| align_to_native_pose(core::pose::Pose &pose) const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| apply_metropolis_criterion(core::Real const &old_energy, core::Real const &new_energy, core::Real const &temperature) const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| centroid_move_generator_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| centroid_sfxn_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| centroid_temperature_generator_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| check_ignore_residues_reasonable(utility::vector1< core::Size > const &ignore_residues, core::pose::PoseCOP const &pose) const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| clone() const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| create_centroid_move_generator() | protocols::helical_bundle_predict::HelicalBundlePredictApplication | static |
| create_centroid_scorefunction() | protocols::helical_bundle_predict::HelicalBundlePredictApplication | static |
| create_final_fullatom_refinement_move_generator() const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| create_fullatom_scorefunction() | protocols::helical_bundle_predict::HelicalBundlePredictApplication | static |
| do_a_simulated_annealing_round(core::pose::PoseOP &pose, core::Size num_steps, HBP_MoveGeneratorCOP move_generator, HBP_TemperatureScheduleGeneratorCOP temperature_generator, core::scoring::ScoreFunction const &sfxn) const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| do_final_fullatom_refinement(core::pose::PoseOP &pose) const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| do_simulated_annealing(core::pose::PoseOP &pose, core::Size const num_rounds, core::Size const num_steps_per_round, HBP_MoveGeneratorOP move_generator, HBP_TemperatureScheduleGeneratorOP temperature_generator, core::scoring::ScoreFunction const &sfxn) const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| final_fullatom_refinement_move_generator_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| fullatom_sfxn_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| HelicalBundlePredictApplication()=delete | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| HelicalBundlePredictApplication(HelicalBundlePredictApplicationOptionsCOP options_in) | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| HelicalBundlePredictApplication(HelicalBundlePredictApplicationOptionsCOP options_in, HBP_MoveGeneratorOP centroid_move_generator_in, core::scoring::ScoreFunctionOP centroid_sfxn_in, core::scoring::ScoreFunctionOP fullatom_sfxn_in) | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| HelicalBundlePredictApplication(HelicalBundlePredictApplication const &src) | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| load_native_pose_from_disk() | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| make_pose_from_fasta_contents() const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| make_pose_from_sequence_file_contents() const | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| native_pose_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| nstruct_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| options_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| outfile_extension_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| outfile_prefix_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| outfile_suffix_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| output_filetype_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| pose_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| run() | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| set_native(core::pose::PoseCOP native) | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| set_nstruct(core::Size const nstruct_in) | protocols::helical_bundle_predict::HelicalBundlePredictApplication | inline |
| set_output_format(core::import_pose::FileType const type) | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| set_output_prefix_and_suffix(std::string const &prefix, std::string const &suffix) | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| set_silent_output() | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
| set_up_centroid_move_generator() | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| silent_output_ | protocols::helical_bundle_predict::HelicalBundlePredictApplication | private |
| ~HelicalBundlePredictApplication() override | protocols::helical_bundle_predict::HelicalBundlePredictApplication | |
1.8.7