| add_additional_low_resolution_step(protocols::moves::MoverOP additional_low_resolution_mover) | protocols::docking::DockingProtocol | |
| add_additional_task_operaration(core::pack::task::operation::TaskOperationOP task_operation) | protocols::docking::DockingProtocol | |
| add_constraints_to_scorefunction() | protocols::docking::DockingProtocol | private |
| add_jump(core::Size const jump_number) | protocols::docking::DockingProtocol | inline |
| additional_low_resolution_steps_ | protocols::docking::DockingProtocol | private |
| apply(core::pose::Pose &pose) override | protocols::docking::DockingProtocol | virtual |
| autofoldtree_ | protocols::docking::DockingProtocol | private |
| check_high_res_protocol() | protocols::docking::DockingProtocol | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::docking::DockingProtocol | virtual |
| create() | protocols::moves::Mover | virtual |
| cst_fa_weight_ | protocols::docking::DockingProtocol | private |
| cst_weight_ | protocols::docking::DockingProtocol | private |
| design_ | protocols::docking::DockingProtocol | private |
| dock_min_ | protocols::docking::DockingProtocol | private |
| docking_constraint_ | protocols::docking::DockingProtocol | private |
| docking_highres_mover() const | protocols::docking::DockingProtocol | |
| docking_highres_mover_ | protocols::docking::DockingProtocol | private |
| docking_local_refine_ | protocols::docking::DockingProtocol | private |
| docking_lowres_mover() const | protocols::docking::DockingProtocol | |
| docking_lowres_mover_ | protocols::docking::DockingProtocol | private |
| docking_scorefxn_high_ | protocols::docking::DockingProtocol | private |
| docking_scorefxn_low_ | protocols::docking::DockingProtocol | private |
| docking_scorefxn_output_ | protocols::docking::DockingProtocol | private |
| docking_scorefxn_pack_ | protocols::docking::DockingProtocol | private |
| DockingProtocol() | protocols::docking::DockingProtocol | |
| DockingProtocol(core::Size const rb_jump_in, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(nullptr), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(nullptr)) | protocols::docking::DockingProtocol | |
| DockingProtocol(DockJumps const movable_jumps, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(nullptr), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(nullptr)) | protocols::docking::DockingProtocol | |
| DockingProtocol(DockingProtocol const &rhs) | protocols::docking::DockingProtocol | |
| ensemble1_ | protocols::docking::DockingProtocol | private |
| ensemble1_filename_ | protocols::docking::DockingProtocol | private |
| ensemble2_ | protocols::docking::DockingProtocol | private |
| ensemble2_filename_ | protocols::docking::DockingProtocol | private |
| finalize_setup(core::pose::Pose &pose) | protocols::docking::DockingProtocol | private |
| first_apply_with_current_setup_ | protocols::docking::DockingProtocol | private |
| flags_and_objects_are_in_sync_ | protocols::docking::DockingProtocol | private |
| fold_tree_ | protocols::docking::DockingProtocol | private |
| fresh_instance() const override | protocols::docking::DockingProtocol | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_additional_task_operarations() | protocols::docking::DockingProtocol | |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_highres_scorefxn() const | protocols::docking::DockingProtocol | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const override | protocols::docking::DockingProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| 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_type() const | protocols::moves::Mover | inline |
| highres_filter_ | protocols::docking::DockingProtocol | private |
| if_ensemble_ | protocols::docking::DockingProtocol | private |
| ignore_default_docking_task_ | protocols::docking::DockingProtocol | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init(DockJumps const movable_jumps, bool const low_res_protocol_only_, bool const docking_local_refine, bool const autofoldtree, core::scoring::ScoreFunctionOP docking_score_low, core::scoring::ScoreFunctionOP docking_score_high) | protocols::docking::DockingProtocol | private |
| init_from_options() | protocols::docking::DockingProtocol | private |
| init_task_factory_ | protocols::docking::DockingProtocol | private |
| initForEqualOperatorAndCopyConstructor(DockingProtocol &lhs, DockingProtocol const &rhs) | protocols::docking::DockingProtocol | private |
| is_ensemble_prepacked(std::string ensemble_filename) | protocols::docking::DockingProtocol | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| low_res_protocol_only_ | protocols::docking::DockingProtocol | private |
| lowres_filter_ | protocols::docking::DockingProtocol | private |
| lowres_inner_cycles_ | protocols::docking::DockingProtocol | private |
| lowres_outer_cycles_ | protocols::docking::DockingProtocol | private |
| mc_ | protocols::docking::DockingProtocol | private |
| movable_jumps() | protocols::docking::DockingProtocol | inline |
| movable_jumps() const | protocols::docking::DockingProtocol | inline |
| movable_jumps_ | protocols::docking::DockingProtocol | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::docking::DockingProtocol | static |
| name() | protocols::moves::Mover | inlinestatic |
| no_filters_ | protocols::docking::DockingProtocol | private |
| operator=(DockingProtocol const &rhs) | protocols::docking::DockingProtocol | |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &) override | protocols::docking::DockingProtocol | virtual |
