| aa(AA const &type) | core::chemical::ResidueType | inline |
| aa(std::string const &type) | core::chemical::ResidueType | inline |
| aa() const | core::chemical::ResidueType | inline |
| aa_ | core::chemical::ResidueType | private |
| abase2(Size const atomno) const | core::chemical::ResidueType | |
| abase2_ | core::chemical::ResidueType | private |
| abase2_indices_ | core::chemical::ResidueType | private |
| acceptor_atoms() | core::chemical::ResidueType | |
| accpt_pos() const | core::chemical::ResidueType | inline |
| accpt_pos_ | core::chemical::ResidueType | private |
| accpt_pos_sc() const | core::chemical::ResidueType | inline |
| accpt_pos_sc_ | core::chemical::ResidueType | private |
| actcoord_atoms() const | core::chemical::ResidueType | inline |
| actcoord_atoms_ | core::chemical::ResidueType | private |
| actcoord_atoms_indices_ | core::chemical::ResidueType | private |
| add_actcoord_atom(std::string const &atom) | core::chemical::ResidueType | |
| add_adduct(Adduct &adduct_in) | core::chemical::ResidueType | inline |
| add_atom(std::string const &atom_name, std::string const &atom_type_name, std::string const &mm_atom_type_name, Real const charge) | core::chemical::ResidueType | |
| add_atom(std::string const &atom_name="") | core::chemical::ResidueType | |
| add_atom_alias(std::string const &rosetta_atom, std::string const &alias) | core::chemical::ResidueType | |
| add_bond(std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel=SingleBond) | core::chemical::ResidueType | |
| add_bond(VD atom1, VD atom2, BondName bondLabel=SingleBond) | core::chemical::ResidueType | |
| add_chi(Size const chino, VD atom1, VD atom2, VD atom3, VD atom4) | core::chemical::ResidueType | |
| add_chi(VD atom1, VD atom2, VD atom3, VD atom4) | core::chemical::ResidueType | |
| add_chi(Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4) | core::chemical::ResidueType | |
| add_chi(std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4) | core::chemical::ResidueType | |
| add_chi_rotamer(Size const chino, Real const mean, Real const sdev) | core::chemical::ResidueType | |
| add_chi_rotamer_to_last_chi(core::Angle const mean, core::Angle const sdev) | core::chemical::ResidueType | |
| add_cut_bond(std::string const &atom_name1, std::string const &atom_name2) | core::chemical::ResidueType | |
| add_metalbinding_atom(std::string const atom_name) | core::chemical::ResidueType | |
| add_nu(core::uint const nu_index, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4) | core::chemical::ResidueType | |
| add_numeric_property(std::string const &tag, core::Real value) | core::chemical::ResidueType | |
| add_orbital(std::string &orbital_name, std::string &orbital_type_name) | core::chemical::ResidueType | |
| add_orbital_bond(std::string const &atom_name1, std::string const &orbital_name) | core::chemical::ResidueType | |
| add_property(std::string const &property) | core::chemical::ResidueType | |
| add_residue_connection(std::string const &atom_name) | core::chemical::ResidueType | |
| add_string_property(std::string const &tag, std::string value) | core::chemical::ResidueType | |
| add_variant_type(VariantType const &variant_type) | core::chemical::ResidueType | |
| all_bb_atoms() const | core::chemical::ResidueType | inline |
| all_bb_atoms_ | core::chemical::ResidueType | private |
| all_sc_atoms() const | core::chemical::ResidueType | inline |
| all_sc_atoms_ | core::chemical::ResidueType | private |
| apolar_hydrogens() | core::chemical::ResidueType | |
| aromatic_atoms() | core::chemical::ResidueType | |
| assign_internal_coordinates() | core::chemical::ResidueType | |
| assign_internal_coordinates(core::chemical::VD new_root) | core::chemical::ResidueType | |
| assign_neighbor_atom() | core::chemical::ResidueType | |
| atom(Size const atom_index) | core::chemical::ResidueType | |
| atom(Size const atom_index) const | core::chemical::ResidueType | |
