| add_aa_virt_rsd_as_root(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| add_protonated_H1_adenosine_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| add_terminal_res_repulsion(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| additional_setup_for_floating_base(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| align_to_native_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| apply(core::pose::Pose &pose) override | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | virtual |
| apply_bulge_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| apply_cutpoint_variants(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| apply_virtual_phosphate_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| apply_virtual_res_variant(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| apply_virtual_res_variant_at_dinucleotide_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| bulge_res_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| copy_DOF_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| correctly_copy_HO2prime_positions(core::pose::Pose &full_pose, utility::vector1< core::pose::Pose > const &start_pose_list) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| create() | protocols::moves::Mover | virtual |
| create_pose_from_input_poses(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| create_starting_pose(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| do_checks_and_apply_protonated_H1_adenosine_variant(core::pose::Pose &pose, core::pose::Pose const &start_pose_with_variant, core::Size const &n, core::Size const &i, utility::vector1< core::Size > const &input_res, std::map< core::Size, core::Size > &full_to_sub) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | 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::legacy::modeler::rna::StepWiseRNA_PoseSetup | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_nearest_dist_to_O2prime(core::Size const O2prime_seq_num, core::pose::Pose const &input_pose, utility::vector1< core::Size > const &input_res_list, utility::vector1< core::Size > const &common_res_list) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| 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 |
| Import_pose(core::Size const &i, core::pose::Pose &import_pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| input_tags_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| instantiate_residue_if_rebuilding_bulge(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| make_extended_pose(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| native_virtual_res_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| output_pdb_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| read_input_pose_and_copy_dofs(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | 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 | |
| rsd_set_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| set_align_to_native(bool const setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_apply_virtual_res_variant_at_dinucleotide(bool const setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_bulge_res(utility::vector1< core::Size > const &bulge_res) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_copy_DOF(bool const setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| 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_input_tags(utility::vector1< std::string > const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_native_virtual_res(utility::vector1< core::Size > const &native_virtual_res_list) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_output_pdb(bool const setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_silent_files_in(utility::vector1< std::string > const &setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_use_phenix_geo(bool const setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_verbose(bool const setting) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| set_virtual_res(utility::vector1< core::Size > const &virtual_res_list) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | inline |
| setup_full_model_info(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | |
| setup_native_pose(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | |
| setup_vdw_cached_rep_screen_info(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| silent_files_in_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| StepWiseRNA_PoseSetup(stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &working_parameters) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | |
| 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 |
| update_fold_tree_at_virtual_sugars(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | |
| use_phenix_geo_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| verbose_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| verify_protonated_H1_adenosine_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| virtual_res_list_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| virtualize_sugar_and_backbone_at_moving_res(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| working_parameters_ | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | private |
| ~StepWiseRNA_PoseSetup() override | protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup | |
1.8.7