| aa() const | core::conformation::Residue | inline |
| abase2(Size const atomno) const | core::conformation::Residue | inline |
| accpt_pos() const | core::conformation::Residue | inline |
| accpt_pos_sc() const | core::conformation::Residue | inline |
| actcoord() const | core::conformation::Residue | inline |
| actcoord() | core::conformation::Residue | inline |
| actcoord_ | core::conformation::Residue | private |
| actcoord_atoms() const | core::conformation::Residue | inline |
| actual_residue_connection(Size resconnid) const | core::conformation::Residue | inline |
| all_bb_atoms() const | core::conformation::Residue | inline |
| annotated_name(bool const show_all_variants=true) const | core::conformation::Residue | |
| apply_transform_downstream(core::Size const atomno, core::Size const upstream_atomno, numeric::xyzMatrix< Real > const &R, Vector const &v) | core::conformation::Residue | private |
| apply_transform_Rx_plus_v(numeric::xyzMatrix< Real > R, Vector v) | core::conformation::Residue | |
| assign_orbitals() | core::conformation::Residue | private |
| atom(Size const atm_index) const | core::conformation::Residue | inline |
| atom(Size const atm_index) | core::conformation::Residue | inline |
| atom(std::string const &atm_name) const | core::conformation::Residue | inline |
| atom(std::string const &atm_name) | core::conformation::Residue | inline |
| atom_base(Size const atomno) const | core::conformation::Residue | inline |
| atom_begin() | core::conformation::Residue | inline |
| atom_begin() const | core::conformation::Residue | inline |
| atom_depends_on_lower(core::Size const atom_index) const | core::conformation::Residue | |
| atom_depends_on_upper(core::Size const atom_index) const | core::conformation::Residue | |
| atom_end() | core::conformation::Residue | inline |
| atom_end() const | core::conformation::Residue | inline |
| atom_index(std::string const &atm) const | core::conformation::Residue | inline |
| atom_is_backbone(Size const atomno) const | core::conformation::Residue | inline |
| atom_is_hydrogen(Size const atomno) const | core::conformation::Residue | inline |
| atom_is_polar_hydrogen(Size ind) const | core::conformation::Residue | inline |
| atom_name(Size const atm) const | core::conformation::Residue | inline |
| atom_type(Size const atomno) const | core::conformation::Residue | inline |
| atom_type_index(Size const atomno) const | core::conformation::Residue | inline |
| atom_type_set() const | core::conformation::Residue | inline |
| atomic_charge(Size const atomno) const | core::conformation::Residue | inline |
| AtomIndices typedef | core::conformation::Residue | |
| atoms() const | core::conformation::Residue | inline |
| atoms() | core::conformation::Residue | inline |
| atoms_ | core::conformation::Residue | private |
| atoms_with_orb_index() const | core::conformation::Residue | inline |
| AtomType typedef | core::conformation::Residue | |
| attached_H_begin(Size const atom) const | core::conformation::Residue | inline |
| attached_H_begin() const | core::conformation::Residue | inline |
| attached_H_end(Size const atom) const | core::conformation::Residue | inline |
| attached_H_end() const | core::conformation::Residue | inline |
| backbone_aa() const | core::conformation::Residue | inline |
| bonded_neighbor(Size const atm) const | core::conformation::Residue | inline |
| bonded_orbitals(Size const atm) const | core::conformation::Residue | inline |
| build_atom_ideal(int const atomno, Conformation const &conformation) const | core::conformation::Residue | inline |
| build_orbital_xyz(Size const orbital_index) const | core::conformation::Residue | inline |
| carbohydrate_info() const | core::conformation::Residue | |
| chain() const | core::conformation::Residue | inline |
| chain(core::Size const setting) | core::conformation::Residue | inline |
| chain_ | core::conformation::Residue | private |
| chi() const | core::conformation::Residue | inline |
| chi() | core::conformation::Residue | inline |
| chi(utility::vector1< Real > const &chis) | core::conformation::Residue | inline |
| chi(Size const chino) const | core::conformation::Residue | inline |
| chi_ | core::conformation::Residue | private |
| chi_atoms() const | core::conformation::Residue | inline |
| chi_atoms(Size const chino) const | core::conformation::Residue | inline |
| chi_rotamers(Size const chino) const | core::conformation::Residue | inline |