| partners() const | protocols::docking::DockingProtocol | inline |
| partners_ | protocols::docking::DockingProtocol | private |
| perturber() const | protocols::docking::DockingProtocol | |
| perturber_ | protocols::docking::DockingProtocol | private |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| previous_sequence_ | protocols::docking::DockingProtocol | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::docking::DockingProtocol | static |
| recover_sidechains_ | protocols::docking::DockingProtocol | private |
| recover_sidechains_filename_ | protocols::docking::DockingProtocol | private |
| register_options() | protocols::docking::DockingProtocol | static |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const override | protocols::docking::DockingProtocol | virtual |
| reporting_ | protocols::docking::DockingProtocol | private |
| reset_status() | protocols::moves::Mover | |
| rt_min_ | protocols::docking::DockingProtocol | private |
| sc_min_ | protocols::docking::DockingProtocol | private |
| score_cutoff_ | protocols::docking::DockingProtocol | private |
| set_additional_task_operarations(utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations) | protocols::docking::DockingProtocol | |
| set_autofoldtree(bool const autofoldtree) | protocols::docking::DockingProtocol | inline |
| set_cst_weight(core::Real const cst_weight) | protocols::docking::DockingProtocol | |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_default() | protocols::docking::DockingProtocol | |
| set_design(bool const design) | protocols::docking::DockingProtocol | inline |
| set_dock_min(bool const dock_min) | protocols::docking::DockingProtocol | |
| set_docking_highres_mover(protocols::docking::DockingHighResOP docking_highres_mover) | protocols::docking::DockingProtocol | |
| set_docking_local_refine(bool const docking_local_refine) | protocols::docking::DockingProtocol | |
| set_ensemble1(std::string const &ensemble1) | protocols::docking::DockingProtocol | inline |
| set_ensemble2(std::string const &ensemble2) | protocols::docking::DockingProtocol | inline |
| set_highres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_high) | protocols::docking::DockingProtocol | |
| set_highres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack) | protocols::docking::DockingProtocol | |
| set_highres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack, core::scoring::ScoreFunctionOP docking_scorefxn_output) | protocols::docking::DockingProtocol | |
| set_ignore_default_docking_task(bool const ignore_default_docking_task) | protocols::docking::DockingProtocol | inline |
| set_inner_cycles(core::Size inner_cycles) | protocols::docking::DockingProtocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_interface_definition_task_operation(protocols::simple_task_operations::InterfaceTaskOperationOP interface_definition) | protocols::docking::DockingProtocol | |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_low_res_protocol_only(bool const low_res_protocol_only) | protocols::docking::DockingProtocol | |
| set_lowres_scorefxn(core::scoring::ScoreFunctionOP docking_scorefxn_low) | protocols::docking::DockingProtocol | |
| set_movable_jumps(DockJumps const jump_numbers) | protocols::docking::DockingProtocol | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_no_filters(bool no_filters) | protocols::docking::DockingProtocol | |
| set_outer_cycles(core::Size outer_cycles) | protocols::docking::DockingProtocol | inline |
| set_partners(std::string const &partners) | protocols::docking::DockingProtocol | inline |
| set_recover_sidechains_filename(std::string const &file) | protocols::docking::DockingProtocol | inline |
| set_reporting(bool report) | protocols::docking::DockingProtocol | inline |
| set_rt_min(bool rt_min) | protocols::docking::DockingProtocol | |
| set_sc_min(bool sc_min) | protocols::docking::DockingProtocol | |
| set_task_factory(core::pack::task::TaskFactoryOP task_factory) | protocols::docking::DockingProtocol | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_use_constraints(bool const use_csts) | protocols::docking::DockingProtocol | |
| set_use_legacy_protocol(bool const use_legacy_protocol) | protocols::docking::DockingProtocol | |
| setup_constraints(core::pose::Pose &pose) | protocols::docking::DockingProtocol | private |
| setup_objects() | protocols::docking::DockingProtocol | private |
| show(std::ostream &out=std::cout) const override | protocols::docking::DockingProtocol | virtual |
| Strings typedef | protocols::moves::Mover | |
| sync_objects_with_flags() | protocols::docking::DockingProtocol | |
| TagCOP typedef | protocols::moves::Mover | |
| task_factory() | protocols::docking::DockingProtocol | inline |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| to_all_atom() const | protocols::docking::DockingProtocol | |
| to_all_atom_ | protocols::docking::DockingProtocol | private |
| to_centroid() const | protocols::docking::DockingProtocol | |
| to_centroid_ | protocols::docking::DockingProtocol | private |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| use_csts_ | protocols::docking::DockingProtocol | private |
| use_legacy_protocol_ | protocols::docking::DockingProtocol | private |
| user_defined_ | protocols::docking::DockingProtocol | private |
| ~DockingProtocol() override | protocols::docking::DockingProtocol | |
1.8.7