| aa(AA const &type) | core::chemical::ResidueTypeBase | inline |
| aa(std::string const &type) | core::chemical::ResidueTypeBase | inline |
| aa() const | core::chemical::ResidueTypeBase | inline |
| aa_ | core::chemical::ResidueTypeBase | private |
| actcoord_atoms() const | core::chemical::MutableResidueType | |
| add_actcoord_atom(std::string const &atom) | core::chemical::MutableResidueType | |
| add_adduct(Adduct &adduct_in) | core::chemical::ResidueTypeBase | 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::MutableResidueType | |
| add_atom(std::string const &atom_name="") | core::chemical::MutableResidueType | |
| add_atom(Atom const &atom, MutableICoorRecord const &icoor) | core::chemical::MutableResidueType | |
| add_atom_alias(std::string const &rosetta_atom, std::string const &alias) | core::chemical::MutableResidueType | |
| add_bond(std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel=SingleBond) | core::chemical::MutableResidueType | |
| add_bond(VD atom1, VD atom2, BondName bondLabel=SingleBond) | core::chemical::MutableResidueType | |
| add_canonical_atom_alias(std::string const &rosetta_atom, std::string const &alias) | core::chemical::MutableResidueType | |
| add_chi(Size const chino, VD atom1, VD atom2, VD atom3, VD atom4) | core::chemical::MutableResidueType | |
| add_chi(VD atom1, VD atom2, VD atom3, VD atom4) | core::chemical::MutableResidueType | |
| 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::MutableResidueType | |
| add_chi(std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4) | core::chemical::MutableResidueType | |
| add_chi_rotamer(Size const chino, Real const mean, Real const sdev) | core::chemical::MutableResidueType | |
| add_chi_rotamer_to_last_chi(core::Angle const mean, core::Angle const sdev) | core::chemical::MutableResidueType | |
| add_cut_bond(std::string const &atom_name1, std::string const &atom_name2) | core::chemical::MutableResidueType | |
| add_metalbinding_atom(std::string const &atom_name) | core::chemical::MutableResidueType | |
| add_metapatch_connect(std::string const &atom) | core::chemical::MutableResidueType | |
| 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::MutableResidueType | |
| add_numeric_property(std::string const &tag, core::Real value) | core::chemical::ResidueTypeBase | |
| add_orbital(std::string &orbital_name, std::string &orbital_type_name) | core::chemical::MutableResidueType | |
| add_orbital_bond(std::string const &atom_name1, std::string const &orbital_name) | core::chemical::MutableResidueType | |
| add_property(std::string const &property) | core::chemical::ResidueTypeBase | |
| add_property(core::chemical::ResidueProperty const property) | core::chemical::ResidueTypeBase | |
| add_residue_connection(std::string const &atom_name) | core::chemical::MutableResidueType | |
| add_ring(core::uint const ring_num, utility::vector1< std::string > const &ring_atoms, core::chemical::rings::RingSaturationType const saturation_type=core::chemical::rings::ALIPHATIC) | core::chemical::MutableResidueType | |
| add_string_property(std::string const &tag, std::string value) | core::chemical::ResidueTypeBase | |
| add_variant_type(VariantType const variant_type) | core::chemical::ResidueTypeBase | |
| add_variant_type(std::string const &variant_type) | core::chemical::ResidueTypeBase | |
| all_atoms() const | core::chemical::MutableResidueType | inline |
| assign_internal_coordinates() | core::chemical::MutableResidueType | |
| assign_internal_coordinates(core::chemical::VD new_root) | core::chemical::MutableResidueType | |
| assign_neighbor_atom() | core::chemical::MutableResidueType | |
| atom(VD const atom_vd) | core::chemical::MutableResidueType | |
| atom(VD const atom_vd) const | core::chemical::MutableResidueType | |
| atom(std::string const &atom_name) | core::chemical::MutableResidueType | |