| clear_residue_connections() | core::conformation::Residue | |
| clone() const | core::conformation::Residue | |
| clone_flipping_chirality(core::chemical::ResidueTypeSet const &residue_type_set) const | core::conformation::Residue | |
| connect_atom(Residue const &other) const | core::conformation::Residue | |
| connect_map(Size resconn_index) const | core::conformation::Residue | inline |
| connect_map_ | core::conformation::Residue | private |
| connect_map_size() const | core::conformation::Residue | inline |
| connected_residue_at_lower() const | core::conformation::Residue | |
| connected_residue_at_resconn(Size const resconn_index) const | core::conformation::Residue | inline |
| connected_residue_at_upper() const | core::conformation::Residue | |
| connection_distance(conformation::Conformation const &conf, Size const resconn_index, Vector const &matchpoint) const | core::conformation::Residue | |
| connection_incomplete(Size resconnid) const | core::conformation::Residue | |
| connections_match(Residue const &other) const | core::conformation::Residue | |
| connections_to_residue(Residue const &other) const | core::conformation::Residue | inline |
| connections_to_residue(Size const other_resid) const | core::conformation::Residue | inline |
| connections_to_residues_ | core::conformation::Residue | private |
| copy_residue_connections(Residue const &src_rsd, bool const suppress_warnings=false) | core::conformation::Residue | |
| copy_residue_connections_from(Residue const &src) | core::conformation::Residue | |
| create_residue() const | core::conformation::Residue | inline |
| create_rotamer() const | core::conformation::Residue | inline |
| cut_bond_neighbor(Size const atm) const | core::conformation::Residue | inline |
| data() const | core::conformation::Residue | inline |
| data_cache_ | core::conformation::Residue | private |
| data_ptr() const | core::conformation::Residue | inline |
| determine_nonstandard_polymer_status() | core::conformation::Residue | private |
| fill_missing_atoms(utility::vector1< bool > &missing, Conformation const &conformation, bool fail=true) | core::conformation::Residue | |
| first_adjacent_heavy_atom(uint const atom_index) const | core::conformation::Residue | |
| first_sidechain_atom() const | core::conformation::Residue | inline |
| first_sidechain_hydrogen() const | core::conformation::Residue | inline |
| get_adjacent_heavy_atoms(uint const atom_index) const | core::conformation::Residue | |
| get_atoms_exocyclic_to_ring_atom(uint const atom_index) const | core::conformation::Residue | |
| get_hydrogens_bonded_to_ring_atom(uint const atom_index) const | core::conformation::Residue | |
| get_metal_binding_atoms(AtomIndices &metal_binding_indices) const | core::conformation::Residue | inline |
| get_pseudobonds_to_residue(Size resid) const | core::conformation::Residue | |
| get_self_ptr() const | core::conformation::Residue | inline |
| get_self_ptr() | core::conformation::Residue | inline |
| get_self_weak_ptr() const | core::conformation::Residue | inline |
| get_self_weak_ptr() | core::conformation::Residue | inline |
| get_substituents_to_ring_atom(uint const atom_index) const | core::conformation::Residue | |
| Haro_index() const | core::conformation::Residue | inline |
| has(std::string const &atm) const | core::conformation::Residue | inline |
| has_incomplete_connection() const | core::conformation::Residue | |
| has_incomplete_connection(core::Size const atomno) const | core::conformation::Residue | |
| has_lower_connect() const | core::conformation::Residue | inline |
| has_property(std::string const &property) const | core::conformation::Residue | inline |
| has_sc_orbitals() const | core::conformation::Residue | inline |
| has_shadow_atoms() const | core::conformation::Residue | inline |
| has_upper_connect() const | core::conformation::Residue | inline |
| has_variant_type(chemical::VariantType const variant_type) const | core::conformation::Residue | inline |
| heavyatom_has_polar_hydrogens(Size ind) const | core::conformation::Residue | inline |
| heavyatom_is_an_acceptor(Size ind) const | core::conformation::Residue | inline |
| heavyAtoms_end() const | core::conformation::Residue | inline |
| Hpol_index() const | core::conformation::Residue | inline |
| Hpos_apolar() const | core::conformation::Residue | inline |
| Hpos_polar() const | core::conformation::Residue | inline |