| atom(std::string const &atom_name) | core::chemical::ResidueType | |
| atom(std::string const &atom_name) const | core::chemical::ResidueType | |
| atom(VD const atom_vd) | core::chemical::ResidueType | |
| atom(VD const atom_vd) const | core::chemical::ResidueType | |
| atom_2_residue_connection_map_ | core::chemical::ResidueType | private |
| atom_aliases_ | core::chemical::ResidueType | private |
| atom_base(Size const atomno) const | core::chemical::ResidueType | |
| atom_base(VD const atomno) const | core::chemical::ResidueType | |
| atom_base_ | core::chemical::ResidueType | private |
| atom_base_indices_ | core::chemical::ResidueType | private |
| atom_being_shadowed(Size atom_shadowing) const | core::chemical::ResidueType | inline |
| atom_forms_residue_connection(Size const atomid) | core::chemical::ResidueType | inline |
| atom_index(std::string const &name) const | core::chemical::ResidueType | |
| atom_index(VD const &vd) const | core::chemical::ResidueType | |
| atom_is_backbone(Size const atomno) const | core::chemical::ResidueType | inline |
| atom_is_hydrogen(Size const atomno) const | core::chemical::ResidueType | inline |
| atom_is_polar_hydrogen(Size atomno) const | core::chemical::ResidueType | inline |
| atom_iterators() const | core::chemical::ResidueType | inline |
| atom_name(Size const index) const | core::chemical::ResidueType | |
| atom_name(VD const vd) const | core::chemical::ResidueType | |
| atom_name_to_vd_ | core::chemical::ResidueType | private |
| atom_shadowed_ | core::chemical::ResidueType | private |
| atom_shadowed_indices_ | core::chemical::ResidueType | private |
| atom_type(Size const atomno) const | core::chemical::ResidueType | |
| atom_type(VD const vd) const | core::chemical::ResidueType | |
| atom_type_set() const | core::chemical::ResidueType | inline |
| atom_type_set_ptr() const | core::chemical::ResidueType | inline |
| atom_types_ | core::chemical::ResidueType | private |
| atom_vertex(std::string const &name) const | core::chemical::ResidueType | |
| atom_vertex(Size const &atomno) const | core::chemical::ResidueType | |
| atoms_are_bonded(core::Size const atomindex1, core::Size const atomindex2) const | core::chemical::ResidueType | |
| atoms_last_controlled_by_chi() const | core::chemical::ResidueType | inline |
| atoms_last_controlled_by_chi(Size chi) const | core::chemical::ResidueType | inline |
| atoms_last_controlled_by_chi_ | core::chemical::ResidueType | private |
| atoms_with_orb_index() const | core::chemical::ResidueType | inline |
| atoms_with_orb_index_ | core::chemical::ResidueType | private |
| atoms_within_one_bond_of_a_residue_connection(Size resconn) const | core::chemical::ResidueType | inline |
| atoms_within_one_bond_of_a_residue_connection_ | core::chemical::ResidueType | private |
| atoms_within_two_bonds_of_a_residue_connection(Size resconn) const | core::chemical::ResidueType | inline |
| atoms_within_two_bonds_of_a_residue_connection_ | core::chemical::ResidueType | private |
| attached_H_begin(Size const atom) const | core::chemical::ResidueType | inline |
| attached_H_begin() const | core::chemical::ResidueType | inline |
| attached_H_begin_ | core::chemical::ResidueType | private |
| attached_H_end(Size const atom) const | core::chemical::ResidueType | inline |
| attached_H_end() const | core::chemical::ResidueType | inline |
| attached_H_end_ | core::chemical::ResidueType | private |
| autodetermine_chi_bonds(core::Size max_proton_chi_samples=500) | core::chemical::ResidueType | |
| backbone_aa(std::string const &type) | core::chemical::ResidueType | inline |
| backbone_aa() const | core::chemical::ResidueType | inline |
| backbone_aa_ | core::chemical::ResidueType | private |
| base_restype_name(std::string const &in) | core::chemical::ResidueType | inline |
| base_restype_name() const | core::chemical::ResidueType | inline |
| base_restype_name_ | core::chemical::ResidueType | private |