| atom(std::string const &atom_name) const | core::chemical::MutableResidueType | |
| atom_alias(std::string const &name) const | core::chemical::ResidueTypeBase | inline |
| atom_aliases() const | core::chemical::ResidueTypeBase | inline |
| atom_aliases() | core::chemical::ResidueTypeBase | inlineprotected |
| atom_aliases_ | core::chemical::ResidueTypeBase | private |
| atom_base(VD const atm) const | core::chemical::MutableResidueType | |
| atom_index(VD const &vd) const | core::chemical::MutableResidueType | |
| atom_iterators() const | core::chemical::MutableResidueType | inline |
| atom_name(VD const vd) const | core::chemical::MutableResidueType | |
| atom_name_to_vd_ | core::chemical::MutableResidueType | private |
| atom_shadowed_ | core::chemical::MutableResidueType | private |
| atom_type(VD const vd) const | core::chemical::MutableResidueType | |
| atom_type_set() const | core::chemical::ResidueTypeBase | inline |
| atom_type_set(AtomTypeSetCOP setting) | core::chemical::ResidueTypeBase | protected |
| atom_type_set_ptr() const | core::chemical::ResidueTypeBase | inline |
| atom_types_ | core::chemical::ResidueTypeBase | private |
| atom_vertex(std::string const &name) const | core::chemical::MutableResidueType | |
| atoms_are_bonded(std::string const &atom1, std::string const &atom2) const | core::chemical::MutableResidueType | |
| autodetermine_chi_bonds(core::Size max_proton_chi_samples=500) | core::chemical::MutableResidueType | |
| backbone_aa(std::string const &type) | core::chemical::ResidueTypeBase | inline |
| backbone_aa(core::chemical::AA const type) | core::chemical::ResidueTypeBase | inline |
| backbone_aa() const | core::chemical::ResidueTypeBase | inline |
| backbone_aa_ | core::chemical::ResidueTypeBase | private |
| backbone_aa_raw() const | core::chemical::ResidueTypeBase | inlineprotected |
| base_analogue(std::string const &type) | core::chemical::ResidueTypeBase | inline |
| base_analogue() const | core::chemical::ResidueTypeBase | inline |
| base_analogue_ | core::chemical::ResidueTypeBase | private |
| base_analogue_raw() const | core::chemical::ResidueTypeBase | inlineprotected |
| base_name() const | core::chemical::ResidueTypeBase | inline |
| base_name(std::string const &base_name_in) | core::chemical::ResidueTypeBase | inline |
| base_name_ | core::chemical::ResidueTypeBase | private |
| base_type_cop_ | core::chemical::MutableResidueType | private |
| bond(ED const ed) | core::chemical::MutableResidueType | |
| bond(ED const ed) const | core::chemical::MutableResidueType | |
| bond(VD vd1, VD vd2) | core::chemical::MutableResidueType | |
| bond(VD vd1, VD vd2) const | core::chemical::MutableResidueType | |
| bond(std::string const &atom1, std::string const &atom2) | core::chemical::MutableResidueType | |
| bond(std::string const &atom1, std::string const &atom2) const | core::chemical::MutableResidueType | |
| bond_iterators() const | core::chemical::MutableResidueType | inline |
| bond_iterators(VD const &atom) const | core::chemical::MutableResidueType | inline |
| bonded_heavyatoms(VD const &atom) const | core::chemical::MutableResidueType | |
| bonded_hydrogens(VD const &atom) const | core::chemical::MutableResidueType | |
| bonded_neighbor_iterators(VD const &atom) const | core::chemical::MutableResidueType | |
| bonded_neighbors(VD const &atom) const | core::chemical::MutableResidueType | |
| canonical_atom_alias(std::string const &name) const | core::chemical::ResidueTypeBase | inline |
| canonical_atom_aliases() const | core::chemical::ResidueTypeBase | inline |
| canonical_atom_aliases() | core::chemical::ResidueTypeBase | inlineprotected |
| canonical_atom_aliases_ | core::chemical::ResidueTypeBase | private |
| change_bond_type(std::string const &atom_name1, std::string const &atom_name2, BondName const new_bond_label) | core::chemical::MutableResidueType | |
