| AA typedef | core::pack::task::PackerTask | |
| add_behavior(std::string const &behavior) override | core::pack::task::PackerTask_ | virtual |
| add_behavior(std::string const &behavior, Size resid) override | core::pack::task::PackerTask_ | virtual |
| adducts(Size resid) const override | core::pack::task::PackerTask_ | virtual |
| and_linmem_ig(bool setting) override | core::pack::task::PackerTask_ | virtual |
| and_max_rotbump_energy(Real setting) override | core::pack::task::PackerTask_ | virtual |
| append_rotamer_operation(rotamer_set::RotamerOperationOP rotop) override | core::pack::task::PackerTask_ | virtual |
| append_rotamerset_operation(rotamer_set::RotamerSetOperationOP rotsetop) override | core::pack::task::PackerTask_ | virtual |
| append_rotamersets_operation(rotamer_set::RotamerSetsOperationOP rotsetsop) override | core::pack::task::PackerTask_ | virtual |
| being_designed(Size resid) const override | core::pack::task::PackerTask_ | inlinevirtual |
| being_packed(Size resid) const override | core::pack::task::PackerTask_ | inlinevirtual |
| bump_check() const override | core::pack::task::PackerTask_ | virtual |
| bump_check_ | core::pack::task::PackerTask_ | private |
| check_threads() const | core::pack::task::PackerTask_ | |
| clean_residue_task(conformation::Residue const &original_residue, Size const seqpos, core::pose::Pose const &pose) override | core::pack::task::PackerTask_ | virtual |
| clone() const override | core::pack::task::PackerTask_ | virtual |
| decrease_double_lazy_ig_memlimit(Size nbytes_for_rpes) override | core::pack::task::PackerTask_ | virtual |
| decrease_linmem_ig_history_size(Size setting) override | core::pack::task::PackerTask_ | virtual |
| design_any() const override | core::pack::task::PackerTask_ | virtual |
| design_residue(int resid) const override | core::pack::task::PackerTask_ | virtual |
| designing_residues() const override | core::pack::task::PackerTask_ | virtual |
| disallow_quench(bool const &disallow_quench) override | core::pack::task::PackerTask_ | virtual |
| disallow_quench() const override | core::pack::task::PackerTask_ | virtual |
| disallow_quench_ | core::pack::task::PackerTask_ | private |
| dlig_mem_limit_ | core::pack::task::PackerTask_ | private |
| double_lazy_ig() const override | core::pack::task::PackerTask_ | virtual |
| double_lazy_ig_ | core::pack::task::PackerTask_ | private |
| double_lazy_ig_memlimit() const override | core::pack::task::PackerTask_ | virtual |
| get_self_ptr() const | core::pack::task::PackerTask | inline |
| get_self_ptr() | core::pack::task::PackerTask | inline |
| has_behavior(std::string const &behavior, Size resid) const override | core::pack::task::PackerTask_ | virtual |
| has_behavior(Size resid) const override | core::pack::task::PackerTask_ | virtual |
| high_temp(Real const &high_temp) override | core::pack::task::PackerTask_ | virtual |
| high_temp() const override | core::pack::task::PackerTask_ | virtual |
| high_temp_ | core::pack::task::PackerTask_ | private |
| IG_edge_reweights_ | core::pack::task::PackerTask_ | private |
| ig_threads_to_request() const override | core::pack::task::PackerTask_ | virtual |
| ig_threads_to_request_ | core::pack::task::PackerTask_ | private |
| IGEdgeReweights() const override | core::pack::task::PackerTask_ | virtual |
| include_current(Size resid) const override | core::pack::task::PackerTask_ | virtual |
| increase_multi_cool_annealer_history_size(Size setting) override | core::pack::task::PackerTask_ | virtual |
| initialize_extra_rotamer_flags_from_command_line() override | core::pack::task::PackerTask_ | virtual |
| initialize_extra_rotamer_flags_from_options(utility::options::OptionCollection const &options) override | core::pack::task::PackerTask_ | virtual |
| initialize_from_command_line() override | core::pack::task::PackerTask_ | virtual |
| initialize_from_options(utility::options::OptionCollection const &options) override | core::pack::task::PackerTask_ | virtual |
| is_initialized() const override | core::pack::task::PackerTask_ | virtual |
| is_initialized_ | core::pack::task::PackerTask_ | private |
| keep_sequence_symmetry() const override | core::pack::task::PackerTask_ | inlinevirtual |
| keep_sequence_symmetry(bool const setting) override | core::pack::task::PackerTask_ | inlinevirtual |
| keep_sequence_symmetry_ | core::pack::task::PackerTask_ | private |
| lazy_ig() const override | core::pack::task::PackerTask_ | virtual |
