| ::FastRelaxTests class | protocols::relax::FastRelax | friend |
| add_cst_files(std::string const &cstfile) | protocols::relax::RelaxProtocolBase | inlineprotected |
| apply(core::pose::Pose &pose) override | protocols::relax::FastRelax | virtual |
| apply_disulfides(core::pose::Pose &pose) | protocols::relax::RelaxProtocolBase | |
| batch_apply(std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=nullptr, core::Real decay_rate=0.5) | protocols::relax::FastRelax | |
| cartesian() const | protocols::relax::RelaxProtocolBase | inline |
| cartesian(bool newval) | protocols::relax::RelaxProtocolBase | |
| check_nonideal_mintype() | protocols::relax::FastRelax | private |
| checkpoints_ | protocols::relax::FastRelax | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::relax::FastRelax | virtual |
| cmd_accept_to_best(const core::scoring::ScoreFunctionOP local_scorefxn, core::pose::Pose &pose, core::pose::Pose &best_pose, const core::pose::Pose &start_pose, core::Real &best_score, core::Size &accept_count) | protocols::relax::FastRelax | protected |
| complex_type_generator_for_fast_relax(utility::tag::XMLSchemaDefinition &) | protocols::relax::FastRelax | static |
| constrain_coords() const | protocols::relax::RelaxProtocolBase | inline |
| constrain_coords(bool constrain_coords) | protocols::relax::RelaxProtocolBase | |
| constrain_relax_segments() const | protocols::relax::RelaxProtocolBase | inline |
| constrain_relax_segments(bool constrain_relax_segments) | protocols::relax::RelaxProtocolBase | |
| constrain_relax_to_native_coords() const | protocols::relax::RelaxProtocolBase | inline |
| constrain_relax_to_native_coords(bool constrain_relax_to_native_coords) | protocols::relax::RelaxProtocolBase | |
| constrain_relax_to_start_coords() const | protocols::relax::RelaxProtocolBase | inline |
| constrain_relax_to_start_coords(bool constrain_relax_to_start_coords) | protocols::relax::RelaxProtocolBase | |
| coord_constrain_sidechains() const | protocols::relax::RelaxProtocolBase | inline |
| coord_constrain_sidechains(bool coord_constrain_sidechains) | protocols::relax::RelaxProtocolBase | |
| create() | protocols::moves::Mover | virtual |
| cst_files(core::Size const i) const | protocols::relax::RelaxProtocolBase | inlineprotected |
| default_repeats() const | protocols::relax::FastRelax | inline |
| default_repeats_ | protocols::relax::FastRelax | private |
| delete_virtual_residues_after_FastRelax_ | protocols::relax::FastRelax | private |
| determine_default_relax_script() | protocols::relax::FastRelax | protected |
| dna_move_ | protocols::relax::FastRelax | private |
| do_md(core::pose::Pose &pose, core::Real nstep, core::Real temp0, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn) | protocols::relax::FastRelax | protected |
| do_minimize(core::pose::Pose &pose, core::Real tolerance, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn) | protocols::relax::FastRelax | protected |
| dry_run() const | protocols::relax::RelaxProtocolBase | inline |
| dry_run(bool setting) | protocols::relax::RelaxProtocolBase | |
| dualspace(bool val) | protocols::relax::FastRelax | |
| dualspace() | protocols::relax::FastRelax | |
| dualspace_ | protocols::relax::FastRelax | private |
| dumpall_ | protocols::relax::FastRelax | private |
| enable_design_ | protocols::relax::FastRelax | private |
| FastRelax(core::Size standard_repeats=0) | protocols::relax::FastRelax | |
| FastRelax(core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0) | protocols::relax::FastRelax | |
| FastRelax(core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file) | protocols::relax::FastRelax | |
| FastRelax(core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats, const std::string &script_file) | protocols::relax::FastRelax | |
| fix_omega() const | protocols::relax::RelaxProtocolBase | inlineprotected |
| fix_omega(bool fix_omega) | protocols::relax::RelaxProtocolBase | inlineprotected |
| force_nonideal_ | protocols::relax::FastRelax | private |
| fresh_instance() const override | protocols::relax::RelaxProtocolBase | inlinevirtual |
