| add_base_residue_type(MutableResidueTypeOP new_type) | core::chemical::ResidueTypeSet | protectedvirtual |
| add_base_residue_type(std::string const &filename) | core::chemical::ResidueTypeSet | protectedvirtual |
| add_metapatch(MetapatchCOP p) | core::chemical::ResidueTypeSet | protectedvirtual |
| add_patch(PatchCOP p) | core::chemical::ResidueTypeSet | protectedvirtual |
| add_patches(utility::vector1< std::string > const &patch_filenames, utility::vector1< std::string > const &metapatch_filenames) | core::chemical::ResidueTypeSet | protectedvirtual |
| add_unpatchable_residue_type(MutableResidueTypeOP new_type) | core::chemical::ResidueTypeSet | protectedvirtual |
| add_unpatchable_residue_type(std::string const &filename) | core::chemical::ResidueTypeSet | protectedvirtual |
| apply_patch(ResidueTypeCOP const &rsd_base_ptr, std::string const &patch_name, std::map< std::string, utility::vector1< PatchCOP > > const &patch_mapping, std::map< std::string, MetapatchCOP > const &metapach_mapping) const | core::chemical::ResidueTypeSet | protected |
| atom_type_set() const | core::chemical::ResidueTypeSet | inline |
| atom_type_set(AtomTypeSetCOP atom_types) | core::chemical::ResidueTypeSet | protected |
| atom_types_ | core::chemical::ResidueTypeSet | private |
| attempt_readin(std::string const &db_filename, std::string const &pdb_id, MutableResidueTypeOP &new_rsd_type, bool &found_file) const | core::chemical::GlobalResidueTypeSet | private |
| base_residue_types() const | core::chemical::ResidueTypeSet | inlinevirtual |
| base_residue_types_ | core::chemical::ResidueTypeSet | private |
| cache_ | core::chemical::ResidueTypeSet | private |
| cache_object() const | core::chemical::ResidueTypeSet | inlineprotected |
| d_to_l_mapping() | core::chemical::ResidueTypeSet | inlineprotected |
| d_to_l_mapping_ | core::chemical::ResidueTypeSet | private |
| database_directory() const | core::chemical::GlobalResidueTypeSet | inline |
| database_directory_ | core::chemical::GlobalResidueTypeSet | private |
| deal_with_patch_special_cases() | core::chemical::GlobalResidueTypeSet | private |
| element_set() const | core::chemical::ResidueTypeSet | inline |
| element_set(ElementSetCOP elements) | core::chemical::ResidueTypeSet | inlineprotected |
| elements_ | core::chemical::ResidueTypeSet | private |
| exclude_pdb_component_ids_ | core::chemical::GlobalResidueTypeSet | private |
| extra_nonparam_restypes_from_commandline() const | core::chemical::GlobalResidueTypeSet | private |
| figure_out_last_patch_from_name(std::string const &rsd_name, std::string &rsd_name_base, std::string &patch_name) const | core::chemical::ResidueTypeSet | protected |
| force_add_base_residue_type_already_write_locked(MutableResidueTypeOP new_type) const | core::chemical::ResidueTypeSet | protectedvirtual |
| generate_all_residue_types() | core::chemical::GlobalResidueTypeSet | private |
| generate_residue_type(std::string const &rsd_name) const | core::chemical::ResidueTypeSet | protectedvirtual |
| generate_residue_type_write_locked(std::string const &rsd_name) const | core::chemical::ResidueTypeSet | protectedvirtual |
| generates_patched_residue_type_with_interchangeability_group(std::string const &base_residue_name, std::string const &interchangeability_group) const | core::chemical::ResidueTypeSet | virtual |
| generates_patched_residue_type_with_name3(std::string const &base_residue_name, std::string const &name3) const | core::chemical::ResidueTypeSet | virtual |
| get_all_types_with_variants_aa(AA aa, utility::vector1< std::string > const &variants) const override | core::chemical::GlobalResidueTypeSet | virtual |
| get_all_types_with_variants_aa(AA aa, utility::vector1< std::string > const &variants, utility::vector1< VariantType > const &exceptions) const override | core::chemical::GlobalResidueTypeSet | virtual |
| get_all_types_with_variants_by_basetype(ResidueTypeCOP base_type, utility::vector1< VariantType > const &variants, utility::vector1< std::string > const &variant_strings, utility::vector1< VariantType > const &exceptions, bool const no_metapatches) const | core::chemical::ResidueTypeSet | |
| get_all_types_with_variants_name1(char name1, utility::vector1< std::string > const &variants) const | core::chemical::ResidueTypeSet | |