| Hpos_polar_sc() const | core::conformation::Residue | inline |
| icoor(Size const atm) const | core::conformation::Residue | inline |
| init_residue_from_other(Residue const &src) | core::conformation::Residue | private |
| inter_residue_connection_partner(int connid, Conformation const &conformation) const | core::conformation::Residue | |
| is_apolar() const | core::conformation::Residue | inline |
| is_aramid() const | core::conformation::Residue | inline |
| is_aromatic() const | core::conformation::Residue | inline |
| is_bonded(Residue const &other) const | core::conformation::Residue | inline |
| is_bonded(Size const other_residue_index) const | core::conformation::Residue | inline |
| is_branch_point() const | core::conformation::Residue | inline |
| is_carbohydrate() const | core::conformation::Residue | inline |
| is_charged() const | core::conformation::Residue | inline |
| is_coarse() const | core::conformation::Residue | inline |
| is_d_rna() const | core::conformation::Residue | inline |
| is_DNA() const | core::conformation::Residue | inline |
| is_l_rna() const | core::conformation::Residue | inline |
| is_ligand() const | core::conformation::Residue | inline |
| is_lower_terminus() const | core::conformation::Residue | inline |
| is_meta_aramid() const | core::conformation::Residue | inline |
| is_metal() const | core::conformation::Residue | inline |
| is_metalbinding() const | core::conformation::Residue | inline |
| is_NA() const | core::conformation::Residue | inline |
| is_ortho_aramid() const | core::conformation::Residue | inline |
| is_para_aramid() const | core::conformation::Residue | inline |
| is_peptoid() const | core::conformation::Residue | inline |
| is_polar() const | core::conformation::Residue | inline |
| is_polymer() const | core::conformation::Residue | inline |
| is_polymer_bonded(Residue const &other) const | core::conformation::Residue | inline |
| is_polymer_bonded(Size const other_index) const | core::conformation::Residue | inline |
| is_post_methylene_meta_aramid() const | core::conformation::Residue | inline |
| is_post_methylene_ortho_aramid() const | core::conformation::Residue | inline |
| is_post_methylene_para_aramid() const | core::conformation::Residue | inline |
| is_pre_methylene_meta_aramid() const | core::conformation::Residue | inline |
| is_pre_methylene_ortho_aramid() const | core::conformation::Residue | inline |
| is_pre_methylene_para_aramid() const | core::conformation::Residue | inline |
| is_pre_methylene_post_methylene_meta_aramid() const | core::conformation::Residue | inline |
| is_pre_methylene_post_methylene_ortho_aramid() const | core::conformation::Residue | inline |
| is_pre_methylene_post_methylene_para_aramid() const | core::conformation::Residue | inline |
| is_protein() const | core::conformation::Residue | inline |
| is_pseudo_bonded(Residue const &other) const | core::conformation::Residue | inline |
| is_pseudo_bonded(Size const other_index) const | core::conformation::Residue | inline |
| is_purine() const | core::conformation::Residue | inline |
| is_pyrimidine() const | core::conformation::Residue | inline |
| is_repulsive(Size const atomno) const | core::conformation::Residue | inline |
| is_RNA() const | core::conformation::Residue | inline |
| is_similar_aa(Residue const &other) const | core::conformation::Residue | inline |
| is_similar_rotamer(Residue const &other) const | core::conformation::Residue | |
| is_sri() const | core::conformation::Residue | inline |
| is_surface() const | core::conformation::Residue | inline |
| is_terminus() const | core::conformation::Residue | inline |
| is_TNA() const | core::conformation::Residue | inline |
| is_triazolemer() const | core::conformation::Residue | inline |
| is_upper_terminus() const | core::conformation::Residue | inline |
| is_virtual(Size const atomno) const | core::conformation::Residue | inline |
| is_virtual_residue() const | core::conformation::Residue | inline |
| is_water() const | core::conformation::Residue | inline |
| last_backbone_atom() const | core::conformation::Residue | inline |
| lower_connect() const | core::conformation::Residue | inline |
| lower_connect_atom() const | core::conformation::Residue | inline |
| mainchain_atom(Size const i) const | core::conformation::Residue | inline |
| mainchain_atoms() const | core::conformation::Residue | inline |
| mainchain_torsion(Size const torsion) const | core::conformation::Residue | inline |