| chi_atom_vds(Size const chino) const | core::chemical::MutableResidueType | inline |
| chi_rotamers(Size const chino) const | core::chemical::MutableResidueType | inline |
| chi_valid(Size const chino) const | core::chemical::MutableResidueType | |
| chis_ | core::chemical::MutableResidueType | private |
| clear_chi_rotamers(core::uint const chi_no) | core::chemical::MutableResidueType | |
| clear_icoor() | core::chemical::MutableResidueType | |
| clear_orbitals() | core::chemical::MutableResidueType | |
| clone() const | core::chemical::MutableResidueType | |
| copy_atom_info(ResidueType const &source) | core::chemical::MutableResidueType | private |
| copy_other_info(ResidueType const &source) | core::chemical::MutableResidueType | private |
| custom_variant_types() const | core::chemical::ResidueTypeBase | |
| defined_adducts() const | core::chemical::ResidueTypeBase | inline |
| defined_adducts_ | core::chemical::ResidueTypeBase | private |
| defines_custom_rama_prepro_map(bool const pre_proline_position) const | core::chemical::ResidueTypeBase | |
| delete_actcoord_atom(std::string const &atom_name) | core::chemical::MutableResidueType | |
| delete_atom(std::string const &name) | core::chemical::MutableResidueType | |
| delete_atom(VD atom) | core::chemical::MutableResidueType | |
| delete_atom_alias(std::string const &alias, bool error=true) | core::chemical::MutableResidueType | |
| delete_bond(VD atom1, VD atom2) | core::chemical::MutableResidueType | |
| delete_chi(Size const chino) | core::chemical::MutableResidueType | |
| delete_child_proton(std::string const &atom) | core::chemical::MutableResidueType | |
| delete_metalbinding_atom(std::string const &atom_name) | core::chemical::MutableResidueType | |
| delete_nu(core::uint const nu_index) | core::chemical::MutableResidueType | |
| delete_property(std::string const &property) | core::chemical::ResidueTypeBase | |
| delete_property(core::chemical::ResidueProperty const property) | core::chemical::ResidueTypeBase | |
| delete_residue_connection(VD atm) | core::chemical::MutableResidueType | |
| delete_ring(core::uint const ring_num) | core::chemical::MutableResidueType | |
| delete_terminal_chi() | core::chemical::MutableResidueType | |
| disulfide_atom_name_ | core::chemical::ResidueTypeBase | private |
| dump_vd_info() const | core::chemical::MutableResidueType | |
| element_set() const | core::chemical::ResidueTypeBase | inline |
| element_set_ptr() const | core::chemical::ResidueTypeBase | inline |
| elements_ | core::chemical::ResidueTypeBase | private |
| enable_custom_variant_types() | core::chemical::ResidueTypeBase | |
| fill_ideal_xyz_from_icoor() | core::chemical::MutableResidueType | |
| force_nbr_atom_orient() const | core::chemical::ResidueTypeBase | inline |
| force_nbr_atom_orient(bool force_orient) | core::chemical::ResidueTypeBase | inline |
| force_nbr_atom_orient_ | core::chemical::ResidueTypeBase | private |
| gasteiger_atom_types_ | core::chemical::ResidueTypeBase | private |
| gasteiger_atom_typeset() const | core::chemical::ResidueTypeBase | |
| get_atom_name_to_vd_map() const | core::chemical::MutableResidueType | inline |
| get_base_type_cop() const override | core::chemical::MutableResidueType | virtual |
| get_disulfide_atom_name() const | core::chemical::ResidueTypeBase | inline |
| get_metal_binding_atoms() const | core::chemical::ResidueTypeBase | inline |
| get_numeric_property(std::string const &tag) const | core::chemical::ResidueTypeBase | |
| get_orbitals() | core::chemical::ResidueTypeBase | inlineprotected |
| get_orbitals_index() | core::chemical::ResidueTypeBase | inlineprotected |
| get_rama_prepro_mainchain_torsion_potential_name(bool const pre_proline_position) const | core::chemical::ResidueTypeBase | |
| get_rama_prepro_map_file_name(bool const pre_proline_position) const | core::chemical::ResidueTypeBase | |