| bond(ED const ed) | core::chemical::ResidueType | |
| bond(ED const ed) const | core::chemical::ResidueType | |
| bond(std::string const &atom1, std::string const &atom2) | core::chemical::ResidueType | |
| bond(std::string const &atom1, std::string const &atom2) const | core::chemical::ResidueType | |
| bond_iterators() const | core::chemical::ResidueType | inline |
| bond_iterators(VD const &atom) const | core::chemical::ResidueType | inline |
| bondangle(Size const bondang) const | core::chemical::ResidueType | inline |
| bondangle_atom_sets_ | core::chemical::ResidueType | private |
| bondangles_for_atom(Size atomno) const | core::chemical::ResidueType | inline |
| bondangles_for_atom_ | core::chemical::ResidueType | private |
| bonded_neighbor(Size const atomno) const | core::chemical::ResidueType | |
| bonded_neighbor_ | core::chemical::ResidueType | private |
| bonded_neighbor_iterators(VD const &atom) const | core::chemical::ResidueType | |
| bonded_neighbor_type_ | core::chemical::ResidueType | private |
| bonded_neighbor_types(Size const atomno) const | core::chemical::ResidueType | |
| bonded_orbitals(Size const atomno) const | core::chemical::ResidueType | inline |
| carbohydrate_info() const | core::chemical::ResidueType | |
| carbohydrate_info_ | core::chemical::ResidueType | private |
| chi_2_proton_chi(Size chi_index) const | core::chemical::ResidueType | inline |
| chi_2_proton_chi_ | core::chemical::ResidueType | private |
| chi_atom_vds(Size const chino) const | core::chemical::ResidueType | inline |
| chi_atoms(Size const chino) const | core::chemical::ResidueType | inline |
| chi_atoms() const | core::chemical::ResidueType | inline |
| chi_atoms_ | core::chemical::ResidueType | private |
| chi_atoms_indices_ | core::chemical::ResidueType | private |
| chi_rotamers(Size const chino) const | core::chemical::ResidueType | inline |
| chi_rotamers_ | core::chemical::ResidueType | private |
| clone() const | core::chemical::ResidueType | |
| conformer_set_ | core::chemical::ResidueType | private |
| cut_bond_neighbor(Size const atomno) const | core::chemical::ResidueType | inline |
| cut_bond_neighbor_ | core::chemical::ResidueType | private |
| cut_bond_neighbor_indices_ | core::chemical::ResidueType | private |
| debug_dump_icoor() const | core::chemical::ResidueType | |
| defined_adducts() const | core::chemical::ResidueType | inline |
| defined_adducts_ | core::chemical::ResidueType | private |
| delete_atom(std::string const &name) | core::chemical::ResidueType | |
| delete_atom(Size const index) | core::chemical::ResidueType | |
| delete_atom_alias(std::string const &alias) | core::chemical::ResidueType | |
| delete_property(std::string const &property) | core::chemical::ResidueType | |
| dihedral(Size const dihe) const | core::chemical::ResidueType | inline |
| dihedral_atom_sets_ | core::chemical::ResidueType | private |
| dihedrals_for_atom(Size atomno) const | core::chemical::ResidueType | inline |
| dihedrals_for_atom_ | core::chemical::ResidueType | private |
| dump_vd_info() const | core::chemical::ResidueType | |
| element_set() const | core::chemical::ResidueType | inline |
| elements_ | core::chemical::ResidueType | private |
| fill_ideal_xyz_from_icoor() | core::chemical::ResidueType | |
| finalize() | core::chemical::ResidueType | |
| finalized_ | core::chemical::ResidueType | private |
| first_sidechain_atom() const | core::chemical::ResidueType | inline |
| first_sidechain_hydrogen() const | core::chemical::ResidueType | inline |
| first_sidechain_hydrogen_ | core::chemical::ResidueType | private |
| force_bb_ | core::chemical::ResidueType | private |
| force_nbr_atom_orient(bool force_orient) | core::chemical::ResidueType | inline |
| force_nbr_atom_orient() const | core::chemical::ResidueType | inline |
| force_nbr_atom_orient_ | core::chemical::ResidueType | private |
| gasteiger_atom_type(Size const atomno) const | core::chemical::ResidueType | |