| mainchain_torsions() const | core::conformation::Residue | inline |
| mainchain_torsions() | core::conformation::Residue | inline |
| mainchain_torsions(utility::vector1< Real > const &torsions) | core::conformation::Residue | inline |
| mainchain_torsions_ | core::conformation::Residue | private |
| mark_connect_incomplete(Size resconn_index) | core::conformation::Residue | |
| mirrored_relative_to_type() const | core::conformation::Residue | inline |
| mirrored_relative_to_type_ | core::conformation::Residue | private |
| misplaced() const | core::conformation::Residue | inline |
| misplaced_ | core::conformation::Residue | private |
| mm_atom_name(Size const atom) const | core::conformation::Residue | inline |
| n_bonded_neighbor_all_res(core::Size const atomno, bool virt=false) const | core::conformation::Residue | |
| n_current_residue_connections() const | core::conformation::Residue | |
| n_hbond_acceptors() const | core::conformation::Residue | inline |
| n_hbond_donors() const | core::conformation::Residue | inline |
| n_mainchain_atoms() const | core::conformation::Residue | inline |
| n_non_polymeric_residue_connections() const | core::conformation::Residue | inline |
| n_nus() const | core::conformation::Residue | inline |
| n_orbitals() const | core::conformation::Residue | inline |
| n_polymeric_residue_connections() const | core::conformation::Residue | inline |
| n_possible_residue_connections() const | core::conformation::Residue | inline |
| n_virtual_atoms() const | core::conformation::Residue | inline |
| na_analogue() const | core::conformation::Residue | inline |
| name() const | core::conformation::Residue | inline |
| name1() const | core::conformation::Residue | inline |
| name3() const | core::conformation::Residue | inline |
| natoms() const | core::conformation::Residue | inline |
| nbr_atom() const | core::conformation::Residue | inline |
| nbr_atom_xyz() const | core::conformation::Residue | inline |
| nbr_radius() const | core::conformation::Residue | inline |
| nbrs(Size const atm) const | core::conformation::Residue | inline |
| nchi() const | core::conformation::Residue | inline |
| nheavyatoms() const | core::conformation::Residue | inline |
| nonconst_data() | core::conformation::Residue | inline |
| nonconst_data_ptr() | core::conformation::Residue | inline |
| nonstandard_polymer_ | core::conformation::Residue | private |
| nu(core::uint const index) const | core::conformation::Residue | inline |
| nu_atoms() const | core::conformation::Residue | inline |
| nu_atoms(core::uint const index) const | core::conformation::Residue | inline |
| nus() const | core::conformation::Residue | inline |
| nus() | core::conformation::Residue | inline |
| nus_ | core::conformation::Residue | private |
| operator=(Residue const &rhs) | core::conformation::Residue | private |
| orbital_name(Size const orbital_index) const | core::conformation::Residue | inline |
| orbital_type(Size const orbital_index) const | core::conformation::Residue | inline |
| orbital_type_index(Size const orbital_index) const | core::conformation::Residue | inline |
| orbital_xyz(Size const orbital_index) const | core::conformation::Residue | inline |
| orbitals_ | core::conformation::Residue | private |
| orient_onto_location(Size center, Size nbr1, Size nbr2, Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton) | core::conformation::Residue | |
| orient_onto_location(Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton) | core::conformation::Residue | |
| orient_onto_residue(Residue const &src) | core::conformation::Residue | |
| orient_onto_residue(Residue const &src, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) | core::conformation::Residue | |
| orient_onto_residue(Residue const &src, Size center, Size nbr1, Size nbr2, Size src_center, Size src_nbr1, Size src_nbr2) | core::conformation::Residue | private |
| orient_onto_residue_peptoid(Residue const &src, Conformation const &conformation) | core::conformation::Residue | |
| path_distance(Size atom) const | core::conformation::Residue | inline |
| path_distance(Size at1, Size at2) const | core::conformation::Residue | inline |
| path_distances() const | core::conformation::Residue | inline |
| place(Residue const &src, Conformation const &conformation, bool preserve_c_beta=false) | core::conformation::Residue | |
| polymeric_oriented_sequence_distance(Residue const &other) const | core::conformation::Residue | inline |
