| ::HBPHelixAssignmentsTests class | protocols::helical_bundle_predict::HBPHelixAssignments | friend |
| add_helix() | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| add_helix(core::Size const startpos, core::Size const endpos, HBPHelix const &reference_helix) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| check_for_helix_merges(HBPHelixCOP const current_helix=nullptr) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| clear() | protocols::helical_bundle_predict::HBPHelixAssignments | |
| clone() const | protocols::helical_bundle_predict::HBPHelixAssignments | |
| common_delta_omega1_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| common_omega0_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| common_r0_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| confine_to_user_defined_helices() const | protocols::helical_bundle_predict::HBPHelixAssignments | inline |
| confine_to_user_defined_helices_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| extension_prob_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| find_adjacent_helix(core::Size seqpos) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| generate_torsion_values_for_helices(utility::vector1< std::map< core::id::TorsionID, core::Real > > &torsion_values_out, core::pose::Pose const &pose_for_reference) const | protocols::helical_bundle_predict::HBPHelixAssignments | |
| get_containing_helix_index(core::Size const seqpos) const | protocols::helical_bundle_predict::HBPHelixAssignments | |
| global_bundle_calculator_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_crick_params_file_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_delta_omega1_max_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_delta_omega1_min_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_fractional_perturbation_magnitude_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_omega0_max_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_omega0_min_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_perturbation_prob_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_r0_max_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| global_r0_min_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| HBPHelixAssignments() | protocols::helical_bundle_predict::HBPHelixAssignments | |
| HBPHelixAssignments(HBPHelixAssignments const &src) | protocols::helical_bundle_predict::HBPHelixAssignments | |
| helices_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| helix_from_seqpos(core::Size const position) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| helix_from_seqpos(core::Size const position) const | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| helix_types_match(HBPHelix const &first_helix, HBPHelix const &second_helix) const | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| initialize_from_file_contents(std::string const &file_contents) | protocols::helical_bundle_predict::HBPHelixAssignments | |
| initialize_global_options_from_file_contents(std::string const &file_contents) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| initialize_helices_from_file_contents(std::string const &file_contents) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| is_in_helix(core::Size const sequence_index) const | protocols::helical_bundle_predict::HBPHelixAssignments | |
| merge_helices(core::Size const first_helix_index, core::Size const second_helix_index, HBPHelixCOP const current_helix=nullptr) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| nucleation_prob_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| operator=(HBPHelixAssignments const &src) | protocols::helical_bundle_predict::HBPHelixAssignments | |
| pull_out_global_block(std::string const &file_contents, std::string &global_block) const | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| pull_out_helix_blocks(std::string const &file_contents, utility::vector1< std::string > &helix_blocks) const | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| remove_helix(HBPHelixOP helix_to_remove) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| resolve_mismatching_helix_overlap(core::Size const helix1_index, core::Size const helix2_index) | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| retraction_prob_ | protocols::helical_bundle_predict::HBPHelixAssignments | private |
| try_elongating_helix(core::Size const seqpos, core::pose::Pose const &pose, HBPHelixAssignments const &reference_helix_assignments) | protocols::helical_bundle_predict::HBPHelixAssignments | |
| try_nucleating_helix(core::Size const seqpos, core::pose::Pose const &pose, HBPHelixAssignments const &reference_helix_assignments) | protocols::helical_bundle_predict::HBPHelixAssignments | |
| try_perturbing_global_helix_parameters() | protocols::helical_bundle_predict::HBPHelixAssignments | |
| try_perturbing_local_helix_parameters() | protocols::helical_bundle_predict::HBPHelixAssignments | |
| try_retracting_helix(core::Size const seqpos, core::pose::Pose const &pose, HBPHelixAssignments const &reference_helix_assignments) | protocols::helical_bundle_predict::HBPHelixAssignments | |
| ~HBPHelixAssignments() override | protocols::helical_bundle_predict::HBPHelixAssignments | |
1.8.7