| gasteiger_atom_types_ | core::chemical::ResidueType | private |
| generate_atom_indices() | core::chemical::ResidueType | private |
| get_metal_binding_atoms(AtomIndices &metal_binding_indices) const | core::chemical::ResidueType | inline |
| get_ncaa_rotlib_n_bin_per_rot(Size n_rot) | core::chemical::ResidueType | inline |
| get_ncaa_rotlib_n_bin_per_rot() const | core::chemical::ResidueType | inline |
| get_ncaa_rotlib_path() const | core::chemical::ResidueType | inline |
| get_numeric_property(std::string const &tag) const | core::chemical::ResidueType | |
| get_peptoid_rotlib_n_bin_per_rot(Size n_rot) | core::chemical::ResidueType | inline |
| get_peptoid_rotlib_n_bin_per_rot() const | core::chemical::ResidueType | inline |
| get_peptoid_rotlib_path() const | core::chemical::ResidueType | inline |
| get_RotamerLibraryName() const | core::chemical::ResidueType | |
| get_string_property(std::string const &tag) const | core::chemical::ResidueType | |
| get_use_ncaa_rotlib() const | core::chemical::ResidueType | inline |
| get_use_peptoid_rotlib() const | core::chemical::ResidueType | inline |
| graph() const | core::chemical::ResidueType | inline |
| graph_ | core::chemical::ResidueType | private |
| Haro_index() const | core::chemical::ResidueType | inline |
| Haro_index_ | core::chemical::ResidueType | private |
| has(std::string const &atom_name) const | core::chemical::ResidueType | inline |
| has(VD const vd) const | core::chemical::ResidueType | inline |
| has_orbital(std::string const &orbital_name) const | core::chemical::ResidueType | inline |
| has_property(std::string const &property) const | core::chemical::ResidueType | |
| has_sc_orbitals() const | core::chemical::ResidueType | |
| has_variant_type(VariantType const &variant_type) const | core::chemical::ResidueType | |
| heavy_atom_with_hydrogens() | core::chemical::ResidueType | |
| heavy_atom_with_polar_hydrogens() | core::chemical::ResidueType | |
| heavy_atoms() | core::chemical::ResidueType | |
| heavyatom_has_polar_hydrogens(Size atomno) const | core::chemical::ResidueType | inline |
| heavyatom_is_an_acceptor(Size atomno) const | core::chemical::ResidueType | inline |
| Hpol_index() const | core::chemical::ResidueType | inline |
| Hpol_index_ | core::chemical::ResidueType | private |
| Hpos_apolar() const | core::chemical::ResidueType | inline |
| Hpos_apolar_ | core::chemical::ResidueType | private |
| Hpos_polar() const | core::chemical::ResidueType | inline |
| Hpos_polar_ | core::chemical::ResidueType | private |
| Hpos_polar_sc() const | core::chemical::ResidueType | inline |
| Hpos_polar_sc_ | core::chemical::ResidueType | private |
| hydrogens() | core::chemical::ResidueType | |
| icoor(Size const atm) const | core::chemical::ResidueType | |
| icoor(VD const atm) const | core::chemical::ResidueType | |
| icoor_ | core::chemical::ResidueType | private |
| improper_dihedral(Size const dihe) const | core::chemical::ResidueType | inline |
| improper_dihedral_atom_sets_ | core::chemical::ResidueType | private |
| improper_dihedrals_for_atom(Size atomno) const | core::chemical::ResidueType | inline |
| improper_dihedrals_for_atom_ | core::chemical::ResidueType | private |
| interchangeability_group() const | core::chemical::ResidueType | inline |
| interchangeability_group(std::string setting) | core::chemical::ResidueType | inline |
| interchangeability_group_ | core::chemical::ResidueType | private |
| is_acetylated_nterminus() const | core::chemical::ResidueType | |
| is_adduct() const | core::chemical::ResidueType | |
| is_alpha_aa() const | core::chemical::ResidueType | |
| is_aromatic() const | core::chemical::ResidueType | |
| is_beta_aa() const | core::chemical::ResidueType | |
| is_branch_lower_terminus() const | core::chemical::ResidueType | |
| is_carbohydrate() const | core::chemical::ResidueType | |
| is_charged() const | core::chemical::ResidueType | |
