| aa(AA const &type) | core::chemical::ResidueTypeBase | inline |
| aa(std::string const &type) | core::chemical::ResidueTypeBase | inline |
| aa() const | core::chemical::ResidueTypeBase | inline |
| abase2(Size const atomno) const | core::chemical::ResidueType | |
| abase2_indices_ | core::chemical::ResidueType | private |
| 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_indices_ | core::chemical::ResidueType | private |
| add_adduct(Adduct &adduct_in) | core::chemical::ResidueTypeBase | inline |
| add_numeric_property(std::string const &tag, core::Real value) | core::chemical::ResidueTypeBase | |
| add_property(std::string const &property) | core::chemical::ResidueTypeBase | |
| add_property(core::chemical::ResidueProperty const property) | core::chemical::ResidueTypeBase | |
| 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_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 |
| atom_2_residue_connection_map_ | core::chemical::ResidueType | private |
| 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_base(Size const atomno) const | core::chemical::ResidueType | |
| atom_base_indices_ | core::chemical::ResidueType | private |
| atom_being_shadowed(Size atom_shadowing) const | core::chemical::ResidueType | inline |
| atom_charge(Size const atomno) const | core::chemical::ResidueType | inline |
| atom_depends_on_connection(core::Size const atom_index, core::Size const connection_id) const | core::chemical::ResidueType | |
| atom_depends_on_connection_ | core::chemical::ResidueType | private |
| atom_depends_on_lower_polymeric_connection(core::Size const atom_index) const | core::chemical::ResidueType | |
| atom_depends_on_lower_polymeric_connection_ | core::chemical::ResidueType | private |
| atom_depends_on_polymeric_connection(core::Size const atom_index) const | core::chemical::ResidueType | |
| atom_depends_on_upper_polymeric_connection(core::Size const atom_index) const | core::chemical::ResidueType | |
| atom_depends_on_upper_polymeric_connection_ | core::chemical::ResidueType | private |
| atom_forms_residue_connection(Size const atomid) const | core::chemical::ResidueType | inline |
| atom_has_property(Size const atomno, AtomProperty const property) const | core::chemical::ResidueType | |
| atom_index(std::string const &atom_name) const | core::chemical::ResidueType | inline |
| atom_is_aro_hydrogen(Size atomno) const | core::chemical::ResidueType | inline |
| 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_is_sidechain(Size const atomno) const | core::chemical::ResidueType | inline |
| atom_name(Size const atomno) const | core::chemical::ResidueType | inline |
| atom_name_to_index_ | core::chemical::ResidueType | private |
| atom_names_ | core::chemical::ResidueType | private |
| atom_properties(Size const atomno) const | core::chemical::ResidueType | inline |
| atom_shadowed_indices_ | core::chemical::ResidueType | private |
| atom_type(Size const atomno) const | core::chemical::ResidueType | inline |
| atom_type_index(core::Size atomno) const | core::chemical::ResidueType | inline |
| 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 |
| atomic_properties_ | core::chemical::ResidueType | private |
| 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 |
| attach_destruction_obs(MemFn fn, Ptr ptr) const | core::chemical::ResidueType | inline |
| attached_H_begin() const | core::chemical::ResidueType | inline |
| attached_H_begin(Size const atom) const | core::chemical::ResidueType | inline |
| attached_H_begin_ | core::chemical::ResidueType | private |
| attached_H_end() const | core::chemical::ResidueType | inline |
| attached_H_end(Size const atom) const | core::chemical::ResidueType | inline |
| attached_H_end_ | core::chemical::ResidueType | private |
| auto_assign_nu_atoms() | core::chemical::ResidueType | private |
| backbone_aa(std::string const &type) | core::chemical::ResidueTypeBase | inline |
