| append_Aform_residue(core::pose::Pose &pose, Size const &n, char const &nt) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| apply(core::pose::Pose &pose) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | virtual |
| apply(core::pose::Pose &pose, std::string const &sequence) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| build_dangle_seq1_3prime(core::pose::Pose &pose, std::string const &dangle_seq) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| build_dangle_seq1_5prime(core::pose::Pose &pose, std::string const &dangle_seq) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| build_dangle_seq2_3prime(core::pose::Pose &pose, std::string const &dangle_seq) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| build_dangle_seq2_5prime(core::pose::Pose &pose, std::string const &dangle_seq) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| build_dangling_ends(core::pose::Pose &pose) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| build_helix(core::pose::Pose &pose, std::string const &full_sequence) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
| build_init_pose(std::string const &seq1, std::string const &seq2) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
| build_on_base_pair(core::pose::Pose &pose, Size const &n, char const &seq1, char const &seq2) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| capping_residues_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | virtual |
| create() | protocols::moves::Mover | virtual |
| dangle_seq1_3prime_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| dangle_seq1_5prime_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| dangle_seq2_3prime_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| dangle_seq2_5prime_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| dump_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| figure_out_and_remove_dangling_ends(std::string const &full_sequence) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| fill_chain_info(core::pose::Pose &pose, std::string const &full_sequence) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| Filters_map typedef | protocols::moves::Mover | |
| finish_scorefxn_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | 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_cutpoint(core::pose::Pose const &pose) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_rid_of_capping_base_pairs(core::pose::Pose &pose) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| get_type() const | protocols::moves::Mover | inline |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| initialize_minimizer() | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| minimize_all_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| minimize_append_res(core::pose::Pose &pose, Size const n) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| minimize_base_step(core::pose::Pose &pose, Size const n, core::scoring::ScoreFunctionOP scorefxn) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| minimize_jump_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| minimize_prepend_res(core::pose::Pose &pose, Size const n) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| minimizer_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| minimizer_options_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| model_and_remove_capping_residues_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | 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 |
| operator=(Mover const &other) | protocols::moves::Mover | |
| 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 |
| perturb_amplitude_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| perturb_torsion(core::pose::Pose &pose, utility::vector1< core::id::TorsionID > const &id_list) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| prepend_Aform_residue(core::pose::Pose &pose, Size const &n, char const &nt) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| put_constraints_on_base_step(core::pose::Pose &pose, Size const &n) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| random_perturbation(bool const &setting) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | inline |
| random_perturbation_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | 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 | |
| RNA_HelixAssembler() | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
| rsd_set_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| scorefxn_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| set_Aform_torsions(core::pose::Pose &pose, Size const &n) const | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_dump(bool const &setting) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | inline |
| set_finish_scorefxn(core::scoring::ScoreFunctionOP setting) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_minimize_all(bool const &setting) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | inline |
| set_model_and_remove_capping_residues(bool setting) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_scorefxn(core::scoring::ScoreFunctionOP setting) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| torsion_info_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| use_phenix_geo(bool const setting) | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
| use_phenix_geo_ | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | private |
| ~Mover() | protocols::moves::Mover | virtual |
| ~RNA_HelixAssembler() | protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler | |
1.8.7