| already_virtualized_res_list_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| apply(core::pose::Pose &pose_to_visualize) override | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | virtual |
| apply(utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &pose_to_visualize) override | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | virtual |
| protocols::moves::MoverForPoseList::apply(utility::vector1< core::pose::PoseOP > &pose_list) | protocols::moves::MoverForPoseList | virtual |
| bulge_chain_closure(utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| bulge_chain_closure_complete(utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| bulge_chain_closure_legacy(utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| bulge_chain_minimize_legacy(utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| choose_random_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| create() | protocols::moves::Mover | virtual |
| distal_partition_res_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| do_chain_closure_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| do_chain_closure_modeler(utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| do_minimize_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| do_screens_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| fast_full_atom_VDW_repulsion_screen(core::pose::Pose const &pose, core::Size const res_1, core::Size const res_2, bool const is_prepend) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| first_minimize_with_fixed_base_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | 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 override | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | 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_sugar_setup_scorefxns(core::scoring::ScoreFunctionOP &sugar_scorefxn, core::scoring::ScoreFunctionOP &sugar_scorefxn_without_ch_bond, core::scoring::ScoreFunctionOP &rescaled_sugar_score_fxn_without_ch_bond) const | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| get_type() const | protocols::moves::Mover | inline |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| initialize_pose_variants_for_chain_closure(utility::vector1< core::pose::PoseOP > &pose_list) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| integration_test_mode_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| keep_base_fixed_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| legacy_mode_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| max_tries_for_random_sugar_setup_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| minimize_sugar(core::pose::Pose &pose_with_sugar) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| MoverForPoseList() | protocols::moves::MoverForPoseList | |
| moving_phosphate_virtualized_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| name() | protocols::moves::Mover | inlinestatic |
| original_constraint_set_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| pose_with_original_terminal_phosphates_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| PoseCOP typedef | protocols::moves::Mover | |
| 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 |
| reinstantiate_backbone_at_moving_res(core::pose::Pose &pose, core::Size const rebuild_res, core::Size const five_prime_chain_break_res) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| reinstantiate_distal_partition(utility::vector1< core::pose::PoseOP > &final_pose_list) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| reinstantiate_distal_partition(core::pose::Pose ¤t_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| reinstate_original_constraints(utility::vector1< core::pose::PoseOP > &pose_list) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| reset_status() | protocols::moves::Mover | |
| restore_pose_variants_after_chain_closure(utility::vector1< core::pose::PoseOP > &pose_list) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| scorefxn_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| set_choose_random(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_do_minimize(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_do_screens(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_integration_test_mode(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_keep_base_fixed(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_legacy_mode(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_scorefxn(core::scoring::ScoreFunctionCOP scorefxn) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | |
| set_tag(std::string const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_use_phenix_geo(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| set_virtual_sugar_is_from_prior_step(bool const &setting) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | inline |
| setup_sugar_conformations(utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| setup_VDW_bin_checker(core::pose::Pose const &input_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| Strings typedef | protocols::moves::Mover | |
| sugar_modeling_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| sugar_setup_success_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| tag_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| 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 |
| use_phenix_geo_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| VDW_bin_checker_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| virtual_sugar_is_from_prior_step_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| virtualize_distal_partition(core::pose::Pose &input_pose) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| VirtualSugarSampler(working_parameters::StepWiseWorkingParametersCOP &working_parameters, SugarModeling &sugar_modeling) | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | |
| working_parameters_ | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | private |
| ~MoverForPoseList() override | protocols::moves::MoverForPoseList | |
| ~VirtualSugarSampler() override | protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler | |
1.8.7