| add_chem_shift_info(core::io::silent::SilentStruct &silent_struct, core::pose::Pose const &const_pose) const | protocols::farna::RNA_DeNovoProtocol | private |
| add_number_base_pairs(core::pose::Pose const &pose_input, core::io::silent::SilentStruct &s) const | protocols::farna::RNA_DeNovoProtocol | private |
| add_number_native_base_pairs(core::pose::Pose &pose, core::io::silent::SilentStruct &s) const | protocols::farna::RNA_DeNovoProtocol | private |
| align_and_output_to_silent_file(core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag) const | protocols::farna::RNA_DeNovoProtocol | |
| all_lores_score_final_ | protocols::farna::RNA_DeNovoProtocol | private |
| all_rna_fragments_ | protocols::farna::RNA_DeNovoProtocol | private |
| all_rna_fragments_file_ | protocols::farna::RNA_DeNovoProtocol | private |
| allow_bulge_ | protocols::farna::RNA_DeNovoProtocol | private |
| allow_consecutive_bulges_ | protocols::farna::RNA_DeNovoProtocol | private |
| allowed_bulge_res_ | protocols::farna::RNA_DeNovoProtocol | private |
| apply(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| apply_chem_shift_data(core::pose::Pose &pose, std::string const out_file_tag) | protocols::farna::RNA_DeNovoProtocol | private |
| autofilter_ | protocols::farna::RNA_DeNovoProtocol | private |
| autofilter_score_quantile_ | protocols::farna::RNA_DeNovoProtocol | private |
| binary_rna_output_ | protocols::farna::RNA_DeNovoProtocol | private |
| bps_moves_ | protocols::farna::RNA_DeNovoProtocol | private |
| calc_rmsds(core::io::silent::SilentStruct &s, core::pose::Pose &pose, std::string const &out_file_tag) const | protocols::farna::RNA_DeNovoProtocol | private |
| chainbreak_weight_ | protocols::farna::RNA_DeNovoProtocol | private |
| check_score_filter(core::Real const lores_score_, std::list< core::Real > &all_lores_score_) | protocols::farna::RNA_DeNovoProtocol | private |
| chem_shift_scorefxn_ | protocols::farna::RNA_DeNovoProtocol | private |
| chunk_coverage_ | protocols::farna::RNA_DeNovoProtocol | private |
| chunk_pdb_files_ | protocols::farna::RNA_DeNovoProtocol | private |
| chunk_silent_files_ | protocols::farna::RNA_DeNovoProtocol | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::farna::RNA_DeNovoProtocol | virtual |
| close_loops_after_each_move_ | protocols::farna::RNA_DeNovoProtocol | private |
| close_loops_at_end_ | protocols::farna::RNA_DeNovoProtocol | private |
| close_loops_in_last_round_ | protocols::farna::RNA_DeNovoProtocol | private |
| constraint_set_ | protocols::farna::RNA_DeNovoProtocol | private |
| create() | protocols::moves::Mover | virtual |
| denovo_scorefxn_ | protocols::farna::RNA_DeNovoProtocol | private |
| do_close_loops_ | protocols::farna::RNA_DeNovoProtocol | private |
| do_random_moves(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| dump_pdb_ | protocols::farna::RNA_DeNovoProtocol | private |
| extra_minimize_chi_res_ | protocols::farna::RNA_DeNovoProtocol | private |
| extra_minimize_res_ | protocols::farna::RNA_DeNovoProtocol | private |
| figure_out_constraint_separation_cutoff(Size const r, Size const max_dist) | protocols::farna::RNA_DeNovoProtocol | private |
| filter_chain_closure_ | protocols::farna::RNA_DeNovoProtocol | private |
| filter_chain_closure_distance_ | protocols::farna::RNA_DeNovoProtocol | private |
| filter_chain_closure_halfway_ | protocols::farna::RNA_DeNovoProtocol | private |
| filter_lores_base_pairs_ | protocols::farna::RNA_DeNovoProtocol | private |
| filter_lores_base_pairs_early_ | protocols::farna::RNA_DeNovoProtocol | private |
| Filters_map typedef | protocols::moves::Mover | |
| final_score(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| final_scorefxn_ | protocols::farna::RNA_DeNovoProtocol | private |
| frag_size_ | protocols::farna::RNA_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_moving_res(core::pose::Pose const &pose) const | protocols::farna::RNA_DeNovoProtocol | private |
| get_name() const | protocols::farna::RNA_DeNovoProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_type() const | protocols::moves::Mover | inline |
| heat_structure_ | protocols::farna::RNA_DeNovoProtocol | private |
| hires_scorefxn_ | protocols::farna::RNA_DeNovoProtocol | private |
| ignore_secstruct(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| ignore_secstruct_ | protocols::farna::RNA_DeNovoProtocol | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| initial_denovo_scorefxn_ | protocols::farna::RNA_DeNovoProtocol | private |
| initialize_constraints(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| initialize_lores_silent_file() | protocols::farna::RNA_DeNovoProtocol | private |