| is_coarse() const | core::chemical::ResidueType | |
| is_cyclic() const | core::chemical::ResidueType | |
| is_d_aa() const | core::chemical::ResidueType | |
| is_DNA() const | core::chemical::ResidueType | |
| is_l_aa() const | core::chemical::ResidueType | |
| is_ligand() const | core::chemical::ResidueType | |
| is_lipid() const | core::chemical::ResidueType | |
| is_lower_terminus() const | core::chemical::ResidueType | |
| is_membrane() const | core::chemical::ResidueType | |
| is_metal() const | core::chemical::ResidueType | |
| is_metalbinding() const | core::chemical::ResidueType | |
| is_methylated_cterminus() const | core::chemical::ResidueType | |
| is_NA() const | core::chemical::ResidueType | |
| is_peptoid() const | core::chemical::ResidueType | |
| is_polar() const | core::chemical::ResidueType | |
| is_polymer() const | core::chemical::ResidueType | |
| is_protein() const | core::chemical::ResidueType | |
| is_proton_chi(Size const chino) const | core::chemical::ResidueType | inline |
| is_proton_chi_ | core::chemical::ResidueType | private |
| is_RNA() const | core::chemical::ResidueType | |
| is_surface() const | core::chemical::ResidueType | |
| is_terminus() const | core::chemical::ResidueType | |
| is_upper_terminus() const | core::chemical::ResidueType | |
| is_virtual(Size const &atomno) const | core::chemical::ResidueType | |
| is_virtual_residue() const | core::chemical::ResidueType | |
| last_backbone_atom() const | core::chemical::ResidueType | inline |
| last_controlling_chi() const | core::chemical::ResidueType | inline |
| last_controlling_chi(Size atomno) const | core::chemical::ResidueType | inline |
| last_controlling_chi_ | core::chemical::ResidueType | private |
| lower_connect() const | core::chemical::ResidueType | |
| lower_connect_atom() const | core::chemical::ResidueType | |
| lower_connect_id() const | core::chemical::ResidueType | inline |
| lower_connect_id_ | core::chemical::ResidueType | private |
| mainchain_atom(Size const atm) const | core::chemical::ResidueType | inline |
| mainchain_atoms() const | core::chemical::ResidueType | inline |
| mainchain_atoms_ | core::chemical::ResidueType | private |
| mainchain_atoms_indices_ | core::chemical::ResidueType | private |
| mass() const | core::chemical::ResidueType | inline |
| mass_ | core::chemical::ResidueType | private |
| metal_binding_atoms_ | core::chemical::ResidueType | private |
| mm_atom_type(Size const atomno) const | core::chemical::ResidueType | |
| mm_atom_types_ | core::chemical::ResidueType | private |
| n_backbone_heavyatoms_ | core::chemical::ResidueType | private |
| n_hbond_acceptors() const | core::chemical::ResidueType | inline |
| n_hbond_acceptors_ | core::chemical::ResidueType | private |
| n_hbond_donors() const | core::chemical::ResidueType | inline |
| n_hbond_donors_ | core::chemical::ResidueType | private |
| n_non_polymeric_residue_connections() const | core::chemical::ResidueType | inline |
| n_non_polymeric_residue_connections_ | core::chemical::ResidueType | private |
| n_nus() const | core::chemical::ResidueType | inline |
| n_orbitals() const | core::chemical::ResidueType | |
| n_polymeric_residue_connections() const | core::chemical::ResidueType | inline |
| n_polymeric_residue_connections_ | core::chemical::ResidueType | private |
| n_proton_chi() const | core::chemical::ResidueType | inline |
| n_residue_connections() const | core::chemical::ResidueType | |
| n_residue_connections_for_atom(Size const atomid) const | core::chemical::ResidueType | inline |
| n_virtual_atoms() const | core::chemical::ResidueType | |
| name() const | core::chemical::ResidueType | inline |
| name(std::string const &name_in) | core::chemical::ResidueType | inline |
| name1() const | core::chemical::ResidueType | inline |
| name1(char const code) | core::chemical::ResidueType | inline |
| name1_ | core::chemical::ResidueType | private |
| name3() const | core::chemical::ResidueType | inline |