| backbone_aa() const | core::chemical::ResidueTypeBase | inline |
| 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_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_type_cop_ | core::chemical::ResidueType | private |
| bond_ringness(core::Size const atomindex1, core::Size const atomindex2) const | core::chemical::ResidueType | |
| bond_type(core::Size const atomindex1, core::Size const atomindex2) const | core::chemical::ResidueType | |
| 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_ringness_ | core::chemical::ResidueType | private |
| bonded_neighbor_ringnesses(Size const atomno) 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 |
| bonded_orbitals_ | core::chemical::ResidueType | private |
| bonds() const | core::chemical::ResidueType | |
| branch_connect_atom_names() const | core::chemical::ResidueType | |
| branch_connect_atoms() const | core::chemical::ResidueType | |
| 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 |
| 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_atoms(Size const chino) const | core::chemical::ResidueType | inline |
| chi_atoms() const | core::chemical::ResidueType | inline |
| chi_atoms_ | core::chemical::ResidueType | private |
| chi_rotamers(Size const chino) const | core::chemical::ResidueType | inline |
| chi_rotamers_ | core::chemical::ResidueType | private |
| clone() const =delete | core::chemical::ResidueType | private |
| copy_atom_info(MutableResidueType const &source, utility::vector1< core::Size > const &old_to_new) | core::chemical::ResidueType | private |
| copy_other_info(MutableResidueType const &source, utility::vector1< core::Size > const &old_to_new) | core::chemical::ResidueType | private |
| custom_variant_types() const | core::chemical::ResidueTypeBase | |
| cut_bond_neighbor(Size const atomno) const | core::chemical::ResidueType | inline |
| cut_bond_neighbor_indices_ | core::chemical::ResidueType | private |
| debug_dump_icoor() const | core::chemical::ResidueType | |
| define_mainchain_atoms() | core::chemical::ResidueType | private |
| defined_adducts() const | core::chemical::ResidueTypeBase | inline |
| defines_custom_rama_prepro_map(bool const pre_proline_position) const | core::chemical::ResidueTypeBase | |
| delete_property(std::string const &property) | core::chemical::ResidueTypeBase | |
| delete_property(core::chemical::ResidueProperty const property) | core::chemical::ResidueTypeBase | |
| destruction_obs_hub_ | core::chemical::ResidueType | mutableprivate |
| detach_destruction_obs(MemFn fn, Ptr ptr) const | core::chemical::ResidueType | inline |
| 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 |
| element(core::Size atomno) const | core::chemical::ResidueType | |
| element_set() const | core::chemical::ResidueTypeBase | inline |
| element_set_ptr() const | core::chemical::ResidueTypeBase | inline |
| element_type(core::Size atomno) const | core::chemical::ResidueType | inline |
| elements_ | core::chemical::ResidueType | private |
| enable_custom_variant_types() | core::chemical::ResidueTypeBase | |
| first_sidechain_atom() const | core::chemical::ResidueType | inline |
| first_sidechain_hydrogen() const | core::chemical::ResidueType | inline |
| first_sidechain_hydrogen_ | core::chemical::ResidueType | private |
| force_nbr_atom_orient() const | core::chemical::ResidueTypeBase | inline |
| force_nbr_atom_orient(bool force_orient) | core::chemical::ResidueTypeBase | inline |
| formal_charge(Size const atomno) const | core::chemical::ResidueType | inline |
| formal_charge_ | core::chemical::ResidueType | private |
| gasteiger_atom_type(core::Size atomno) const | core::chemical::ResidueType | |
| gasteiger_atom_type_index_ | core::chemical::ResidueType | private |
| gasteiger_atom_typeset() const | core::chemical::ResidueTypeBase | |
| get_base_type_cop() const override | core::chemical::ResidueType | virtual |
| get_disulfide_atom_name() const | core::chemical::ResidueTypeBase | inline |
