| add_new_RNA_jump(core::pose::Pose &pose, core::Size const &which_jump, bool &success) const | protocols::farna::RNA_StructureParameters | private |
| add_virtual_anchor_ | protocols::farna::RNA_StructureParameters | private |
| allow_cuts_inside_base_pair_steps_ | protocols::farna::RNA_StructureParameters | private |
| allow_insert() | protocols::farna::RNA_StructureParameters | |
| allow_insert_ | protocols::farna::RNA_StructureParameters | private |
| allow_insert_res_ | protocols::farna::RNA_StructureParameters | private |
| append_virtual_anchor(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | private |
| assume_non_stem_is_loop | protocols::farna::RNA_StructureParameters | private |
| bps_moves_ | protocols::farna::RNA_StructureParameters | private |
| chain_connections_ | protocols::farna::RNA_StructureParameters | private |
| check_base_pairs(core::pose::Pose &pose) const | protocols::farna::RNA_StructureParameters | |
| check_forward_backward(core::pose::Pose &pose, core::Size const jump_pos) const | protocols::farna::RNA_StructureParameters | private |
| check_in_chain_connections(core::Size const &pos1, core::Size const &pos2) const | protocols::farna::RNA_StructureParameters | private |
| check_in_pairing_sets(utility::vector1< utility::vector1< core::Size > > pairing_sets, RNA_Pairing const &rna_pairing_check) const | protocols::farna::RNA_StructureParameters | private |
| connections() const | protocols::farna::RNA_StructureParameters | |
| cutpoints_closed_ | protocols::farna::RNA_StructureParameters | private |
| cutpoints_open_ | protocols::farna::RNA_StructureParameters | private |
| fill_in_default_jump_atoms(core::kinematics::FoldTree &f, core::pose::Pose const &pose) const | protocols::farna::RNA_StructureParameters | private |
| get_base_pair_steps() const | protocols::farna::RNA_StructureParameters | |
| get_obligate_pairing_sets() | protocols::farna::RNA_StructureParameters | inline |
| get_pairings_from_line(std::istringstream &line_stream, bool const in_stem) | protocols::farna::RNA_StructureParameters | private |
| get_rna_pairing_list() | protocols::farna::RNA_StructureParameters | inline |
| get_stem_residues(core::pose::Pose const &pose) const | protocols::farna::RNA_StructureParameters | |
| initialize(core::pose::Pose &pose, std::string const rna_params_file, std::string const jump_library_file, bool const ignore_secstruct) | protocols::farna::RNA_StructureParameters | |
| initialize_allow_insert(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | private |
| initialize_secstruct(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | private |
| insert_base_pair_jumps(core::pose::Pose &pose, bool &success) const | protocols::farna::RNA_StructureParameters | private |
| obligate_pairing_sets_ | protocols::farna::RNA_StructureParameters | private |
| override_secstruct(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | private |
| random_jump_change(core::pose::Pose &pose) const | protocols::farna::RNA_StructureParameters | |
| read_chain_connection(std::istringstream &line_stream) | protocols::farna::RNA_StructureParameters | private |
| read_parameters_from_file(std::string const &pairing_file) | protocols::farna::RNA_StructureParameters | private |
| read_secstruct_from_file(std::string const &rna_secstruct_file) | protocols::farna::RNA_StructureParameters | private |
| rna_jump_library_ | protocols::farna::RNA_StructureParameters | private |
| rna_pairing_list_ | protocols::farna::RNA_StructureParameters | private |
| rna_secstruct_ | protocols::farna::RNA_StructureParameters | private |
| RNA_StructureParameters() | protocols::farna::RNA_StructureParameters | |
| root_at_first_rigid_body_ | protocols::farna::RNA_StructureParameters | private |
| sample_alternative_chain_connection(core::pose::Pose &pose, core::Size const &which_jump) const | protocols::farna::RNA_StructureParameters | private |
| save_res_lists_to_chain_connections_and_clear(utility::vector1< Size > &res_list1, utility::vector1< Size > &res_list2) | protocols::farna::RNA_StructureParameters | private |
| secstruct_defined_ | protocols::farna::RNA_StructureParameters | private |
| set_allow_insert(toolbox::AllowInsertOP allow_insert) | protocols::farna::RNA_StructureParameters | |
| set_bps_moves(Size const setting) | protocols::farna::RNA_StructureParameters | inline |
| set_jump_library(RNA_JumpLibraryOP rna_jump_library) | protocols::farna::RNA_StructureParameters | private |
| set_root_at_first_rigid_body(bool const setting) | protocols::farna::RNA_StructureParameters | inline |
| set_suppress_bp_constraint(core::Real const setting) | protocols::farna::RNA_StructureParameters | inline |
| setup_base_pair_constraints(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | |
| setup_chainbreak_variants(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | private |
| setup_fold_tree_and_jumps_and_variants(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | |
| setup_jumps(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | private |
| setup_virtual_phosphate_variants(core::pose::Pose &pose) | protocols::farna::RNA_StructureParameters | |
| stem_pairing_sets_ | protocols::farna::RNA_StructureParameters | private |
| suppress_bp_constraint_ | protocols::farna::RNA_StructureParameters | private |
| virtual_anchor_attachment_points_ | protocols::farna::RNA_StructureParameters | private |
| ~RNA_StructureParameters() | protocols::farna::RNA_StructureParameters | virtual |
1.8.7