| lazy_ig_ | core::pack::task::PackerTask_ | private |
| limit_ig_setup_threads(core::Size const setting) override | core::pack::task::PackerTask_ | virtual |
| linmem_ig() const override | core::pack::task::PackerTask_ | virtual |
| linmem_ig_ | core::pack::task::PackerTask_ | private |
| linmem_ig_history_size() const override | core::pack::task::PackerTask_ | virtual |
| linmem_ig_history_size_ | core::pack::task::PackerTask_ | private |
| linmem_ig_history_size_at_default_ | core::pack::task::PackerTask_ | private |
| list_options_read(utility::options::OptionKeyList &read_options) | core::pack::task::PackerTask | static |
| low_temp(Real const &low_temp) override | core::pack::task::PackerTask_ | virtual |
| low_temp() const override | core::pack::task::PackerTask_ | virtual |
| low_temp_ | core::pack::task::PackerTask_ | private |
| max_rotbump_energy() const override | core::pack::task::PackerTask_ | virtual |
| max_rotbump_energy_ | core::pack::task::PackerTask_ | private |
| mca_history_size_ | core::pack::task::PackerTask_ | private |
| multi_cool_annealer() const override | core::pack::task::PackerTask_ | virtual |
| multi_cool_annealer_ | core::pack::task::PackerTask_ | private |
| multi_cool_annealer_history_size() const override | core::pack::task::PackerTask_ | virtual |
| n_to_be_packed_ | core::pack::task::PackerTask_ | mutableprivate |
| n_to_be_packed_up_to_date_ | core::pack::task::PackerTask_ | mutableprivate |
| nonconst_residue_task(Size resid) override | core::pack::task::PackerTask_ | virtual |
| nres_ | core::pack::task::PackerTask_ | private |
| num_to_be_packed() const override | core::pack::task::PackerTask_ | virtual |
| operator=(PackerTask const &) | core::pack::task::PackerTask_ | privatevirtual |
| optimize_H_ | core::pack::task::PackerTask_ | private |
| or_adducts(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_adducts(bool setting, Size resid) override | core::pack::task::PackerTask_ | virtual |
| or_double_lazy_ig(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_fix_his_tautomer(utility::vector1< int > const &positions, bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_flip_HNQ(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_include_current(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_include_current(bool setting, Size resid) override | core::pack::task::PackerTask_ | virtual |
| or_lazy_ig(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_linmem_ig(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_multi_cool_annealer(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_optimize_h_mode(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_precompute_ig(bool setting) override | core::pack::task::PackerTask_ | virtual |
| or_preserve_c_beta(bool setting) override | core::pack::task::PackerTask_ | virtual |
| pack_residue(int resid) const override | core::pack::task::PackerTask_ | virtual |
| pack_residue_ | core::pack::task::PackerTask_ | private |
| packer_palette_ | core::pack::task::PackerTask_ | private |
| PackerTask_(core::Size const ig_threads_to_request=0) | core::pack::task::PackerTask_ | |
| PackerTask_(pose::Pose const &pose, core::Size const ig_threads_to_request=0) | core::pack::task::PackerTask_ | |
| PackerTask_(pose::Pose const &pose, core::pack::palette::PackerPaletteCOP const &packer_palette, core::Size const ig_threads_to_request=0) | core::pack::task::PackerTask_ | |
| precompute_ig() const override | core::pack::task::PackerTask_ | virtual |
| precompute_ig_ | core::pack::task::PackerTask_ | private |
| remap_residue_level_tasks(core::id::SequenceMappingCOP seqmap, core::pose::Pose const &pose) override | core::pack::task::PackerTask_ | virtual |
| repacking_residues() const override | core::pack::task::PackerTask_ | virtual |
| request_symmetrize_by_intersection() override | core::pack::task::PackerTask_ | virtual |
| request_symmetrize_by_union() override | core::pack::task::PackerTask_ | virtual |
| residue_task(Size resid) const override | core::pack::task::PackerTask_ | virtual |
| residue_tasks_ | core::pack::task::PackerTask_ | private |
| restrict_to_repacking() override | core::pack::task::PackerTask_ | virtual |
| restrict_to_residues(utility::vector1< bool > const &residues_allowed_to_be_packed) override | core::pack::task::PackerTask_ | virtual |
| rotamer_couplings() const override | core::pack::task::PackerTask_ | virtual |
| rotamer_couplings(RotamerCouplingsCOP setting) override | core::pack::task::PackerTask_ | virtual |