| get_metal_binding_atoms(AtomIndices &metal_binding_indices) const | core::chemical::ResidueType | inline |
| core::chemical::ResidueTypeBase::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_self_ptr() const | core::chemical::ResidueType | inline |
| get_self_ptr() | core::chemical::ResidueType | inline |
| get_self_weak_ptr() const | core::chemical::ResidueType | inline |
| get_self_weak_ptr() | core::chemical::ResidueType | inline |
| get_string_property(std::string const &tag) const | core::chemical::ResidueTypeBase | |
| Haro_index() const | core::chemical::ResidueType | inline |
| Haro_index_ | core::chemical::ResidueType | private |
| has(std::string const &atom_name) const override | core::chemical::ResidueType | inlinevirtual |
| has_orbital(std::string const &orbital_name) const | core::chemical::ResidueTypeBase | inline |
| has_orbital_types() const | core::chemical::ResidueTypeBase | inline |
| has_polymer_dependent_groups() const | core::chemical::ResidueType | inline |
| has_polymer_dependent_groups_ | core::chemical::ResidueType | private |
| has_property(std::string const &property) const | core::chemical::ResidueTypeBase | |
| has_property(ResidueProperty const property) const | core::chemical::ResidueTypeBase | |
| has_sc_orbitals() const | core::chemical::ResidueType | |
| has_shadow_atoms() const | core::chemical::ResidueType | inline |
| has_variant_type(VariantType const variant_type) const | core::chemical::ResidueTypeBase | |
| has_variant_type(std::string const &variant_type) const | core::chemical::ResidueTypeBase | |
| heavyatom_has_polar_hydrogens(Size atomno) const | core::chemical::ResidueType | |
| heavyatom_has_polar_hydrogens_ | core::chemical::ResidueType | private |
| 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 |
| icoor(Size const atm) const | core::chemical::ResidueType | |
| icoor_ | core::chemical::ResidueType | private |
| ideal_xyz(Size const atomno) const | core::chemical::ResidueType | inline |
| ideal_xyz(std::string const &atomname) const | core::chemical::ResidueType | inline |
| ideal_xyz_ | core::chemical::ResidueType | private |
| initialize_derived_data() | core::chemical::ResidueType | private |
| interchangeability_group() const | core::chemical::ResidueTypeBase | inline |
| interchangeability_group(std::string setting) | core::chemical::ResidueTypeBase | inline |
| is_acetylated_nterminus() const | core::chemical::ResidueType | |
| is_achiral_backbone() const | core::chemical::ResidueTypeBase | inline |
| is_achiral_sidechain() const | core::chemical::ResidueTypeBase | inline |
| is_adduct() const | core::chemical::ResidueType | |
| is_alpha_aa() const | core::chemical::ResidueType | inline |
| is_aramid() const | core::chemical::ResidueType | inline |
| is_aromatic() const | core::chemical::ResidueType | |
| is_base_type() const override | core::chemical::ResidueType | virtual |
| is_beta_aa() const | core::chemical::ResidueType | inline |
| is_branch_point() const | core::chemical::ResidueType | |
| is_canonical() const | core::chemical::ResidueType | |
| is_canonical_aa() const | core::chemical::ResidueType | |
| is_canonical_nucleic() 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::ResidueTypeBase | inline |
| is_d_rna() const | core::chemical::ResidueTypeBase | inline |
| is_disulfide_bonded() const | core::chemical::ResidueType | inline |
| is_DNA() const | core::chemical::ResidueTypeBase | inline |
| is_gamma_aa() const | core::chemical::ResidueType | inline |
| is_inverted_virtual_residue() const | core::chemical::ResidueType | |
| is_l_aa() const | core::chemical::ResidueTypeBase | inline |
| is_l_rna() const | core::chemical::ResidueTypeBase | inline |
| 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_meta_aramid() const | core::chemical::ResidueType | inline |
| is_metal() const | core::chemical::ResidueType | |
| is_metalbinding() const | core::chemical::ResidueType | |
