| aa(core::chemical::AA const &setting) | core::chemical::ResidueTypeFinder | inline |
| aa_ | core::chemical::ResidueTypeFinder | private |
| adds_any_property(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| adds_any_variant(PatchCOP patch) const | core::chemical::ResidueTypeFinder | private |
| apply_basic_filters(ResidueTypeCOPs rsd_types) const | core::chemical::ResidueTypeFinder | private |
| apply_filters_after_patches(ResidueTypeCOPs rsd_types, bool const allow_extra_variants=false) const | core::chemical::ResidueTypeFinder | private |
| apply_metapatches_recursively(utility::vector1< ResidueTypeCOP > const &rsd_types, Size const metapatch_number, bool const get_first_totally_ok_residue_type=false) const | core::chemical::ResidueTypeFinder | private |
| apply_patches_recursively(utility::vector1< ResidueTypeCOP > const &rsd_types, Size const patch_number, bool const get_first_totally_ok_residue_type=false) const | core::chemical::ResidueTypeFinder | private |
| apply_preferences_and_discouragements(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| atom_names_soft(utility::vector1< std::string > const &setting) | core::chemical::ResidueTypeFinder | inline |
| atom_names_soft_ | core::chemical::ResidueTypeFinder | private |
| base_property(ResidueProperty const setting) | core::chemical::ResidueTypeFinder | inline |
| base_property_ | core::chemical::ResidueTypeFinder | private |
| base_type(ResidueTypeCOP const &basetype) | core::chemical::ResidueTypeFinder | inline |
| base_type_ | core::chemical::ResidueTypeFinder | private |
| changes_to_wrong_aa(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| check_candidate_has_all_variant_sets(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| check_nucleic_acid_virtual_phosphates(bool const setting) | core::chemical::ResidueTypeFinder | inline |
| check_nucleic_acid_virtual_phosphates_ | core::chemical::ResidueTypeFinder | private |
| check_variant_sets_have_all_candidate_variants(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| connect_atoms(utility::vector1< std::string > const &setting) | core::chemical::ResidueTypeFinder | inline |
| connect_atoms_ | core::chemical::ResidueTypeFinder | private |
| custom_variants_ | core::chemical::ResidueTypeFinder | private |
| deletes_any_property(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| deletes_any_variant(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| disable_metapatches() | core::chemical::ResidueTypeFinder | inline |
| disallow_carboxyl_conjugation_at_glu_asp_ | core::chemical::ResidueTypeFinder | private |
| disallow_properties(utility::vector1< ResidueProperty > const &setting) | core::chemical::ResidueTypeFinder | inline |
| disallow_properties_ | core::chemical::ResidueTypeFinder | private |
| disallow_variants(utility::vector1< VariantType > const &setting, bool const clear_existing=true) | core::chemical::ResidueTypeFinder | |
| disallow_variants_ | core::chemical::ResidueTypeFinder | private |
| discouraged_properties(utility::vector1< ResidueProperty > const &setting) | core::chemical::ResidueTypeFinder | inline |
| discouraged_properties_ | core::chemical::ResidueTypeFinder | private |
| filter_all_patch_names(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_all_properties(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_all_variants_matched(ResidueTypeCOPs const &rsd_types, bool const allow_extra_variants=false) const | core::chemical::ResidueTypeFinder | private |
| filter_by_aa(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_by_base_property(ResidueTypeCOPs const &base_rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_by_interchangeability_group(ResidueTypeCOPs const &rsd_types, bool const keep_if_base_type_generates_interchangeability_group) const | core::chemical::ResidueTypeFinder | private |
| filter_by_name1(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_by_name3(ResidueTypeCOPs const &rsd_types, bool const keep_if_base_type_generates_aa) const | core::chemical::ResidueTypeFinder | private |
| filter_by_residue_type_base_name(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_connections(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_disallow_properties(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_disallow_variants(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| filter_special_cases(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| fixes_connects(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| fixes_interchangeability_group(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| fixes_name3(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| get_all_possible_residue_types(bool const allow_extra_variants=false) const | core::chemical::ResidueTypeFinder | |
