| add_base_pair_constraints_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| all_rna_fragments_file_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| apply(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| check_new_pairing_dists(core::pose::Pose &pose, Size const &frag_pos) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| check_pairing_dists_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| choose_best_solution_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| chunk_silent_files_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | virtual |
| close_loops_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| CoarseRNA_DeNovoProtocol(Size const nstruct, Size const monte_carlo_cycles, std::string const silent_file) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | |
| constraint_set_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| create() | protocols::moves::Mover | virtual |
| denovo_scorefxn_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| do_random_fragment_insertions(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| domain_move_frequency_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| dump_pdb_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| figure_out_constraint_separation_cutoff(Size const &r, Size const &rounds, Size const &max_dist) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| fill_pairing_dists(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| Filters_map typedef | protocols::moves::Mover | |
| force_ideal_chainbreak_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| frag_mover_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| frag_size_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| freeze_domains_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_temperature(Size const &r, Size const &rounds) const | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| get_type() const | protocols::moves::Mover | inline |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| initialize_constraints(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| initialize_movers(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| initialize_tag_is_done() | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| input_res_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| jump_library_file_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| lores_scorefxn_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| m_Temperature_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| monte_carlo_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| monte_carlo_cycles_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| multiple_domain_mover_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| name() | protocols::moves::Mover | inlinestatic |
| nstruct_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| operator=(Mover const &other) | protocols::moves::Mover | |
| output_to_silent_file(core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag, bool const score_only=false) const | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | |
| pairing_dists_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) | protocols::moves::Mover | virtual |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) | protocols::moves::Mover | virtual |
| parse_state(SerializableState const &state) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| random_domain_move_trial(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| random_fragment_trial(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | 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 | |
| rna_chunk_library_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| rna_data_file_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| rna_data_reader_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| rna_loop_closer_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| RNA_move_trial(core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| rna_params_file_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| rna_structure_parameters_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| rounds_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| set_add_base_pair_constraints(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_check_pairing_dists(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_choose_best_solution(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_chunk_silent_files(utility::vector1< std::string > const &chunk_silent_files) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_close_loops(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_dump_pdb(bool const setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_force_ideal_chainbreak(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_freeze_domains(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_input_res(utility::vector1< core::Size > const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_jump_library_file(std::string const jump_library_file) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_lores_scorefxn(std::string const &lores_scorefxn) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_rna_data_file(std::string const file) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_rna_params_file(std::string const file) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_sim_anneal(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_staged_constraints(bool const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| set_temperature(core::Real const &setting) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| silent_file_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| sim_anneal_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| staged_constraints_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| Strings typedef | protocols::moves::Mover | |
| tag_is_done_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| update_domain_rot_trans_mag(Size const &r, Size const &rounds) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| update_pose_constraints(Size const &r, Size const &rounds, core::pose::Pose &pose) | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| view_monte_carlo_ | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | private |
| ~CoarseRNA_DeNovoProtocol() | protocols::coarse_rna::CoarseRNA_DeNovoProtocol | |
| ~Mover() | protocols::moves::Mover | virtual |
1.8.7