| add_capping_base_pairs_to_full_sequence() | core::import_pose::RNA_HelixAssembler | private |
| append_Aform_residue(core::pose::Pose &pose, Size const &n, std::string const &nt) const | core::import_pose::RNA_HelixAssembler | private |
| apply(core::pose::Pose &pose) | core::import_pose::RNA_HelixAssembler | |
| apply(core::pose::Pose &pose, std::string const &full_sequence_in) | core::import_pose::RNA_HelixAssembler | |
| build_dangle_seq1_3prime(core::pose::Pose &pose, std::string const &dangle_seq) const | core::import_pose::RNA_HelixAssembler | private |
| build_dangle_seq1_5prime(core::pose::Pose &pose, std::string const &dangle_seq) const | core::import_pose::RNA_HelixAssembler | private |
| build_dangle_seq2_3prime(core::pose::Pose &pose, std::string const &dangle_seq) const | core::import_pose::RNA_HelixAssembler | private |
| build_dangle_seq2_5prime(core::pose::Pose &pose, std::string const &dangle_seq) const | core::import_pose::RNA_HelixAssembler | private |
| build_dangling_ends(core::pose::Pose &pose) const | core::import_pose::RNA_HelixAssembler | private |
| build_helix(core::pose::Pose &pose) | core::import_pose::RNA_HelixAssembler | |
| build_init_pose(std::string const &seq1, std::string const &seq2) | core::import_pose::RNA_HelixAssembler | |
| build_on_base_pair(core::pose::Pose &pose, Size const &n, std::string const &seq1, std::string const &seq2) const | core::import_pose::RNA_HelixAssembler | private |
| capping_residues_ | core::import_pose::RNA_HelixAssembler | private |
| dangle_seq1_3prime_ | core::import_pose::RNA_HelixAssembler | private |
| dangle_seq1_5prime_ | core::import_pose::RNA_HelixAssembler | private |
| dangle_seq2_3prime_ | core::import_pose::RNA_HelixAssembler | private |
| dangle_seq2_5prime_ | core::import_pose::RNA_HelixAssembler | private |
| dump_ | core::import_pose::RNA_HelixAssembler | private |
| figure_out_and_remove_dangling_ends() | core::import_pose::RNA_HelixAssembler | private |
| fill_chain_info(core::pose::Pose &pose) | core::import_pose::RNA_HelixAssembler | private |
| finish_scorefxn_ | core::import_pose::RNA_HelixAssembler | private |
| full_sequence_ | core::import_pose::RNA_HelixAssembler | private |
| get_cutpoint(core::pose::Pose const &pose) const | core::import_pose::RNA_HelixAssembler | private |
| get_name() const | core::import_pose::RNA_HelixAssembler | virtual |
| get_residue(std::string const &nt) const | core::import_pose::RNA_HelixAssembler | private |
| get_rid_of_capping_base_pairs(core::pose::Pose &pose) | core::import_pose::RNA_HelixAssembler | private |
| get_sequence(core::Size const n) | core::import_pose::RNA_HelixAssembler | private |
| initialize_minimizer() | core::import_pose::RNA_HelixAssembler | private |
| minimize_all_ | core::import_pose::RNA_HelixAssembler | private |
| minimize_append_res(core::pose::Pose &pose, Size const n) const | core::import_pose::RNA_HelixAssembler | private |
| minimize_base_step(core::pose::Pose &pose, Size const n, core::scoring::ScoreFunctionOP scorefxn) const | core::import_pose::RNA_HelixAssembler | private |
| minimize_jump_ | core::import_pose::RNA_HelixAssembler | private |
| minimize_prepend_res(core::pose::Pose &pose, Size const n) const | core::import_pose::RNA_HelixAssembler | private |
| minimizer_ | core::import_pose::RNA_HelixAssembler | private |
| minimizer_options_ | core::import_pose::RNA_HelixAssembler | private |
| model_and_remove_capping_residues_ | core::import_pose::RNA_HelixAssembler | private |
| non_standard_residues_ | core::import_pose::RNA_HelixAssembler | private |
| perturb_amplitude_ | core::import_pose::RNA_HelixAssembler | private |
| perturb_torsion(core::pose::Pose &pose, utility::vector1< core::id::TorsionID > const &id_list) const | core::import_pose::RNA_HelixAssembler | private |
| prepend_Aform_residue(core::pose::Pose &pose, Size const &n, std::string const &nt) const | core::import_pose::RNA_HelixAssembler | private |
| put_constraints_on_base_step(core::pose::Pose &pose, Size const &n) const | core::import_pose::RNA_HelixAssembler | private |
| random_perturbation(bool const &setting) | core::import_pose::RNA_HelixAssembler | inline |
| random_perturbation_ | core::import_pose::RNA_HelixAssembler | private |
| remove_first_base_pair(std::string &full_sequence, std::map< Size, std::string > &non_standard_residues, std::string &sequence_helix1, std::string &sequence_helix2) const | core::import_pose::RNA_HelixAssembler | private |
| remove_last_base_pair(std::string &full_sequence, std::map< Size, std::string > &non_standard_residues, std::string &sequence_helix1, std::string &sequence_helix2) const | core::import_pose::RNA_HelixAssembler | private |
| RNA_HelixAssembler() | core::import_pose::RNA_HelixAssembler | |
| rsd_set_ | core::import_pose::RNA_HelixAssembler | private |
| scorefxn_ | core::import_pose::RNA_HelixAssembler | private |
| set_Aform_torsions(core::pose::Pose &pose, Size const &n) const | core::import_pose::RNA_HelixAssembler | private |
| set_dump(bool const &setting) | core::import_pose::RNA_HelixAssembler | inline |
| set_finish_scorefxn(core::scoring::ScoreFunctionOP setting) | core::import_pose::RNA_HelixAssembler | |
| set_minimize_all(bool const &setting) | core::import_pose::RNA_HelixAssembler | inline |
| set_model_and_remove_capping_residues(bool setting) | core::import_pose::RNA_HelixAssembler | inline |
| set_scorefxn(core::scoring::ScoreFunctionOP setting) | core::import_pose::RNA_HelixAssembler | |
| torsion_info_ | core::import_pose::RNA_HelixAssembler | private |
| use_phenix_geo(bool const setting) | core::import_pose::RNA_HelixAssembler | |
| use_phenix_geo_ | core::import_pose::RNA_HelixAssembler | private |
| ~RNA_HelixAssembler() | core::import_pose::RNA_HelixAssembler | virtual |
1.8.7