| get_all_types_with_variants_name3(std::string const &name3, utility::vector1< std::string > const &variants) const | core::chemical::ResidueTypeSet | |
| get_base_types_aa(AA aa) const | core::chemical::ResidueTypeSet | |
| get_base_types_name1(char name1) const | core::chemical::ResidueTypeSet | |
| get_base_types_name3(std::string const &name3) const | core::chemical::ResidueTypeSet | |
| get_d_equivalent(ResidueTypeCOP l_rsd) const | core::chemical::ResidueTypeSet | virtual |
| get_l_equivalent(ResidueTypeCOP d_rsd) const | core::chemical::ResidueTypeSet | virtual |
| get_mirrored_type(ResidueTypeCOP original_rsd) const | core::chemical::ResidueTypeSet | virtual |
| get_patches(std::string const &name) const | core::chemical::ResidueTypeSet | virtual |
| get_patches(std::string const &name, std::map< std::string, utility::vector1< PatchCOP > > const &patch_mapping, std::map< std::string, MetapatchCOP > const &metapach_mapping) const | core::chemical::ResidueTypeSet | protectedvirtual |
| get_representative_type_aa(AA aa, utility::vector1< std::string > const &variants) const | core::chemical::ResidueTypeSet | |
| get_representative_type_aa(AA aa) const | core::chemical::ResidueTypeSet | |
| get_representative_type_base_name(std::string const &base_name) const | core::chemical::ResidueTypeSet | |
| get_representative_type_name1(char name1, utility::vector1< std::string > const &variants) const | core::chemical::ResidueTypeSet | |
| get_representative_type_name1(char name1) const | core::chemical::ResidueTypeSet | |
| get_representative_type_name3(std::string const &name3, utility::vector1< std::string > const &variants) const | core::chemical::ResidueTypeSet | |
| get_representative_type_name3(std::string const &name3) const | core::chemical::ResidueTypeSet | |
| get_residue_type_with_custom_variant_added(ResidueType const &init_rsd, std::string const &new_type) const | core::chemical::ResidueTypeSet | |
| get_residue_type_with_variant_added(ResidueType const &init_rsd, VariantType const new_type) const | core::chemical::ResidueTypeSet | |
| get_residue_type_with_variant_added(ResidueType const &init_rsd, std::string const &new_type) const | core::chemical::ResidueTypeSet | |
| get_residue_type_with_variant_removed(ResidueType const &init_rsd, VariantType const old_type) const | core::chemical::ResidueTypeSet | |
| get_self_ptr() const | core::chemical::ResidueTypeSet | inline |
| get_self_weak_ptr() const | core::chemical::ResidueTypeSet | inline |
| GlobalResidueTypeSet()=delete | core::chemical::GlobalResidueTypeSet | |
| GlobalResidueTypeSet(std::string const &name, std::string const &directory) | core::chemical::GlobalResidueTypeSet | |
| GlobalResidueTypeSet(GlobalResidueTypeSet const &)=delete | core::chemical::GlobalResidueTypeSet | private |
| has_interchangeability_group(std::string const &name) const | core::chemical::ResidueTypeSet | |
| has_metapatch(std::string const &name) const | core::chemical::ResidueTypeSet | inlinevirtual |
| has_name(std::string const &name) const | core::chemical::ResidueTypeSet | virtual |
| has_name3(std::string const &name3) const | core::chemical::ResidueTypeSet | |
| has_name_write_locked(std::string const &name) const | core::chemical::ResidueTypeSet | protectedvirtual |
| init_patches_from_commandline() | core::chemical::GlobalResidueTypeSet | private |
| init_patches_from_database() | core::chemical::GlobalResidueTypeSet | private |
| init_restypes_from_commandline() | core::chemical::GlobalResidueTypeSet | private |
| init_restypes_from_database() | core::chemical::GlobalResidueTypeSet | private |
| l_to_d_mapping() | core::chemical::ResidueTypeSet | inlineprotected |
| l_to_d_mapping_ | core::chemical::ResidueTypeSet | private |
| lazy_load_base_type_already_write_locked(std::string const &rsd_base_name) const override | core::chemical::GlobalResidueTypeSet | protectedvirtual |
| load_exclude_pdb_component_ids(std::string const &directory, std::string const &file="exclude_pdb_component_list.txt") | core::chemical::GlobalResidueTypeSet | private |
| load_pdb_component(std::string const &pdb_id) const | core::chemical::GlobalResidueTypeSet | private |
