| add_aa_virt_rsd_as_root(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| add_protonated_H1_adenosine_variants(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| add_terminal_res_repulsion(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| additional_setup_for_floating_base(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| align_to_native_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| apply(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| apply_bulge_variants(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| apply_cutpoint_variants(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| apply_virtual_phosphate_variants(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| apply_virtual_res_variant(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| apply_virtual_res_variant_at_dinucleotide_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| bulge_res_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| copy_DOF_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| correctly_copy_HO2prime_positions(pose::Pose &full_pose, utility::vector1< pose::Pose > const &start_pose_list) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| create() | protocols::moves::Mover | virtual |
| create_pose_from_input_poses(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| create_starting_pose(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| do_checks_and_apply_protonated_H1_adenosine_variant(pose::Pose &pose, pose::Pose const &start_pose_with_variant, Size const &n, Size const &i, utility::vector1< Size > const &input_res, std::map< Size, Size > &full_to_sub) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| 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::legacy::StepWiseRNA_PoseSetup | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_nearest_dist_to_O2prime(Size const O2prime_seq_num, pose::Pose const &input_pose, utility::vector1< Size > const &input_res_list, utility::vector1< Size > const &common_res_list) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| get_type() const | protocols::moves::Mover | inline |
| Import_pose(Size const &i, pose::Pose &import_pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| input_tags_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| instantiate_residue_if_rebuilding_bulge(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| job_parameters_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| make_extended_pose(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| native_virtual_res_list_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| operator=(Mover const &other) | protocols::moves::Mover | |
| output_pdb_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | 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 | |
| read_input_pose_and_copy_dofs(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::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::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| set_align_to_native(bool const setting) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_apply_virtual_res_variant_at_dinucleotide(bool const setting) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_bulge_res(utility::vector1< Size > const &bulge_res) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_copy_DOF(bool const setting) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| 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_input_tags(utility::vector1< std::string > const &setting) | protocols::stepwise::sampling::rna::legacy::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< Size > const &native_virtual_res_list) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_output_pdb(bool const setting) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_silent_files_in(utility::vector1< std::string > const &setting) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_use_phenix_geo(bool const setting) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_verbose(bool const setting) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| set_virtual_res(utility::vector1< Size > const &virtual_res_list) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | inline |
| setup_native_pose(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | |
| setup_pdb_info_with_working_residue_numbers(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| silent_files_in_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| StepWiseRNA_PoseSetup(StepWiseRNA_JobParametersOP &job_parameters) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | |
| Strings typedef | protocols::moves::Mover | |
| 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 |
| update_fold_tree_at_virtual_sugars(pose::Pose &pose) | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | |
| use_phenix_geo_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| verbose_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| verify_protonated_H1_adenosine_variants(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| virtual_res_list_ | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| virtualize_sugar_and_backbone_at_moving_res(pose::Pose &pose) const | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | private |
| ~Mover() | protocols::moves::Mover | virtual |
| ~StepWiseRNA_PoseSetup() | protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup | |
1.8.7