| polymeric_sequence_distance(Residue const &other) const | core::conformation::Residue | inline |
| pseudobonds() const | core::conformation::Residue | inline |
| pseudobonds_ | core::conformation::Residue | private |
| requires_actcoord() const | core::conformation::Residue | inline |
| Residue(ResidueTypeCOP rsd_type_in, bool const dummy_arg) | core::conformation::Residue | |
| Residue(ResidueType const &rsd_type_in, bool const dummy_arg) | core::conformation::Residue | |
| Residue(ResidueType const &rsd_type_in, Residue const ¤t_rsd, Conformation const &conformation, bool preserve_c_beta=false, bool allow_alternate_backbone_matching=false) | core::conformation::Residue | |
| Residue(Residue const &src) | core::conformation::Residue | |
| Residue(Residue const &src, core::chemical::ResidueTypeCOP new_restype, bool flip_chirality) | core::conformation::Residue | private |
| residue_connect_atom_index(Size const resconn_id) const | core::conformation::Residue | inline |
| residue_connection(Size const resconn_index) const | core::conformation::Residue | inline |
| residue_connection_conn_id(Size const resconn_index) const | core::conformation::Residue | inline |
| residue_connection_partner(Size const resconn_index) const | core::conformation::Residue | inline |
| residue_connection_partner(Size const resconn_index, Size const otherres, Size const other_connid) | core::conformation::Residue | |
| ResidueType typedef | core::conformation::Residue | |
| ResidueTypeCOP typedef | core::conformation::Residue | |
| resolve_partial_atom_id(id::PartialAtomID const &partial_id) const | core::conformation::Residue | |
| ring_conformer(core::uint const ring_num, core::Real limit=90.0) const | core::conformation::Residue | |
| RNA_info() const | core::conformation::Residue | inline |
| rsd_type_ | core::conformation::Residue | private |
| rsd_type_ptr_ | core::conformation::Residue | private |
| select_orient_atoms(Size ¢er, Size &nbr1, Size &nbr2) const | core::conformation::Residue | |
| seqpos() const | core::conformation::Residue | inline |
| seqpos(Size const setting) | core::conformation::Residue | inline |
| seqpos_ | core::conformation::Residue | private |
| set_all_chi(utility::vector1< Real > const &chis) | core::conformation::Residue | |
| set_all_nu(utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) | core::conformation::Residue | |
| set_all_ring_nu(Size start, Size end, utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) | core::conformation::Residue | |
| set_chi(int const chino, Real const setting) | core::conformation::Residue | |
| set_d(int const chino, Real const setting) | core::conformation::Residue | |
| set_mirrored_relative_to_type(bool const setting) | core::conformation::Residue | inline |
| set_orbital_xyz(core::Size const orbital_index, Vector const &xyz_in) | core::conformation::Residue | inline |
| set_pseudobonds_to_residue(Size resid, PseudoBondCollectionCOP pbs) | core::conformation::Residue | |
| set_tau(Size const nuno, Real const setting) | core::conformation::Residue | |
| set_theta(int const chino, Real const setting) | core::conformation::Residue | |
| set_xyz(core::Size const atm_index, Vector const &xyz_in) | core::conformation::Residue | |
| set_xyz(std::string const &atm_name, Vector const &xyz_in) | core::conformation::Residue | |
| show(std::ostream &output=std::cout, bool output_atomic_details=false) const | core::conformation::Residue | |
| sidechainAtoms_begin() const | core::conformation::Residue | inline |
| type() const | core::conformation::Residue | inline |
| type_ptr() const | core::conformation::Residue | inline |
| update_actcoord() | core::conformation::Residue | |
| update_connections_to_other_residue(Residue const &other_rsd) | core::conformation::Residue | |
| update_connections_to_residues() | core::conformation::Residue | private |
| update_nus() | core::conformation::Residue | |
| update_orbital_coords() | core::conformation::Residue | inline |
| update_sequence_numbering(utility::vector1< Size > const &old2new) | core::conformation::Residue | |
| upper_connect() const | core::conformation::Residue | inline |
| upper_connect_atom() const | core::conformation::Residue | inline |
| xyz(Size const atm_index) const | core::conformation::Residue | inline |
| xyz(std::string const &atm_name) const | core::conformation::Residue | inline |
| ~Residue() override | core::conformation::Residue | |
1.8.7