| append_virtual_anchor(core::pose::Pose &pose) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| assume_non_stem_is_loop | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| bps_moves_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| center_jumps_in_single_stranded_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| dock_chunks_res_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| dock_each_chunk_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| dock_each_chunk_per_chain_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| initialize_for_de_novo_protocol(core::pose::Pose &pose, bool const ignore_secstruct=false) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | |
| initialize_secstruct(core::pose::Pose &pose) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| insert_base_pair_jumps(core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &jump_mover, bool &success) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| model_with_density() const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| model_with_density_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| new_fold_tree_initializer() const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| new_fold_tree_initializer_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| override_secstruct(core::pose::Pose &pose) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| RNA_DeNovoPoseInitializer(core::import_pose::RNA_DeNovoParameters const &rna_params_file_info) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | |
| rna_params() const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| rna_params_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| root_at_first_rigid_body_ | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| set_bps_moves(bool const &setting) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| set_center_jumps_in_single_stranded(bool const &setting) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| set_dock_chunks_res(utility::vector1< core::Size > const &dock_chunks_res) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| set_dock_each_chunk(bool const &setting) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| set_dock_each_chunk_per_chain(bool const &setting) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| set_model_with_density(bool const &setting) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| set_new_fold_tree_initializer(bool const &setting) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| set_root_at_first_rigid_body(bool const setting) | protocols::rna::denovo::RNA_DeNovoPoseInitializer | inline |
| setup_block_stack_variants(core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| setup_chainbreak_variants(core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | |
| setup_chainbreak_variants(core::pose::Pose &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map, core::import_pose::RNA_JumpMover const &rna_jump_mover, core::import_pose::libraries::RNA_ChunkLibrary const &rna_chunk_library, bool const &enumerate=false) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| setup_fold_tree_and_jumps_and_variants(core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &rna_jump_mover, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map, core::import_pose::libraries::RNA_ChunkLibrary const &rna_chunk_library, bool const &enumerate=false) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | |
| setup_fold_tree_and_jumps_and_variants(core::pose::Pose &pose) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | |
| setup_fold_tree_legacy(core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &rna_jump_mover) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| setup_fold_tree_through_build_full_model_info(core::pose::Pose &pose, core::import_pose::libraries::RNA_ChunkLibrary const &chunk_library, bool const &enumerate=false) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| setup_jumps(core::pose::Pose &pose, core::import_pose::RNA_JumpMover const &rna_jump_mover, core::import_pose::libraries::RNA_ChunkLibrary const &rna_chunk_library, bool const enumerate=false) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| setup_virtual_phosphate_variants(core::pose::Pose &pose) const | protocols::rna::denovo::RNA_DeNovoPoseInitializer | private |
| ~RNA_DeNovoPoseInitializer() override | protocols::rna::denovo::RNA_DeNovoPoseInitializer | |
1.8.7