| 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_movemap() const | protocols::relax::RelaxProtocolBase | |
| get_movemap() | protocols::relax::RelaxProtocolBase | |
| get_name() const override | protocols::relax::FastRelax | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_possible_relax_script_names(std::string const &prefix) const | protocols::relax::FastRelax | private |
| get_scorefxn() const | protocols::relax::RelaxProtocolBase | |
| get_scorefxn() | protocols::relax::RelaxProtocolBase | protected |
| 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_task_factory() const | protocols::relax::RelaxProtocolBase | |
| get_type() const | protocols::moves::Mover | inline |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| initialize_movemap(core::pose::Pose const &pose, core::kinematics::MoveMap &movemap) | protocols::relax::RelaxProtocolBase | protected |
| inner_loop_accept_to_best_command(core::scoring::ScoreFunctionOP const &local_scorefxn, core::pose::Pose &pose, core::Real &best_score, core::Size &accept_count, core::pose::Pose &best_pose, core::pose::Pose const &start_pose, std::vector< core::Real > &best_score_log, std::vector< core::Real > &curr_score_log, int const ) | protocols::relax::FastRelax | private |
| inner_loop_dumpall_command(RelaxScriptCommand const &cmd) | protocols::relax::FastRelax | private |
| inner_loop_md_command(RelaxScriptCommand const &cmd, core::Size &chk_counter, core::pose::Pose &pose, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn) | protocols::relax::FastRelax | private |
| inner_loop_min_command(RelaxScriptCommand const &cmd, core::pose::Pose &pose, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn, core::Size &chk_counter, int &dump_counter) | protocols::relax::FastRelax | private |
| inner_loop_ramp_repack_min_command(RelaxScriptCommand const &cmd, int const total_repeat_count, bool const do_rama_repair, core::scoring::EnergyMap &full_weights, core::pose::Pose &pose, minimization_packing::PackRotamersMoverOP const &pack_full_repack, int const repeat_count, int const total_count, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn, core::Size &chk_counter, int &dump_counter) | protocols::relax::FastRelax | private |
| inner_loop_reference_command(RelaxScriptCommand const &cmd, core::scoring::ScoreFunctionOP const &local_scorefxn) const | protocols::relax::FastRelax | private |
| inner_loop_repack_command(core::Size const chk_counter, core::pose::Pose &pose, core::scoring::ScoreFunctionOP const &local_scorefxn, minimization_packing::PackRotamersMoverOP const &pack_full_repack, int &dump_counter) | protocols::relax::FastRelax | private |
| inner_loop_reset_reference_command(core::scoring::ScoreFunctionOP const &local_scorefxn) const | protocols::relax::FastRelax | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| limit_aroma_chi2() const | protocols::relax::RelaxProtocolBase | inlineprotected |
| max_iter() const | protocols::relax::RelaxProtocolBase | inline |
| max_iter(core::Size max_iter) | protocols::relax::RelaxProtocolBase | |
| min_type() const | protocols::relax::RelaxProtocolBase | inline |
| min_type(std::string min_type) | protocols::relax::RelaxProtocolBase | |
| minimize_bond_angles() const | protocols::relax::RelaxProtocolBase | inline |
| minimize_bond_angles(bool minimize_bond_angles) | protocols::relax::RelaxProtocolBase | |
| minimize_bond_lengths() const | protocols::relax::RelaxProtocolBase | inline |
| minimize_bond_lengths(bool minimize_bond_lengths) | protocols::relax::RelaxProtocolBase | |
| minimize_bondangle_subset() const | protocols::relax::RelaxProtocolBase | inlineprotected |
| minimize_bondangle_subset(int minimize_bondangle_subset) | protocols::relax::RelaxProtocolBase | inlineprotected |
| minimize_bondlength_subset() const | protocols::relax::RelaxProtocolBase | inlineprotected |
| minimize_bondlength_subset(int minimize_bondlength_subset) | protocols::relax::RelaxProtocolBase | inlineprotected |
| movemap_disables_packing_of_fixed_chi_positions() const | protocols::relax::FastRelax | inline |
| movemap_disables_packing_of_fixed_chi_positions_ | protocols::relax::FastRelax | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::relax::FastRelax | static |