| get_string_property(std::string const &tag) const | core::chemical::ResidueTypeBase | |
| graph() const | core::chemical::MutableResidueType | inline |
| graph_ | core::chemical::MutableResidueType | private |
| has(std::string const &atom_name) const override | core::chemical::MutableResidueType | inlinevirtual |
| has(VD const vd) const | core::chemical::MutableResidueType | inline |
| has(std::string const &atom_name) const=0 | core::chemical::MutableResidueType | |
| has_orbital(std::string const &orbital_name) const | core::chemical::ResidueTypeBase | inline |
| has_orbital_types() const | core::chemical::ResidueTypeBase | inline |
| has_property(std::string const &property) const | core::chemical::ResidueTypeBase | |
| has_property(ResidueProperty const property) const | core::chemical::ResidueTypeBase | |
| has_variant_type(VariantType const variant_type) const | core::chemical::ResidueTypeBase | |
| has_variant_type(std::string const &variant_type) const | core::chemical::ResidueTypeBase | |
| icoor(VD const atm) const | core::chemical::MutableResidueType | |
| interchangeability_group() const | core::chemical::ResidueTypeBase | inline |
| interchangeability_group(std::string const &setting) | core::chemical::ResidueTypeBase | inline |
| interchangeability_group_ | core::chemical::ResidueTypeBase | private |
| is_achiral_backbone() const | core::chemical::ResidueTypeBase | inline |
| is_achiral_sidechain() const | core::chemical::ResidueTypeBase | inline |
| is_backbone_heavyatom(VD atom) const | core::chemical::MutableResidueType | |
| is_base_type() const override | core::chemical::MutableResidueType | virtual |
| is_d_aa() const | core::chemical::ResidueTypeBase | inline |
| is_d_rna() const | core::chemical::ResidueTypeBase | inline |
| is_DNA() const | core::chemical::ResidueTypeBase | inline |
| is_l_aa() const | core::chemical::ResidueTypeBase | inline |
| is_l_rna() const | core::chemical::ResidueTypeBase | inline |
| is_metapatched() const | core::chemical::ResidueTypeBase | inline |
| is_metapatched_ | core::chemical::ResidueTypeBase | private |
| is_peptoid() const | core::chemical::ResidueTypeBase | inline |
| is_polymer() const | core::chemical::ResidueTypeBase | inline |
| is_protein() const | core::chemical::ResidueTypeBase | inline |
| is_proton_chi(Size const chino) const | core::chemical::MutableResidueType | inline |
| is_r_peptoid() const | core::chemical::ResidueTypeBase | inline |
| is_RNA() const | core::chemical::ResidueTypeBase | inline |
| is_s_peptoid() const | core::chemical::ResidueTypeBase | inline |
| low_ring_conformers(core::uint const ring_num) const | core::chemical::MutableResidueType | inline |
| low_ring_conformers_ | core::chemical::MutableResidueType | private |
| lower_connect() const | core::chemical::MutableResidueType | |
| lower_connect_atom() const | core::chemical::MutableResidueType | |
| lower_connect_id() const | core::chemical::MutableResidueType | inline |
| lower_connect_id_ | core::chemical::MutableResidueType | private |
| lowest_ring_conformer(core::uint const ring_num) const | core::chemical::MutableResidueType | inline |
| lowest_ring_conformer_ | core::chemical::MutableResidueType | private |
| mainchain_atoms() const | core::chemical::MutableResidueType | inline |
| mainchain_atoms_ | core::chemical::MutableResidueType | private |
| mainchain_potentials_match(ResidueTypeBase const &other) const | core::chemical::ResidueTypeBase | |
| metal_binding_atoms() | core::chemical::ResidueTypeBase | inlineprotected |
| metal_binding_atoms_ | core::chemical::ResidueTypeBase | private |
| mm_atom_types_ | core::chemical::ResidueTypeBase | private |
| mm_atom_types_ptr() const | core::chemical::ResidueTypeBase | inline |
| mode() const | core::chemical::ResidueTypeBase | inline |
| mode_ | core::chemical::ResidueTypeBase | private |
