| allow_virtual_o2prime_hydrogens_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| apply(core::pose::Pose &pose) override | protocols::stepwise::modeler::StepWiseMinimizer | virtual |
| atom_level_domain_map_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| atom_tree_minimizer_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| cartesian_minimizer_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| check_pose_list(core::pose::Pose const &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| close_chainbreaks(core::pose::Pose &pose, core::kinematics::MoveMap &mm) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| create() | protocols::moves::Mover | virtual |
| current_job_ | protocols::moves::Mover | private |
| current_tag_ | protocols::moves::Mover | private |
| do_clustering(core::pose::Pose &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| do_full_minimizing(core::pose::Pose &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| do_minimize(core::pose::Pose &pose, core::kinematics::MoveMap &mm) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| figure_out_working_minimize_res(core::pose::Pose const &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| final_scorefxn_ | protocols::stepwise::modeler::StepWiseMinimizer | 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_move_map_and_atom_level_domain_map(core::kinematics::MoveMap &mm, core::pose::Pose const &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| get_name() const override | protocols::stepwise::modeler::StepWiseMinimizer | inlinevirtual |
| 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 |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| info_ | protocols::moves::Mover | private |
| initialize_parameters() | protocols::stepwise::modeler::StepWiseMinimizer | private |
| input_pose_ | protocols::moves::Mover | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| last_status_ | protocols::moves::Mover | private |
| let_neighboring_side_chains_minimize(core::kinematics::MoveMap &mm, core::pose::Pose const &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| minimize_scorefxn_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| minimizer_options_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| move_side_chain(core::kinematics::MoveMap &mm, core::pose::Pose const &pose, core::Size const j) | protocols::stepwise::modeler::StepWiseMinimizer | 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 |
| num_pose_minimize() const | protocols::stepwise::modeler::StepWiseMinimizer | inline |
| num_pose_minimize_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| options_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| output_empty_minimizer_silent_file() const | protocols::stepwise::modeler::StepWiseMinimizer | private |
| output_minimized_pose_list() const | protocols::stepwise::modeler::StepWiseMinimizer | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| pose_list() const | protocols::stepwise::modeler::StepWiseMinimizer | inline |
| pose_list_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| PoseCOP typedef | protocols::moves::Mover | |
| protein_ccd_closer_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| 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::stepwise::modeler::StepWiseMinimizer | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_scorefxn(core::scoring::ScoreFunctionOP const &scorefxn) | protocols::stepwise::modeler::StepWiseMinimizer | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_working_pack_res(utility::vector1< core::Size > const &setting) | protocols::stepwise::modeler::StepWiseMinimizer | inline |
| setup_all_moving_res(core::pose::Pose const &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| setup_minimizers() | protocols::stepwise::modeler::StepWiseMinimizer | private |
| setup_scorefxns(core::pose::Pose const &pose) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| setup_vary_bond_geometry(core::pose::Pose &pose, core::kinematics::MoveMap &mm) | protocols::stepwise::modeler::StepWiseMinimizer | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| StepWiseMinimizer(utility::vector1< core::pose::PoseOP > const &pose_list, working_parameters::StepWiseWorkingParametersCOP working_parameters, options::StepWiseModelerOptionsCOP options, core::scoring::ScoreFunctionCOP scorefxn) | protocols::stepwise::modeler::StepWiseMinimizer | |
| Strings typedef | protocols::moves::Mover | |
| 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 |
| working_calc_rms_res_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| working_fixed_res_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| working_minimize_res() const | protocols::stepwise::modeler::StepWiseMinimizer | inline |
| working_minimize_res_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| working_moving_res_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| working_pack_res() const | protocols::stepwise::modeler::StepWiseMinimizer | inline |
| working_pack_res_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| working_parameters_ | protocols::stepwise::modeler::StepWiseMinimizer | private |
| ~StepWiseMinimizer() override | protocols::stepwise::modeler::StepWiseMinimizer | |