| is_metapatched() const | core::chemical::ResidueTypeBase | inline |
| is_methylated_cterminus() const | core::chemical::ResidueType | |
| is_mirrored_type() const | core::chemical::ResidueType | inline |
| is_n_methylated() const | core::chemical::ResidueType | inline |
| is_NA() const | core::chemical::ResidueType | inline |
| is_oligourea() const | core::chemical::ResidueType | inline |
| is_ortho_aramid() const | core::chemical::ResidueType | inline |
| is_para_aramid() const | core::chemical::ResidueType | inline |
| is_peptoid() const | core::chemical::ResidueTypeBase | inline |
| is_PNA() const | core::chemical::ResidueType | inline |
| is_polar() const | core::chemical::ResidueType | |
| is_polymer() const | core::chemical::ResidueTypeBase | inline |
| is_post_methylene_meta_aramid() const | core::chemical::ResidueType | inline |
| is_post_methylene_ortho_aramid() const | core::chemical::ResidueType | inline |
| is_post_methylene_para_aramid() const | core::chemical::ResidueType | inline |
| is_pre_methylene_meta_aramid() const | core::chemical::ResidueType | inline |
| is_pre_methylene_ortho_aramid() const | core::chemical::ResidueType | inline |
| is_pre_methylene_para_aramid() const | core::chemical::ResidueType | inline |
| is_pre_methylene_post_methylene_meta_aramid() const | core::chemical::ResidueType | inline |
| is_pre_methylene_post_methylene_ortho_aramid() const | core::chemical::ResidueType | inline |
| is_pre_methylene_post_methylene_para_aramid() const | core::chemical::ResidueType | inline |
| is_protein() const | core::chemical::ResidueTypeBase | inline |
| is_proton_chi(Size const chino) const | core::chemical::ResidueType | inline |
| is_proton_chi_ | core::chemical::ResidueType | private |
| is_purine() const | core::chemical::ResidueType | |
| is_pyrimidine() const | core::chemical::ResidueType | |
| is_r_peptoid() const | core::chemical::ResidueTypeBase | inline |
| is_repulsive(Size const atomno) const | core::chemical::ResidueType | |
| is_ring_atom(uint const ring_num, uint const atom_id) const | core::chemical::ResidueType | |
| is_RNA() const | core::chemical::ResidueTypeBase | inline |
| is_s_peptoid() const | core::chemical::ResidueTypeBase | inline |
| is_sidechain_amine() const | core::chemical::ResidueType | inline |
| is_sidechain_thiol() const | core::chemical::ResidueType | inline |
| is_solvent() const | core::chemical::ResidueType | |
| is_sri() const | core::chemical::ResidueType | |
| is_surface() const | core::chemical::ResidueType | |
| is_terminus() const | core::chemical::ResidueType | inline |
| is_TNA() const | core::chemical::ResidueType | inline |
| is_TP3() const | core::chemical::ResidueType | |
| is_triazolemer() 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 | |
| is_virtualizable_by_packer() const | core::chemical::ResidueType | inline |
| is_VRT1() const | core::chemical::ResidueType | |
| is_water() const | core::chemical::ResidueType | inline |
| 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 |
| low_ring_conformers() const | core::chemical::ResidueType | inline |
| low_ring_conformers_ | 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 |
| lowest_ring_conformer_ | core::chemical::ResidueType | private |
| lowest_ring_conformers() const | core::chemical::ResidueType | inline |
| mainchain_atom(Size const mainchain_index) const | core::chemical::ResidueType | inline |
| mainchain_atoms() const | core::chemical::ResidueType | inline |
| mainchain_atoms_indices_ | core::chemical::ResidueType | private |
| mainchain_potentials_match(ResidueTypeBase const &other) const | core::chemical::ResidueTypeBase | |
| make(MutableResidueType const &residue_type) | core::chemical::ResidueType | static |
| mass() const | core::chemical::ResidueType | inline |
| mass_ | core::chemical::ResidueType | private |
| metal_binding_atoms() | core::chemical::ResidueTypeBase | inlineprotected |