| initialize_movers(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| initialize_scorefxn(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| initialize_tag_is_done() | protocols::farna::RNA_DeNovoProtocol | private |
| input_res_ | protocols::farna::RNA_DeNovoProtocol | private |
| jump_change_frequency(core::Real const value) | protocols::farna::RNA_DeNovoProtocol | inline |
| jump_change_frequency_ | protocols::farna::RNA_DeNovoProtocol | private |
| jump_library_file_ | protocols::farna::RNA_DeNovoProtocol | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| linear_chainbreak_weight_ | protocols::farna::RNA_DeNovoProtocol | private |
| local_rna_low_resolution_potential_ | protocols::farna::RNA_DeNovoProtocol | private |
| lores_score_early_ | protocols::farna::RNA_DeNovoProtocol | private |
| lores_score_final_ | protocols::farna::RNA_DeNovoProtocol | private |
| lores_scorefxn_ | protocols::farna::RNA_DeNovoProtocol | private |
| lores_silent_file_ | protocols::farna::RNA_DeNovoProtocol | private |
| m_Temperature_ | protocols::farna::RNA_DeNovoProtocol | private |
| minimize_structure_ | protocols::farna::RNA_DeNovoProtocol | private |
| minimizer_use_coordinate_constraints_ | protocols::farna::RNA_DeNovoProtocol | private |
| monte_carlo_ | protocols::farna::RNA_DeNovoProtocol | private |
| monte_carlo_cycles_ | protocols::farna::RNA_DeNovoProtocol | private |
| monte_carlo_cycles_max_default_ | protocols::farna::RNA_DeNovoProtocol | private |
| move_first_rigid_body_ | protocols::farna::RNA_DeNovoProtocol | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| nstruct_ | protocols::farna::RNA_DeNovoProtocol | private |
| operator=(Mover const &other) | protocols::moves::Mover | |
| output_filters_ | protocols::farna::RNA_DeNovoProtocol | private |
| output_lores_silent_file(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| output_lores_silent_file_ | protocols::farna::RNA_DeNovoProtocol | private |
| output_silent_struct(core::io::silent::SilentStruct &s, core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, core::pose::Pose &pose, std::string const out_file_tag, bool const score_only=false) const | protocols::farna::RNA_DeNovoProtocol | private |
| 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::farna::RNA_DeNovoProtocol | |
| 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_chunk_trial(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| random_fragment_trial(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| random_jump_trial(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| randomize_rigid_body_orientations(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| refine_from_silent_ | protocols::farna::RNA_DeNovoProtocol | private |
| refine_pose_ | protocols::farna::RNA_DeNovoProtocol | private |
| refine_pose_list_ | protocols::farna::RNA_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 |
| relax_structure_ | protocols::farna::RNA_DeNovoProtocol | private |
| reset_status() | protocols::moves::Mover | |
| rigid_body_mover_ | protocols::farna::RNA_DeNovoProtocol | private |
| rna_chunk_library_ | protocols::farna::RNA_DeNovoProtocol | private |
| rna_data_file_ | protocols::farna::RNA_DeNovoProtocol | private |
| rna_data_reader_ | protocols::farna::RNA_DeNovoProtocol | private |
| RNA_DeNovoProtocol(Size const nstruct, std::string const silent_file, bool const heat_structure=true, bool const minimize_structure=false, bool const relax_structure=false, bool const allow_bulge=false) | protocols::farna::RNA_DeNovoProtocol | |
| rna_fragment_mover_ | protocols::farna::RNA_DeNovoProtocol | private |
| rna_loop_closer_ | protocols::farna::RNA_DeNovoProtocol | private |
| rna_minimizer_ | protocols::farna::RNA_DeNovoProtocol | private |
| RNA_move_trial(core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| rna_params_file_ | protocols::farna::RNA_DeNovoProtocol | private |
| rna_relaxer_ | protocols::farna::RNA_DeNovoProtocol | private |
| rna_structure_parameters_ | protocols::farna::RNA_DeNovoProtocol | private |
| root_at_first_rigid_body_ | protocols::farna::RNA_DeNovoProtocol | private |