| get_best_match_residue_type_for_atom_names(utility::vector1< std::string > const &atom_names) | core::chemical::ResidueTypeFinder | |
| get_possible_base_residue_types(bool const include_unpatchable=true, bool const apply_all_filters=false) const | core::chemical::ResidueTypeFinder | |
| get_possible_base_unpatchable_residue_types() const | core::chemical::ResidueTypeFinder | |
| get_possible_unpatchable_residue_types() const | core::chemical::ResidueTypeFinder | |
| get_representative_type(bool const metapatches=true) const | core::chemical::ResidueTypeFinder | |
| has_disallowed_variant(PatchCOP patch) const | core::chemical::ResidueTypeFinder | private |
| ignore_atom_named_H(bool const setting) | core::chemical::ResidueTypeFinder | inline |
| ignore_atom_named_H_ | core::chemical::ResidueTypeFinder | private |
| initialize_relevant_pdb_components() const | core::chemical::ResidueTypeFinder | private |
| interchangeability_group(std::string const &setting) | core::chemical::ResidueTypeFinder | inline |
| interchangeability_group_ | core::chemical::ResidueTypeFinder | private |
| matches_any_atom_name(PatchCOP patch, ResidueTypeCOP rsd_type) const | core::chemical::ResidueTypeFinder | private |
| matches_any_patch_name(PatchCOP patch) const | core::chemical::ResidueTypeFinder | private |
| name1(char const &setting) | core::chemical::ResidueTypeFinder | inline |
| name1_ | core::chemical::ResidueTypeFinder | private |
| name3(std::string const &setting) | core::chemical::ResidueTypeFinder | inline |
| name3_ | core::chemical::ResidueTypeFinder | private |
| no_CCD_on_name3_match_ | core::chemical::ResidueTypeFinder | private |
| no_metapatches() const | core::chemical::ResidueTypeFinder | inline |
| no_metapatches_ | core::chemical::ResidueTypeFinder | private |
| patch_names(utility::vector1< std::string > const &setting) | core::chemical::ResidueTypeFinder | inline |
| patch_names_ | core::chemical::ResidueTypeFinder | private |
| preferred_properties(utility::vector1< ResidueProperty > const &setting) | core::chemical::ResidueTypeFinder | inline |
| preferred_properties_ | core::chemical::ResidueTypeFinder | private |
| prioritize_rosetta_types_over_pdb_components(ResidueTypeCOPs const &rsd_types) const | core::chemical::ResidueTypeFinder | private |
| properties(utility::vector1< ResidueProperty > const &setting) | core::chemical::ResidueTypeFinder | inline |
| properties_ | core::chemical::ResidueTypeFinder | private |
| residue_base_name(std::string const &setting) | core::chemical::ResidueTypeFinder | inline |
| residue_type_base_name_ | core::chemical::ResidueTypeFinder | private |
| residue_type_set_ | core::chemical::ResidueTypeFinder | private |
| ResidueTypeFinder(core::chemical::ResidueTypeSet const &residue_type_set) | core::chemical::ResidueTypeFinder | |
| set_no_CCD_on_name3_match(bool setting) | core::chemical::ResidueTypeFinder | inline |
| variant_exceptions(utility::vector1< std::string > const &setting, bool const clear_existing=true) | core::chemical::ResidueTypeFinder | |
| variant_exceptions(utility::vector1< VariantType > const &setting, bool const clear_existing=true) | core::chemical::ResidueTypeFinder | |
| variant_exceptions_ | core::chemical::ResidueTypeFinder | private |
| variants(utility::vector1< VariantType > const &setting, bool const clear_existing=true) | core::chemical::ResidueTypeFinder | |
| variants(utility::vector1< std::string > const &setting) | core::chemical::ResidueTypeFinder | |
| variants(utility::vector1< VariantType > const &std_variants, utility::vector1< std::string > const &custom_variants, bool const clear_existing=true) | core::chemical::ResidueTypeFinder | |
| variants(utility::vector1< VariantType > const &setting) const | core::chemical::ResidueTypeFinder | private |
| variants_in_sets(utility::vector1< utility::vector1< VariantType > > const &setting) | core::chemical::ResidueTypeFinder | inline |
| variants_in_sets_ | core::chemical::ResidueTypeFinder | private |
| ~ResidueTypeFinder() override | core::chemical::ResidueTypeFinder | |
1.8.7