| name3(std::string const &name_in) | core::chemical::ResidueType | inline |
| name3_ | core::chemical::ResidueType | private |
| name_ | core::chemical::ResidueType | private |
| natoms() const | core::chemical::ResidueType | inline |
| nbonds() const | core::chemical::ResidueType | inline |
| nbonds(Size atom) const | core::chemical::ResidueType | inline |
| nbonds(VD atom) const | core::chemical::ResidueType | inline |
| nbr_atom(std::string const &atom_name) | core::chemical::ResidueType | inline |
| nbr_atom(VD vertex) | core::chemical::ResidueType | inline |
| nbr_atom() const | core::chemical::ResidueType | inline |
| nbr_atom_ | core::chemical::ResidueType | private |
| nbr_atom_indices_ | core::chemical::ResidueType | private |
| nbr_radius(Real const radius) | core::chemical::ResidueType | inline |
| nbr_radius() const | core::chemical::ResidueType | inline |
| nbr_radius_ | core::chemical::ResidueType | private |
| nbr_vertex() const | core::chemical::ResidueType | inline |
| nbrs(Size const atomno) const | core::chemical::ResidueType | inline |
| ncaa_rotlib_n_bins_per_rot_ | core::chemical::ResidueType | private |
| ncaa_rotlib_n_rots_ | core::chemical::ResidueType | private |
| ncaa_rotlib_path_ | core::chemical::ResidueType | private |
| nchi() const | core::chemical::ResidueType | inline |
| ndihe() const | core::chemical::ResidueType | inline |
| new_orbital_icoor_data(Size const orbital_index) const | core::chemical::ResidueType | |
| nheavyatoms() const | core::chemical::ResidueType | inline |
| nheavyatoms_ | core::chemical::ResidueType | private |
| nonadduct_variants_match(ResidueType const &other) const | core::chemical::ResidueType | |
| nondefault(bool in) | core::chemical::ResidueType | inline |
| nondefault_ | core::chemical::ResidueType | private |
| note_chi_controls_atom(Size chi, Size atomno) | core::chemical::ResidueType | private |
| nu_atoms(core::uint const nu_index) const | core::chemical::ResidueType | inline |
| nu_atoms() const | core::chemical::ResidueType | inline |
| nu_atoms_ | core::chemical::ResidueType | private |
| nu_atoms_indices_ | core::chemical::ResidueType | private |
| null_vertex | core::chemical::ResidueType | static |
| num_bondangles() const | core::chemical::ResidueType | inline |
| number_bonded_heavyatoms(Size const atomno) const | core::chemical::ResidueType | |
| number_bonded_hydrogens(Size const atomno) const | core::chemical::ResidueType | inline |
| orbital(Size const orbital_index) const | core::chemical::ResidueType | |
| orbital(std::string const &orbital_name) const | core::chemical::ResidueType | |
| orbital_icoor_data(Size const orbital_index) const | core::chemical::ResidueType | |
| orbital_index(std::string const &name) const | core::chemical::ResidueType | |
| orbital_type(int const orbital_index) const | core::chemical::ResidueType | |
| orbital_types_ | core::chemical::ResidueType | private |
| orbitals_ | core::chemical::ResidueType | private |
| orbitals_index_ | core::chemical::ResidueType | private |
| order_atoms() | core::chemical::ResidueType | private |
| ordered_atoms_ | core::chemical::ResidueType | private |
| path_distance(Size at1, Size at2) const | core::chemical::ResidueType | inline |
| path_distance(Size atom) const | core::chemical::ResidueType | inline |
| path_distance_ | core::chemical::ResidueType | private |
| path_distances() const | core::chemical::ResidueType | inline |
| peptoid_rotlib_n_bins_per_rot_ | core::chemical::ResidueType | private |
| peptoid_rotlib_n_rots_ | core::chemical::ResidueType | private |
| peptoid_rotlib_path_ | core::chemical::ResidueType | private |
| perform_checks() | core::chemical::ResidueType | private |
| polar_hydrogens() | core::chemical::ResidueType | |
| print_bondangles() const | core::chemical::ResidueType | |
| print_dihedrals() const | core::chemical::ResidueType | |
| print_pretty_path_distances() const | core::chemical::ResidueType | |