| rounds_ | protocols::farna::RNA_DeNovoProtocol | private |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| set_all_rna_fragments_file(std::string const file) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_allow_consecutive_bulges(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_allowed_bulge_res(utility::vector1< core::Size > const &setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_autofilter(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_binary_rna_output(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_bps_moves(Size const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_chainbreak_weight(core::Real setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_chunk_pdb_files(utility::vector1< std::string > const &chunk_pdb_files) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_chunk_silent_files(utility::vector1< std::string > const &chunk_silent_files) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_close_loops(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_close_loops_after_each_move(bool const setting) | protocols::farna::RNA_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::farna::RNA_DeNovoProtocol | inline |
| set_extra_minimize_chi_res(utility::vector1< core::Size > setting) | protocols::farna::RNA_DeNovoProtocol | |
| set_extra_minimize_res(utility::vector1< core::Size > setting) | protocols::farna::RNA_DeNovoProtocol | |
| set_filter_chain_closure(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_filter_chain_closure_distance(core::Real const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_filter_chain_closure_halfway(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_filter_lores_base_pairs(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_filter_lores_base_pairs_early(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_input_res(utility::vector1< Size > const &input_res) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_jump_library_file(std::string const jump_library_file) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_linear_chainbreak_weight(core::Real setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_lores_scorefxn(std::string const &lores_scorefxn) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_minimizer_use_coordinate_constraints(Size const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_monte_carlo_cycles(Size const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_move_first_rigid_body(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_output_filters(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_refine_pose(Size const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_refine_pose_list(utility::vector1< core::pose::PoseOP > const &setting) | protocols::farna::RNA_DeNovoProtocol | |
| set_rna_data_file(std::string const file) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_rna_params_file(std::string const file) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_root_at_first_rigid_body(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_rounds(Size const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_staged_constraints(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_suppress_bp_constraint(core::Real const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_temperature(core::Real const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_vall_torsions_file(std::string const file) | protocols::farna::RNA_DeNovoProtocol | inline |
| set_vary_bond_geometry(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| setup_monte_carlo_cycles(core::pose::Pose const &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| setup_rigid_body_mover(core::pose::Pose const &pose, core::Size const r) | protocols::farna::RNA_DeNovoProtocol | private |
| show(std::ostream &output=std::cout) const | protocols::farna::RNA_DeNovoProtocol | virtual |
| silent_file_ | protocols::farna::RNA_DeNovoProtocol | private |
| simple_rmsd_cutoff_relax(bool const setting) | protocols::farna::RNA_DeNovoProtocol | inline |
| simple_rmsd_cutoff_relax_ | protocols::farna::RNA_DeNovoProtocol | private |
| staged_constraints_ | protocols::farna::RNA_DeNovoProtocol | private |
| Strings typedef | protocols::moves::Mover | |
| suppress_bp_constraint_ | protocols::farna::RNA_DeNovoProtocol | private |
| tag_is_done_ | protocols::farna::RNA_DeNovoProtocol | private |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| titrate_stack_bonus_ | protocols::farna::RNA_DeNovoProtocol | private |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| update_denovo_scorefxn_weights(Size const r) | protocols::farna::RNA_DeNovoProtocol | private |
| update_frag_size(Size const r) | protocols::farna::RNA_DeNovoProtocol | private |
| update_pose_constraints(Size const r, core::pose::Pose &pose) | protocols::farna::RNA_DeNovoProtocol | private |
| use_chem_shift_data_ | protocols::farna::RNA_DeNovoProtocol | private |
| user_defined_cycles_ | protocols::farna::RNA_DeNovoProtocol | private |
| vary_bond_geometry_ | protocols::farna::RNA_DeNovoProtocol | private |
| ~Mover() | protocols::moves::Mover | virtual |
| ~RNA_DeNovoProtocol() | protocols::farna::RNA_DeNovoProtocol | |
1.8.7