| abort_on_failed_loop_ | protocols::LoopRebuild | private |
| acceptable_rmsd_change(core::pose::Pose &pose1, core::pose::Pose &pose2) | protocols::LoopRebuild | private |
| allowed_failure_before_extend_ | protocols::LoopRebuild | private |
| allowed_failure_before_stop | protocols::LoopRebuild | |
| allowed_failure_before_stop_ | protocols::LoopRebuild | private |
| apply(core::pose::Pose &pose) override | protocols::LoopRebuild | virtual |
| barcode_extend_stems(core::pose::Pose &pose, int &barcst_extend_begin, int &barcst_extend_end, int &loop_begin, int &loop_end, int const &old_loop_begin, int const &old_loop_end, int const &nres, int const &selected_loop, int const &total_combine, int const &backward_combine) | protocols::LoopRebuild | private |
| build_loop_with_ccd_closure(core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int &cutpoint, bool const &extend_this_loop) | protocols::LoopRebuild | private |
| build_random_loops(core::pose::Pose &pose) | protocols::LoopRebuild | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::LoopRebuild | virtual |
| create() | protocols::moves::Mover | virtual |
| current_job_ | protocols::moves::Mover | private |
| current_tag_ | protocols::moves::Mover | private |
| desired_loops() | protocols::LoopRebuild | |
| extend_barcode_regions_if_chain_break(core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int &n_chain_break_fail, bool &is_chain_break, int &barcst_extend_begin, int &barcst_extend_end) | protocols::LoopRebuild | private |
| extend_loops | protocols::LoopRebuild | private |
| extended_loop() | protocols::LoopRebuild | |
| fast_ccd_close_loops(core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int const &cutpoint, core::kinematics::MoveMap &mm) | protocols::LoopRebuild | private |
| frag_libs_ | protocols::LoopRebuild | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| get_abort_on_failed_loop() | protocols::LoopRebuild | inline |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_allowed_failure_before_extend() | protocols::LoopRebuild | inline |
| get_allowed_failure_before_stop() | protocols::LoopRebuild | inline |
| get_ccd_closure_exist() | protocols::LoopRebuild | |
| get_chain_break_tolerance() | protocols::LoopRebuild | |
| get_combine_if_fail_exist() | protocols::LoopRebuild | |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_desired_loops_exist() | protocols::LoopRebuild | |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_loop_combine_rate() | protocols::LoopRebuild | |
| get_looprlx_cycle_ratio() | protocols::LoopRebuild | private |
| get_mc(core::pose::Pose &pose) | protocols::LoopRebuild | |
| get_name() const override | protocols::LoopRebuild | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_random_loop_flag() | protocols::LoopRebuild | inline |
| get_rmsd_tolerance() | protocols::LoopRebuild | |
| get_score_filter_cutoff() | protocols::LoopRebuild | private |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_success() | protocols::LoopRebuild | inline |
| get_type() const | protocols::moves::Mover | inline |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| info_ | protocols::moves::Mover | private |
| input_pose_ | protocols::moves::Mover | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| last_status_ | protocols::moves::Mover | private |
| loop_model() | protocols::LoopRebuild | |
| LoopRebuild(core::scoring::ScoreFunctionOP scorefxn, protocols::loops::Loops Loops_in) | protocols::LoopRebuild | |
| Loops_in_ | protocols::LoopRebuild | private |
| m_Temperature_ | protocols::LoopRebuild | private |
| mc_ | protocols::LoopRebuild | private |
| mc_created | protocols::LoopRebuild | private |
| movemap_ | protocols::LoopRebuild | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| native_pose_ | protocols::moves::Mover | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| pose_ | protocols::LoopRebuild | private |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| random_loop_flag_ | protocols::LoopRebuild | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| reset_status() | protocols::moves::Mover | |
| scorefxn_ | protocols::LoopRebuild | private |
| select_one_loop(int nres, int &selected_loop, std::vector< int > &folded_loops, std::vector< int > &inter_res, int &loop_begin, int &loop_end, int &cutpoint, bool &extend_this_loop, bool &are_loops_combined, int &combine_interval, int &loop_counter) | protocols::LoopRebuild | private |
| set_abort_on_failed_loop(bool setting=true) | protocols::LoopRebuild | inline |
| set_allowed_failure_before_extend(int setting) | protocols::LoopRebuild | inline |
| set_allowed_failure_before_stop(int setting) | protocols::LoopRebuild | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_default_mc(core::pose::Pose &pose) | protocols::LoopRebuild | |
| set_default_settings() | protocols::LoopRebuild | |
| set_extended_loop(bool val) | protocols::LoopRebuild | |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_looprlx_allow_move_map(int const &loop_begin, int const &loop_end, core::kinematics::MoveMap &mm) | protocols::LoopRebuild | private |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_random_loop_flag(bool setting=true) | protocols::LoopRebuild | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| shorten_long_terminal_loop() | protocols::LoopRebuild | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| Strings typedef | protocols::moves::Mover | |
| success | protocols::LoopRebuild | private |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| type_ | protocols::moves::Mover | private |
| use_default_extend_loops | protocols::LoopRebuild | private |
| ~LoopRebuild() override | protocols::LoopRebuild | |
