molsysmt.Topology# add(to_item, item[, keep_ids, skip_digestion]) append_structures(item[, structure_id, ...]) copy(item[, skip_digestion]) extract(item[, atom_indices, ...]) get_topological_attributes has_attribute(molecular_system, attribute[, ...]) Checking instance-aware attribute availability for native topology. is_form(item) TopologyIterator(molecular_system[, ...]) merge(items[, atom_indices, keep_ids, ...]) set to_file_h5msm to_file_pdb to_file_psf to_mdtraj_Topology to_networkx_Graph to_nglview_NGLWidget to_openmm_Topology to_parmed_Structure to_pytraj_Topology to_string_amino_acids_1 to_string_amino_acids_3 to_string_pdb_text