| rotamer_couplings_ | core::pack::task::PackerTask_ | private |
| rotamer_couplings_exist() const override | core::pack::task::PackerTask_ | virtual |
| rotamer_links() const override | core::pack::task::PackerTask_ | virtual |
| rotamer_links(RotamerLinksCOP setting) override | core::pack::task::PackerTask_ | virtual |
| rotamer_links_ | core::pack::task::PackerTask_ | private |
| rotamer_links_exist() const override | core::pack::task::PackerTask_ | virtual |
| rotamer_sets_operation_begin() const override | core::pack::task::PackerTask_ | virtual |
| rotamer_sets_operation_end() const override | core::pack::task::PackerTask_ | virtual |
| RotamerCouplingsCOP typedef | core::pack::task::PackerTask | |
| RotamerLinksCOP typedef | core::pack::task::PackerTask | |
| rotsetsops_ | core::pack::task::PackerTask_ | private |
| seq_sym_uid_prefix_ | core::pack::task::PackerTask_ | private |
| sequence_symmetric_uid_prefix() const override | core::pack::task::PackerTask_ | inlinevirtual |
| sequence_symmetric_uid_prefix(std::string const &prefix) override | core::pack::task::PackerTask_ | inlinevirtual |
| set_bump_check(bool setting) override | core::pack::task::PackerTask_ | virtual |
| set_IGEdgeReweights() override | core::pack::task::PackerTask_ | virtual |
| set_smart_annealer(bool setting) override | core::pack::task::PackerTask_ | inlinevirtual |
| set_smart_annealer_cutoff(core::Real setting) override | core::pack::task::PackerTask_ | inlinevirtual |
| set_smart_annealer_disable_during_quench(bool setting) override | core::pack::task::PackerTask_ | inlinevirtual |
| set_smart_annealer_model(std::string const &setting) override | core::pack::task::PackerTask_ | inlinevirtual |
| set_smart_annealer_pick_again(bool setting) override | core::pack::task::PackerTask_ | inlinevirtual |
| show(std::ostream &out) const override | core::pack::task::PackerTask_ | virtual |
| show() const override | core::pack::task::PackerTask_ | virtual |
| show_all_residue_tasks(std::ostream &out) const override | core::pack::task::PackerTask_ | virtual |
| show_all_residue_tasks() const override | core::pack::task::PackerTask_ | virtual |
| show_residue_task(std::ostream &out, Size resid) const override | core::pack::task::PackerTask_ | virtual |
| show_residue_task(Size resid) const override | core::pack::task::PackerTask_ | virtual |
| smart_annealer() const override | core::pack::task::PackerTask_ | inlinevirtual |
| smart_annealer_ | core::pack::task::PackerTask_ | private |
| smart_annealer_cutoff() const override | core::pack::task::PackerTask_ | inlinevirtual |
| smart_annealer_cutoff_ | core::pack::task::PackerTask_ | private |
| smart_annealer_disable_during_quench() const override | core::pack::task::PackerTask_ | inlinevirtual |
| smart_annealer_disable_during_quench_ | core::pack::task::PackerTask_ | private |
| smart_annealer_model() const override | core::pack::task::PackerTask_ | inlinevirtual |
| smart_annealer_model_ | core::pack::task::PackerTask_ | private |
| smart_annealer_pick_again() const override | core::pack::task::PackerTask_ | inlinevirtual |
| smart_annealer_pick_again_ | core::pack::task::PackerTask_ | private |
| symmetrize_by_intersection() const override | core::pack::task::PackerTask_ | virtual |
| symmetrize_by_union() const override | core::pack::task::PackerTask_ | virtual |
| symmetry_status_ | core::pack::task::PackerTask_ | private |
| target_type(Size resid) const | core::pack::task::PackerTask_ | virtual |
| task_string(pose::Pose const &pose) const override | core::pack::task::PackerTask_ | virtual |
| temporarily_fix_everything() override | core::pack::task::PackerTask_ | virtual |
| temporarily_set_pack_residue(int resid, bool setting) override | core::pack::task::PackerTask_ | virtual |
| total_residue() const override | core::pack::task::PackerTask_ | virtual |
| update_commutative(PackerTask const &tark_in) override | core::pack::task::PackerTask_ | virtual |
| update_n_to_be_packed() const | core::pack::task::PackerTask_ | private |
| update_residue_commutative(Size resid, ResidueLevelTask const &res_task_in) | core::pack::task::PackerTask_ | virtual |
| update_residue_intersection(Size resid, ResidueLevelTask const &res_task_in) | core::pack::task::PackerTask_ | virtual |
| update_residue_union(Size resid, ResidueLevelTask const &res_task_in) | core::pack::task::PackerTask_ | virtual |
| ~PackerTask_() override | core::pack::task::PackerTask_ | |
1.8.7