| load_residue_types_from_sql_database() | core::chemical::GlobalResidueTypeSet | private |
| merge_split_behavior_manager() const | core::chemical::ResidueTypeSet | |
| merge_split_behavior_manager_ | core::chemical::ResidueTypeSet | private |
| metapatch(std::string const &name) const | core::chemical::ResidueTypeSet | inlinevirtual |
| metapatch_map() const | core::chemical::ResidueTypeSet | inlinevirtual |
| metapatch_map_ | core::chemical::ResidueTypeSet | private |
| metapatches() const | core::chemical::ResidueTypeSet | inlinevirtual |
| metapatches_ | core::chemical::ResidueTypeSet | private |
| mm_atom_type_set() const | core::chemical::ResidueTypeSet | inline |
| mm_atom_type_set(MMAtomTypeSetCOP mm_atom_types) | core::chemical::ResidueTypeSet | inlineprotected |
| mm_atom_types_ | core::chemical::ResidueTypeSet | private |
| mode() const | core::chemical::ResidueTypeSet | inline |
| mode(TypeSetMode setting) | core::chemical::ResidueTypeSet | inlineprotected |
| mode_ | core::chemical::ResidueTypeSet | private |
| name() const | core::chemical::GlobalResidueTypeSet | inline |
| name(std::string const &setting) | core::chemical::GlobalResidueTypeSet | inlineprivate |
| name_ | core::chemical::GlobalResidueTypeSet | private |
| name_map(std::string const &name) const | core::chemical::ResidueTypeSet | virtual |
| name_mapOP(std::string const &name) const | core::chemical::ResidueTypeSet | virtual |
| name_mapOP_write_locked(std::string const &name) const | core::chemical::ResidueTypeSet | protectedvirtual |
| operator=(GlobalResidueTypeSet const &)=delete | core::chemical::GlobalResidueTypeSet | private |
| core::chemical::ResidueTypeSet::operator=(ResidueTypeSet const &)=delete | core::chemical::ResidueTypeSet | protected |
| orbital_type_set() const | core::chemical::ResidueTypeSet | inline |
| orbital_type_set(orbitals::OrbitalTypeSetCOP orbital_types) | core::chemical::ResidueTypeSet | inlineprotected |
| orbital_types_ | core::chemical::ResidueTypeSet | private |
| params_files_from_commandline() const | core::chemical::GlobalResidueTypeSet | private |
| patch_map() const | core::chemical::ResidueTypeSet | inlinevirtual |
| patch_map_ | core::chemical::ResidueTypeSet | private |
| patches() const | core::chemical::ResidueTypeSet | inlinevirtual |
| patches_ | core::chemical::ResidueTypeSet | private |
| pdb_components_directory(std::string const &setting) | core::chemical::GlobalResidueTypeSet | inlineprivate |
| pdb_components_directory() const | core::chemical::GlobalResidueTypeSet | inlineprivate |
| pdb_components_directory_ | core::chemical::GlobalResidueTypeSet | private |
| pdb_components_overrides(utility::vector1< std::string > const &setting) | core::chemical::GlobalResidueTypeSet | inlineprivate |
| pdb_components_overrides() const | core::chemical::GlobalResidueTypeSet | inlineprivate |
| pdb_components_overrides_ | core::chemical::GlobalResidueTypeSet | private |
| place_adducts() | core::chemical::GlobalResidueTypeSet | private |
| prep_restype(MutableResidueTypeOP new_type) const | core::chemical::ResidueTypeSet | protected |
| read_files_for_base_residue_types(utility::vector1< std::string > const &filenames) | core::chemical::ResidueTypeSet | protectedvirtual |
| read_files_for_unpatchable_residue_types(utility::vector1< std::string > const &filenames) | core::chemical::ResidueTypeSet | protectedvirtual |
| remove_base_residue_type(std::string const &name) override | core::chemical::GlobalResidueTypeSet | protectedvirtual |
| remove_unpatchable_residue_type(std::string const &name) override | core::chemical::GlobalResidueTypeSet | protectedvirtual |
| ResidueTypeSet(TypeSetMode mode=INVALID_t) | core::chemical::ResidueTypeSet | |
| ResidueTypeSet(ResidueTypeSet const &) | core::chemical::ResidueTypeSet | protected |
| set_merge_split_behavior_manager(io::MergeAndSplitBehaviorManagerCOP mbm) | core::chemical::ResidueTypeSet | protectedvirtual |
| unpatchable_residue_types() const | core::chemical::ResidueTypeSet | inlinevirtual |
| unpatchable_residue_types_ | core::chemical::ResidueTypeSet | private |
| update_base_residue_types_if_replaced(ResidueTypeCOP rsd_type, ResidueTypeCOP rsd_type_new) | core::chemical::ResidueTypeSet | protected |