| MutableResidueType() | core::chemical::MutableResidueType | private |
| MutableResidueType(AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types) | core::chemical::MutableResidueType | |
| MutableResidueType(MutableResidueType const &residue_type) | core::chemical::MutableResidueType | |
| MutableResidueType(ResidueType const &residue_type) | core::chemical::MutableResidueType | explicit |
| MutableResidueType(MutableResidueType &&residue_type)=default | core::chemical::MutableResidueType | |
| n_nus() const | core::chemical::MutableResidueType | inline |
| n_orbitals() const | core::chemical::ResidueTypeBase | |
| n_polymeric_residue_connections() const | core::chemical::MutableResidueType | inline |
| n_possible_residue_connections() const | core::chemical::MutableResidueType | |
| n_proton_chi() const | core::chemical::MutableResidueType | |
| n_residue_connections_for_atom(VD const atomid) const | core::chemical::MutableResidueType | |
| n_rings() const | core::chemical::MutableResidueType | inline |
| n_virtual_atoms() const override | core::chemical::MutableResidueType | virtual |
| na_analogue(std::string const &type) | core::chemical::ResidueTypeBase | inline |
| na_analogue() const | core::chemical::ResidueTypeBase | inline |
| na_analogue_ | core::chemical::ResidueTypeBase | private |
| na_analogue_raw() const | core::chemical::ResidueTypeBase | inlineprotected |
| name() const | core::chemical::ResidueTypeBase | inline |
| name(std::string const &name_in) | core::chemical::ResidueTypeBase | inline |
| name1() const | core::chemical::ResidueTypeBase | inline |
| name1(char const code) | core::chemical::ResidueTypeBase | inline |
| name1_ | core::chemical::ResidueTypeBase | private |
| name3() const | core::chemical::ResidueTypeBase | inline |
| name3(std::string const &name_in) | core::chemical::ResidueTypeBase | inline |
| name3_ | core::chemical::ResidueTypeBase | private |
| name_ | core::chemical::ResidueTypeBase | private |
| natoms() const override | core::chemical::MutableResidueType | inlinevirtual |
| nbonds() const override | core::chemical::MutableResidueType | inlinevirtual |
| nbonds(VD atom) const | core::chemical::MutableResidueType | inline |
| nbr_atom(std::string const &atom_name) | core::chemical::MutableResidueType | inline |
| nbr_atom(VD vertex) | core::chemical::MutableResidueType | inline |
| nbr_atom_ | core::chemical::MutableResidueType | private |
| nbr_radius(Real const radius) | core::chemical::MutableResidueType | inline |
| nbr_radius() const | core::chemical::MutableResidueType | inline |
| nbr_radius_ | core::chemical::MutableResidueType | private |
| nbr_vertex() const | core::chemical::MutableResidueType | inline |
| nchi() const | core::chemical::MutableResidueType | inline |
| net_formal_charge() const | core::chemical::ResidueTypeBase | inline |
| net_formal_charge(signed long int charge_in) | core::chemical::ResidueTypeBase | inline |
| net_formal_charge_ | core::chemical::ResidueTypeBase | private |
| nheavyatoms() const override | core::chemical::MutableResidueType | virtual |
| nu_atoms(core::uint const nu_index) const | core::chemical::MutableResidueType | inline |
| nu_atoms_ | core::chemical::MutableResidueType | private |
| null_vertex | core::chemical::MutableResidueType | static |
| number_bonded_heavyatoms(VD atomvd) const | core::chemical::MutableResidueType | |
| number_bonded_hydrogens(VD atomvd) const | core::chemical::MutableResidueType | |
| operator=(MutableResidueType const &src) | core::chemical::MutableResidueType | |
| operator=(MutableResidueType &&)=default | core::chemical::MutableResidueType | |
| core::chemical::ResidueTypeBase::operator=(ResidueTypeBase const &)=default | core::chemical::ResidueTypeBase | protected |
| orbital(Size const orbital_index) const | core::chemical::ResidueTypeBase | |
| orbital(std::string const &orbital_name) const | core::chemical::ResidueTypeBase | |