| mm_atom_type(Size const atomno) const | core::chemical::ResidueType | |
| mm_atom_type_index(core::Size atomno) const | core::chemical::ResidueType | inline |
| mm_atom_type_index_ | core::chemical::ResidueType | private |
| mm_atom_types_ptr() const | core::chemical::ResidueTypeBase | inline |
| mm_name(core::Size atomno) const | core::chemical::ResidueType | |
| mode() const | core::chemical::ResidueTypeBase | inline |
| 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::ResidueTypeBase | |
| n_polymeric_residue_connections() const | core::chemical::ResidueType | inline |
| n_polymeric_residue_connections_ | core::chemical::ResidueType | private |
| n_possible_residue_connections() const | core::chemical::ResidueType | |
| n_proton_chi() const | core::chemical::ResidueType | inline |
| n_residue_connections_for_atom(Size const atomid) const | core::chemical::ResidueType | inline |
| n_ring_conformer_sets() const | core::chemical::ResidueType | |
| n_rings() const | core::chemical::ResidueType | inline |
| n_virtual_atoms() const override | core::chemical::ResidueType | virtual |
| na_analogue(std::string const &type) | core::chemical::ResidueTypeBase | inline |
| na_analogue() const | core::chemical::ResidueTypeBase | inline |
| 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 |
| name3() const | core::chemical::ResidueTypeBase | inline |
| name3(std::string const &name_in) | core::chemical::ResidueTypeBase | inline |
| natoms() const override | core::chemical::ResidueType | inlinevirtual |
| natoms_ | core::chemical::ResidueType | private |
| nbonds() const override | core::chemical::ResidueType | inlinevirtual |
| nbonds(Size atom) const | core::chemical::ResidueType | inline |
| nbonds_ | core::chemical::ResidueType | private |
| nbr_atom() const | core::chemical::ResidueType | inline |
| nbr_atom_ | core::chemical::ResidueType | private |
| nbr_radius() const | core::chemical::ResidueType | inline |
| nbr_radius_ | core::chemical::ResidueType | private |
| nbrs(Size const atomno) const | core::chemical::ResidueType | inline |
| nchi() const | core::chemical::ResidueType | inline |
| ndihe() const | core::chemical::ResidueType | inline |
| net_formal_charge() const | core::chemical::ResidueTypeBase | inline |
| net_formal_charge(signed long int charge_in) | core::chemical::ResidueTypeBase | inline |
| new_orbital_icoor_data(Size const orbital_index) const | core::chemical::ResidueType | |
| nheavyatoms() const override | core::chemical::ResidueType | inlinevirtual |
| nheavyatoms_ | 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 |
| 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 |
| operator=(ResidueType const &src)=delete | core::chemical::ResidueType | private |
| 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_icoor_data(Size const orbital_index) const | core::chemical::ResidueType | |
| orbital_index(std::string const &name) const | core::chemical::ResidueTypeBase | |
| orbital_type(Size const orbital_index) const | core::chemical::ResidueTypeBase | |
| orbital_types_ptr() const | core::chemical::ResidueTypeBase | inline |
| partial_charge_ | 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 |
| perform_checks() const | core::chemical::ResidueType | private |
| placeholder_clone() const =delete | core::chemical::ResidueType | private |
| print_bondangles() const | core::chemical::ResidueType | |
| print_pretty_path_distances() const | core::chemical::ResidueType | |
| properties() const | core::chemical::ResidueTypeBase | inline |
| 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 |
| remap_pdb_atom_names(bool rename) | core::chemical::ResidueTypeBase | inline |
| remap_pdb_atom_names() const | core::chemical::ResidueTypeBase | inline |
| remove_variant_type(VariantType const variant_type) | core::chemical::ResidueTypeBase | |
| remove_variant_type(std::string const &variant_type) | core::chemical::ResidueTypeBase | |