| properties() const | core::chemical::ResidueType | |
| properties_ | core::chemical::ResidueType | private |
| proton_chi_2_chi(Size proton_chi_id) const | core::chemical::ResidueType | inline |
| proton_chi_extra_samples(Size proton_chi) const | core::chemical::ResidueType | inline |
| proton_chi_extra_samples_ | core::chemical::ResidueType | private |
| proton_chi_samples(Size proton_chi) const | core::chemical::ResidueType | inline |
| proton_chi_samples_ | core::chemical::ResidueType | private |
| proton_chis_ | core::chemical::ResidueType | private |
| redefine_chi(Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4) | core::chemical::ResidueType | |
| remap_pdb_atom_names(bool rename) | core::chemical::ResidueType | inline |
| remap_pdb_atom_names() const | core::chemical::ResidueType | inline |
| remap_pdb_atom_names_ | core::chemical::ResidueType | private |
| report_adducts() | core::chemical::ResidueType | |
| require_final() const | core::chemical::ResidueType | inline |
| requires_actcoord() const | core::chemical::ResidueType | |
| residue_connect_atom_index(Size const resconn_id) const | core::chemical::ResidueType | |
| residue_connection(Size const i) const | core::chemical::ResidueType | |
| residue_connection(Size const i) | core::chemical::ResidueType | |
| residue_connection_id_for_atom(Size const atomid) const | core::chemical::ResidueType | inline |
| residue_connection_is_polymeric(Size const resconn_id) const | core::chemical::ResidueType | inline |
| residue_connections_ | core::chemical::ResidueType | private |
| residue_connections_for_atom(Size const atomid) const | core::chemical::ResidueType | inline |
| residue_type_set() const | core::chemical::ResidueType | |
| residue_type_set(ResidueTypeSetCAP set_in) | core::chemical::ResidueType | |
| residue_type_set_ | core::chemical::ResidueType | private |
| ResidueType(AtomTypeSetCAP atom_types, ElementSetCAP element_types, MMAtomTypeSetCAP mm_atom_types, orbitals::OrbitalTypeSetCAP orbital_types) | core::chemical::ResidueType | |
| ResidueType(ResidueType const &residue_type) | core::chemical::ResidueType | |
| ring_conformer_set() const | core::chemical::ResidueType | |
| rings() | core::chemical::ResidueType | inline |
| rings_and_their_edges_ | core::chemical::ResidueType | private |
| rna_residue_type_ | core::chemical::ResidueType | private |
| RNA_type() const | core::chemical::ResidueType | |
| root_atom() const | core::chemical::ResidueType | inline |
| root_atom_ | core::chemical::ResidueType | private |
| rotamer_aa(AA const &type) | core::chemical::ResidueType | inline |
| rotamer_aa(std::string const &type) | core::chemical::ResidueType | inline |
| rotamer_aa() const | core::chemical::ResidueType | inline |
| rotamer_aa_ | core::chemical::ResidueType | private |
| rotamer_library_name_ | core::chemical::ResidueType | private |
| select_orient_atoms(Size ¢er, Size &nbr1, Size &nbr2) const | core::chemical::ResidueType | |
| serialized_ | core::chemical::ResidueType | mutable |
| set_adduct_flag(bool adduct_in) | core::chemical::ResidueType | |
| set_atom_base(std::string const &atom_name1, std::string const &atom_name2) | core::chemical::ResidueType | |
| set_atom_base(VD const &atom1, VD const &atom2) | core::chemical::ResidueType | |
| set_atom_type(std::string const &atom_name, std::string const &atom_type_name) | core::chemical::ResidueType | inline |
| set_atom_type(VD atom, std::string const &atom_type_name) | core::chemical::ResidueType | |
| set_backbone_heavyatom(std::string const &name) | core::chemical::ResidueType | |
| set_gasteiger_atom_type(std::string const &atom_name, std::string const &gasteiger_atom_type_name) | core::chemical::ResidueType | |
| set_gasteiger_typeset(gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types) | core::chemical::ResidueType | |
| set_icoor(std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false) | core::chemical::ResidueType | |