| orbital_index(std::string const &name) const | core::chemical::ResidueTypeBase | |
| orbital_type(Size const orbital_index) const | core::chemical::ResidueTypeBase | |
| orbital_types_ | core::chemical::ResidueTypeBase | private |
| orbital_types_ptr() const | core::chemical::ResidueTypeBase | inline |
| orbitals_ | core::chemical::ResidueTypeBase | private |
| orbitals_index_ | core::chemical::ResidueTypeBase | private |
| ordered_atoms_ | core::chemical::MutableResidueType | private |
| placeholder_clone() const | core::chemical::MutableResidueType | |
| properties() const | core::chemical::ResidueTypeBase | inline |
| properties_ | core::chemical::ResidueTypeBase | private |
| proton_chi_extra_samples_for_chi(Size chino) const | core::chemical::MutableResidueType | inline |
| proton_chi_samples_for_chi(Size chino) const | core::chemical::MutableResidueType | inline |
| rama_prepro_mainchain_torsion_potential_name_ | core::chemical::ResidueTypeBase | private |
| rama_prepro_mainchain_torsion_potential_name_beforeproline_ | core::chemical::ResidueTypeBase | private |
| rama_prepro_map_file_name_ | core::chemical::ResidueTypeBase | private |
| rama_prepro_map_file_name_beforeproline_ | core::chemical::ResidueTypeBase | 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::MutableResidueType | |
| remap_pdb_atom_names(bool rename) | core::chemical::ResidueTypeBase | inline |
| remap_pdb_atom_names() const | core::chemical::ResidueTypeBase | inline |
| remap_pdb_atom_names_ | core::chemical::ResidueTypeBase | private |
| remove_variant_type(VariantType const variant_type) | core::chemical::ResidueTypeBase | |
| remove_variant_type(std::string const &variant_type) | core::chemical::ResidueTypeBase | |
| rename_atom(VD atom, std::string const &name) | core::chemical::MutableResidueType | |
| report_adducts() const | core::chemical::ResidueTypeBase | |
| reset_base_type_cop() | core::chemical::MutableResidueType | |
| reset_bond_distance_to_atom(std::string const &atm, core::Distance const d) | core::chemical::MutableResidueType | |
| reset_mainchain_torsion_potential_names() | core::chemical::ResidueTypeBase | |
| residue_connect_atom(Size const resconn_id) const | core::chemical::MutableResidueType | |
| residue_connection(Size const i) const | core::chemical::MutableResidueType | |
| residue_connection(Size const i) | core::chemical::MutableResidueType | |
| residue_connection_is_polymeric(Size const resconn_id) const | core::chemical::MutableResidueType | inline |
| residue_connections_ | core::chemical::MutableResidueType | private |
| ResidueTypeBase() | core::chemical::ResidueTypeBase | protected |
| ResidueTypeBase(AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types) | core::chemical::ResidueTypeBase | protected |
| ResidueTypeBase(ResidueTypeBase const &)=default | core::chemical::ResidueTypeBase | protected |
| ring_atoms(core::uint const ring_num) const | core::chemical::MutableResidueType | inline |
| ring_atoms_ | core::chemical::MutableResidueType | private |
| ring_saturation_type(uint const ring_num) const | core::chemical::MutableResidueType | inline |
| ring_saturation_types_ | core::chemical::MutableResidueType | private |
| root_atom() const | core::chemical::MutableResidueType | inline |
| root_atom_ | core::chemical::MutableResidueType | private |
| rotamer_library_specification(rotamers::RotamerLibrarySpecificationOP) | core::chemical::ResidueTypeBase | |
| rotamer_library_specification() const | core::chemical::ResidueTypeBase | |
| rotamer_library_specification_ | core::chemical::ResidueTypeBase | private |
| rotamer_library_specification_nonconst() | core::chemical::ResidueTypeBase | |
| set_adduct_flag(bool adduct_in) | core::chemical::ResidueTypeBase | |
| set_atom_type(std::string const &name, std::string const &atom_type_name) | core::chemical::MutableResidueType | inline |