| report_adducts() const | core::chemical::ResidueTypeBase | |
| requires_actcoord() const | core::chemical::ResidueType | |
| reset_mainchain_torsion_potential_names() | core::chemical::ResidueTypeBase | |
| residue_connect_atom_index(Size const resconn_id) const | core::chemical::ResidueType | |
| residue_connection(Size const i) const | 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 |
| ResidueType() | core::chemical::ResidueType | private |
| ResidueType(MutableResidueType const &residue_type) | core::chemical::ResidueType | private |
| ResidueType(ResidueType const &residue_type)=delete | core::chemical::ResidueType | 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(uint const ring_num) const | core::chemical::ResidueType | inline |
| ring_atoms() const | core::chemical::ResidueType | inline |
| ring_atoms_ | core::chemical::ResidueType | private |
| ring_conformer_set(core::uint ring_num) const | core::chemical::ResidueType | |
| ring_conformer_sets_ | core::chemical::ResidueType | private |
| ring_saturation_type(uint const ring_num) const | core::chemical::ResidueType | inline |
| ring_saturation_types() const | core::chemical::ResidueType | inline |
| ring_saturation_types_ | core::chemical::ResidueType | private |
| RNA_info() const | core::chemical::ResidueType | |
| rna_info_ | core::chemical::ResidueType | private |
| root_atom() const | core::chemical::ResidueType | inline |
| root_atom_ | core::chemical::ResidueType | private |
| rotamer_library_specification(rotamers::RotamerLibrarySpecificationOP) | core::chemical::ResidueTypeBase | |
| rotamer_library_specification() const | core::chemical::ResidueTypeBase | |
| rotamer_library_specification_nonconst() | core::chemical::ResidueTypeBase | |
| select_orient_atoms(Size ¢er, Size &nbr1, Size &nbr2) const | core::chemical::ResidueType | |
| select_orient_atoms() const | core::chemical::ResidueType | |
| select_orient_atoms_standard_logic(Size ¢er, Size &nbr1, Size &nbr2, bool const ignore_virtuals) const | core::chemical::ResidueType | |
| self_pointer_updates() | core::chemical::ResidueType | private |
| set_adduct_flag(bool adduct_in) | core::chemical::ResidueTypeBase | |
| set_disulfide_atom_name(std::string const &n) | core::chemical::ResidueTypeBase | inline |
| set_gasteiger_atom_typeset(gasteiger::GasteigerAtomTypeSetCOP setting) | core::chemical::ResidueTypeBase | |
| set_metapatched() | core::chemical::ResidueTypeBase | inline |
| set_orbital_typeset(orbitals::OrbitalTypeSetCOP setting) | core::chemical::ResidueTypeBase | inline |
| set_properties(ResiduePropertiesOP properties) | core::chemical::ResidueTypeBase | |
| 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 | |
| setup_atom_ordering(MutableResidueType const &source) | core::chemical::ResidueType | private |
| show(std::ostream &output=std::cout, bool output_atomic_details=false) const override | core::chemical::ResidueType | virtual |
| show_all_atom_names(std::ostream &out) const override | core::chemical::ResidueType | virtual |
| strip_rotamer_library_specification() | core::chemical::ResidueTypeBase | |
| update_derived_data() | core::chemical::ResidueType | private |
| update_last_controlling_chi() | core::chemical::ResidueType | private |
| update_ncaa_rotamer_library_specification_if_present() | core::chemical::ResidueType | private |
| update_nonpolymer_dependent_groups() | core::chemical::ResidueType | private |
| update_polymer_dependent_groups() | core::chemical::ResidueType | private |
| update_ring_conformer_sets() | 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 |
| variant_type_enums() const | core::chemical::ResidueTypeBase | |
| variant_types() const | core::chemical::ResidueTypeBase | |
| vec_atom_type_indexes_ | core::chemical::ResidueType | private |
| vec_atom_types_ | 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() override | core::chemical::ResidueType | |
1.8.7