| name() | protocols::moves::Mover | inlinestatic |
| output_debug_structure(core::pose::Pose &pose, std::string prefix) | protocols::relax::RelaxProtocolBase | protected |
| parent typedef | protocols::relax::RelaxProtocolBase | |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override | protocols::relax::FastRelax | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const override | protocols::relax::FastRelax | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::relax::FastRelax | static |
| ramady_ | protocols::relax::FastRelax | private |
| ramady_cutoff_ | protocols::relax::FastRelax | private |
| ramady_force_ | protocols::relax::FastRelax | private |
| ramady_num_rebuild_ | protocols::relax::FastRelax | private |
| ramady_rms_limit_ | protocols::relax::FastRelax | private |
| ramp_down_constraints() const | protocols::relax::RelaxProtocolBase | inline |
| ramp_down_constraints(bool ramp_down_constraints) | protocols::relax::RelaxProtocolBase | |
| read_script_file(std::string script_file, core::Size standard_repeats=5) | protocols::relax::FastRelax | private |
| register_options() | protocols::relax::RelaxProtocolBase | static |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| RelaxProtocolBase(core::scoring::ScoreFunctionOP) | protocols::relax::RelaxProtocolBase | |
| RelaxProtocolBase(std::string const &movername="RelaxProtocol") | protocols::relax::RelaxProtocolBase | |
| RelaxProtocolBase(std::string const &movername, core::scoring::ScoreFunctionOP) | protocols::relax::RelaxProtocolBase | |
| repack_ | protocols::relax::FastRelax | private |
| reset_status() | protocols::moves::Mover | |
| script_ | protocols::relax::FastRelax | private |
| script_max_accept_ | protocols::relax::FastRelax | private |
| set_constraint_weight(core::scoring::ScoreFunctionOP local_scorefxn, core::scoring::EnergyMap const &full_weights, core::Real const weight, core::pose::Pose &pose) const | protocols::relax::FastRelax | protectedvirtual |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_default_coordinate_settings() | protocols::relax::RelaxProtocolBase | |
| set_default_minimization_settings() | protocols::relax::RelaxProtocolBase | |
| set_default_movemap() | protocols::relax::RelaxProtocolBase | |
| set_defaults() | protocols::relax::RelaxProtocolBase | |
| set_enable_design(bool const val) | protocols::relax::FastRelax | inline |
| set_force_nonideal(bool val) | protocols::relax::FastRelax | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_movemap(core::kinematics::MoveMapOP movemap) | protocols::relax::RelaxProtocolBase | |
| set_movemap_disables_packing_of_fixed_chi_positions(bool const setting) | protocols::relax::FastRelax | |
| set_movemap_factory(core::select::movemap::MoveMapFactoryOP mm_factory) | protocols::relax::RelaxProtocolBase | |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_scorefxn(core::scoring::ScoreFunctionOP scorefxn) | protocols::relax::RelaxProtocolBase | |
| set_script_from_lines(std::vector< std::string > const &filelines) | protocols::relax::FastRelax | |
| set_script_to_batchrelax_default(core::Size standard_repeats=0) | protocols::relax::FastRelax | |
| set_task_factory(core::pack::task::TaskFactoryOP task_factory) | protocols::relax::RelaxProtocolBase | |
| set_to_default() | protocols::relax::FastRelax | |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_up_constraints(core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap) | protocols::relax::RelaxProtocolBase | protected |
| setup_local_tf(core::pose::Pose const &pose, core::kinematics::MoveMapOP const &local_movemap) | protocols::relax::FastRelax | protected |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| Strings typedef | protocols::moves::Mover | |
| symmetric_rmsd_ | protocols::relax::FastRelax | private |
| TagCOP typedef | protocols::moves::Mover | |
| test_cycles_ | protocols::relax::FastRelax | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| ~FastRelax() override | protocols::relax::FastRelax | |
| ~RelaxProtocolBase() override | protocols::relax::RelaxProtocolBase | |
1.8.7