifreader_PdbxContainers_DataContainer.iterators.StructuresIterator(molecular_system, atom_indices='all', start=0, stop=None, step=1, chunk=1, structure_indices=None, output_type='values', skip_digestion=False, **kwargs)

Bases: object

class molsysmt.form.bcifreader_PdbxContainers_DataContainer.iterators.TopologyIterator(molecular_system, element='atom', indices='all', start=0, stop=None, step=1, chunk=1, output_type='values', skip_digestion=False, **kwargs)

Bases: object

molsysmt.form.bcifreader_PdbxContainers_DataContainer.merge module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.merge.merge(items, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.set module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_bcifreader_PdbxContainers_DataContainer module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_bcifreader_PdbxContainers_DataContainer.to_bcifreader_PdbxContainers_DataContainer(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_file_pdb module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_file_pdb.to_file_pdb(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_mdtraj_Trajectory module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_mdtraj_Trajectory.to_mdtraj_Trajectory(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys.to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bck module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bck.to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bueno module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolSys_bueno.to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolecularMechanics module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanics(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Structures module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Structures.to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Topology module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_molsysmt_Topology.to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_openmm_Topology module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_openmm_Topology.to_openmm_Topology(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_1 module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_1.to_string_amino_acids_1(item, group_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_3 module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_amino_acids_3.to_string_amino_acids_3(item, group_indices='all', skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_id module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_id.to_string_pdb_id(item, skip_digestion=False)

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_text module

molsysmt.form.bcifreader_PdbxContainers_DataContainer.to_string_pdb_text.to_string_pdb_text(item, atom_indices='all', structure_indices='all', skip_digestion=False)

Module contents