| set_atom_type(VD atom, std::string const &atom_type_name) | core::chemical::MutableResidueType | |
| set_backbone_heavyatom(std::string const &name) | core::chemical::MutableResidueType | |
| set_base_type_cop(ResidueTypeCOP new_base_type) | core::chemical::MutableResidueType | |
| set_disulfide_atom_name(std::string const &n) | core::chemical::ResidueTypeBase | inline |
| set_gasteiger_atom_type(std::string const &atom_name, std::string const &gasteiger_atom_type_name) | core::chemical::MutableResidueType | |
| set_gasteiger_atom_type(VD atom, std::string const &gasteiger_atom_type_name) | core::chemical::MutableResidueType | |
| set_gasteiger_atom_typeset(gasteiger::GasteigerAtomTypeSetCOP setting) | core::chemical::ResidueTypeBase | |
| 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::MutableResidueType | |
| 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::MutableResidueType | |
| set_icoor(VD 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::MutableResidueType | |
| set_ideal_xyz(std::string const &atm, Vector const &xyz_in) | core::chemical::MutableResidueType | |
| set_ideal_xyz(VD atm, Vector const &xyz_in) | core::chemical::MutableResidueType | |
| set_low_energy_ring_conformers(core::uint const ring_num, utility::vector1< std::string > const &conformers) | core::chemical::MutableResidueType | |
| set_lower_connect_atom(std::string const &atm_name) | core::chemical::MutableResidueType | |
| set_lowest_energy_ring_conformer(core::uint const ring_num, std::string const &conformer) | core::chemical::MutableResidueType | |
| set_mainchain_atoms(utility::vector1< VD > const &mainchain) | core::chemical::MutableResidueType | inline |
| set_metapatched() | core::chemical::ResidueTypeBase | 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::MutableResidueType | |
| set_orbital_typeset(orbitals::OrbitalTypeSetCOP setting) | core::chemical::ResidueTypeBase | inline |
| set_properties(ResiduePropertiesOP properties) | core::chemical::ResidueTypeBase | |
| set_proton_chi(Size chino, utility::vector1< Real > const &dihedral_samples, utility::vector1< Real > const &extra_samples) | core::chemical::MutableResidueType | |
| set_rama_prepro_mainchain_torsion_potential_name(std::string const &name_in, bool const pre_proline_position) | core::chemical::ResidueTypeBase | |
| set_rama_prepro_map_file_name(std::string const &filename_in, bool const pre_proline_position) | core::chemical::ResidueTypeBase | |
| set_shadowing_atom(std::string const &atom, std::string const &atom_being_shadowed) | core::chemical::MutableResidueType | |
| set_upper_connect_atom(std::string const &atm_name) | core::chemical::MutableResidueType | |
| shadow_atoms() const | core::chemical::MutableResidueType | inline |
| show(std::ostream &output=std::cout, bool output_atomic_details=false) const override | core::chemical::MutableResidueType | virtual |
| show_all_atom_names(std::ostream &out) const override | core::chemical::MutableResidueType | virtual |
| strip_rotamer_library_specification() | core::chemical::ResidueTypeBase | |
| update_atom_type_set(AtomTypeSetCOP setting) | core::chemical::MutableResidueType | |
| update_icoors_after_connection_deletion(core::Size const conn_id_deleted) | core::chemical::MutableResidueType | private |
| upper_connect() const | core::chemical::MutableResidueType | |
| upper_connect_atom() const | core::chemical::MutableResidueType | |
| upper_connect_id() const | core::chemical::MutableResidueType | inline |
| upper_connect_id_ | core::chemical::MutableResidueType | private |
| validate_residue_type() const | core::chemical::MutableResidueType | |
| variant_type_enums() const | core::chemical::ResidueTypeBase | |
| variant_types() const | core::chemical::ResidueTypeBase | |
| ~MutableResidueType() override | core::chemical::MutableResidueType | |