| set_icoor(VD const &atm, Real const phi, Real const theta, Real const d, VD const &stub_atom1, VD const &stub_atom2, VD const &stub_atom3, bool const update_xyz=false) | core::chemical::ResidueType | |
| set_ideal_xyz(std::string const &atm, Vector const &xyz_in) | core::chemical::ResidueType | |
| set_ideal_xyz(Size index, Vector const &xyz_in) | core::chemical::ResidueType | |
| set_ideal_xyz(VD atm, Vector const &xyz_in) | core::chemical::ResidueType | |
| set_lower_connect_atom(std::string const &atm_name) | core::chemical::ResidueType | |
| set_mainchain_atoms(AtomIndices const &mainchain) | core::chemical::ResidueType | |
| set_mm_atom_type(std::string const &atom_name, std::string const &mm_atom_type_name) | core::chemical::ResidueType | |
| set_ncaa_rotlib_n_bin_per_rot(utility::vector1< Size > n_bins_per_rot) | core::chemical::ResidueType | |
| set_ncaa_rotlib_n_rotameric_bins(Size n_rots) | core::chemical::ResidueType | inline |
| set_ncaa_rotlib_n_rotameric_bins() const | core::chemical::ResidueType | inline |
| set_ncaa_rotlib_path(std::string const &path) | core::chemical::ResidueType | inline |
| set_orbital_icoor_id(std::string const &orbital, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3) | core::chemical::ResidueType | |
| set_peptoid_rotlib_n_bin_per_rot(utility::vector1< Size > n_bins_per_rot) | core::chemical::ResidueType | |
| set_peptoid_rotlib_n_rotameric_bins(Size n_rots) | core::chemical::ResidueType | inline |
| set_peptoid_rotlib_n_rotameric_bins() const | core::chemical::ResidueType | inline |
| set_peptoid_rotlib_path(std::string const &path) | core::chemical::ResidueType | inline |
| set_proton_chi(Size chino, utility::vector1< Real > const &dihedral_samples, utility::vector1< Real > const &extra_samples) | core::chemical::ResidueType | |
| set_RotamerLibraryName(std::string const &filename) | core::chemical::ResidueType | |
| set_shadowing_atom(std::string const &atom, std::string const &atom_being_shadowed) | core::chemical::ResidueType | |
| set_upper_connect_atom(std::string const &atm_name) | core::chemical::ResidueType | |
| set_use_ncaa_rotlib(bool flag) | core::chemical::ResidueType | inline |
| set_use_peptoid_rotlib(bool flag) | core::chemical::ResidueType | inline |
| setup_atom_ordering() | core::chemical::ResidueType | private |
| show(std::ostream &output=std::cout, bool output_atomic_details=false) const | core::chemical::ResidueType | |
| show_all_atom_names(std::ostream &out) const | core::chemical::ResidueType | |
| smallest_ring_size(VD const &atom, core::Size const &max_size=999999) const | core::chemical::ResidueType | |
| update_actcoord(conformation::Residue &rot) const | core::chemical::ResidueType | |
| update_derived_data() | core::chemical::ResidueType | private |
| update_last_controlling_chi() | core::chemical::ResidueType | private |
| update_residue_connection_mapping() | core::chemical::ResidueType | private |
| upper_connect() const | core::chemical::ResidueType | |
| upper_connect_atom() const | core::chemical::ResidueType | |
| upper_connect_id() const | core::chemical::ResidueType | inline |
| upper_connect_id_ | core::chemical::ResidueType | private |
| use_ncaa_rotlib_ | core::chemical::ResidueType | private |
| use_peptoid_rotlib_ | core::chemical::ResidueType | private |
| variant_types() const | core::chemical::ResidueType | |
| variants_match(ResidueType const &other) const | core::chemical::ResidueType | |
| vd_to_index_ | core::chemical::ResidueType | private |
| within1bonds_sets_for_atom(Size atomid) const | core::chemical::ResidueType | inline |
| within1bonds_sets_for_atom_ | core::chemical::ResidueType | private |
| within2bonds_sets_for_atom(Size atomid) const | core::chemical::ResidueType | inline |
| within2bonds_sets_for_atom_ | core::chemical::ResidueType | private |
| ~ResidueType() | core::chemical::ResidueType | virtual |
1.8.7