| anchor_sugar_modeling() | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| apply(pose::Pose &pose_to_visualize) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| create() | protocols::moves::Mover | virtual |
| do_sugar_sampling(pose::Pose &viewer_pose, SugarModeling &sugar_modeling, std::string const name) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| do_the_sampling(core::pose::Pose &pose) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| Filters_map typedef | protocols::moves::Mover | |
| 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 | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_sugar_modeling_set(pose::Pose &viewer_pose, Size const i) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| get_sugar_modeling_sets_for_chainbreak() const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| get_type() const | protocols::moves::Mover | inline |
| include_current_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| instantiate_sugar(pose::Pose &pose, SugarModeling const &sugar_modeling, Size const sugar_ID) const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| instantiate_sugars_recursively(pose::Pose const &pose, utility::vector1< pose::PoseOP > &pose_data_list, utility::vector1< SugarModelingOP > const &sugar_modeling_sets, utility::vector1< Size > const &sugar_modeling_set_indices) const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| job_parameters_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| keep_base_fixed_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| minimize_sugar_sets_legacy(pose::Pose const &pose, utility::vector1< pose::PoseOP > &pose_data_list) const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| moving_res_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| moving_res_legacy_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| name() | protocols::moves::Mover | inlinestatic |
| num_sets() const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | inline |
| operator=(Mover const &other) | protocols::moves::Mover | |
| options_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| 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 | |
| prepare_from_prior_sampled_sugar_jobs(pose::Pose const &pose, utility::vector1< pose::PoseOP > &starting_pose_data_list, bool const pose_explosion_legacy) const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| prepare_from_prior_sampled_sugar_jobs_for_chain_break(pose::Pose const &pose, utility::vector1< pose::PoseOP > &starting_pose_data_list) const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| rebuild_bulge_mode_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| reference_res_for_each_virtual_sugar_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | 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 |
| reset_status() | protocols::moves::Mover | |
| residue_alternative_set(Size const n) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| residue_alternative_sets_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| sampled_sugar_index(Size const i) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| sampling_sugar() const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| sampling_sugar_at_chain_break() const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| scorefxn_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_keep_base_fixed(bool const &setting) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_options(StepWiseRNA_ModelerOptionsCOP options) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| set_scorefxn(core::scoring::ScoreFunctionOP const &scorefxn) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| setup_sugar_modeling(pose::Pose const &pose, Size const moving_res, SugarModeling &sugar_modeling) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| StepWiseRNA_VirtualSugarJustInTimeInstantiator(StepWiseRNA_JobParametersCOP &job_parameters_) | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| Strings typedef | protocols::moves::Mover | |
| success() const | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | inline |
| success_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| sugar_modeling_sets_ | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | private |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| ~Mover() | protocols::moves::Mover | virtual |
| ~StepWiseRNA_VirtualSugarJustInTimeInstantiator() | protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator | |
1.8.7