| all_rigid_body_settings_save_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| alpha_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| alpha_increment_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| alpha_max_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| alpha_min_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| apply_input_samples(pose::Pose &pose, std::string const rigid_body_sample_file) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| apply_rigid_body_settings(pose::Pose &pose, pose::Pose const &pose_start, Real const alpha, Real const beta, Real const gamma, Real const x, Real const y, Real const z) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| assign_WC_edges_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| assign_WC_edges_to_base_pair12(pose::Pose &pose, io::silent::SilentStruct &s) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| best_energy_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| beta_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| check_contact(Vector const &translation, utility::vector1< Vector > const &moving_atoms, utility::vector1< Vector > const &partner_atoms) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| check_fa_rep(pose::Pose &pose) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| check_num_hbonds(pose::Pose &pose) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| check_o2prime_needs_optimization(pose::Pose const &pose) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| check_steric_overlap(Vector const &translation, utility::vector1< Vector > const &moving_atoms, utility::vector1< Vector > const &partner_atoms) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| CONTACT_CUTOFF_squared_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| cosbeta_increment_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| cosbeta_max_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| cosbeta_min_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| count_clash_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| count_good_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| count_no_contact_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| count_total_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| delx_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| dely_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| delz_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| do_the_sampling(pose::Pose &pose) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| fa_rep_cutoff_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| figure_out_reference_energy(pose::Pose &pose) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| fixed_res_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| force_antiparallel() | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| force_coplanar() | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| force_parallel() | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| gamma_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| gamma_increment_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| gamma_max_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| gamma_min_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| ignore_o2prime_hbonds_in_filter_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| initialize_counters() | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| initialize_reference_axes_and_centroid(conformation::Residue const &rsd) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| min_hbonds_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| MIN_NUM_CONTACTS_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| moving_res_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| native_pose_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| o2prime_pack_scorefxn_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| o2prime_trials_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| output_histogram(utility::io::ozstream &out) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| output_results(utility::io::ozstream &out) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| output_silent_file(std::string const silent_file, bool const write_score_only=false) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| reference_axes_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| reference_centroid_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| reference_energy_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| RigidBodySampler(utility::vector1< Size > const &fixed_res, utility::vector1< Size > const &moving_res) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| rmsd_cutoff_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| save_rigid_body_settings(Real const energy) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| save_silent_struct(pose::Pose &pose, std::string const tag) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| score_cutoff_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| score_function() | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| scorefxn_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| search_rotations_and_translations(pose::Pose &pose) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| search_translations(pose::Pose &pose, pose::Pose const &pose_to_translate) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| set_alpha_increment(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_alpha_max(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_alpha_min(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_assign_WC_edges(bool const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_contact_cutoff(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_cosbeta_increment(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_cosbeta_max(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_cosbeta_min(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_fa_rep_cutoff(Real const value) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_gamma_increment(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_gamma_max(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_gamma_min(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_ignore_o2prime_hbonds_in_filter(bool const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_min_hbonds(Size const value) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_min_num_contacts(Size const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_n_sample_alpha_full_range(Size const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_n_sample_cosbeta_full_range(Size const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_n_sample_gamma_full_range(Size const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_native_pose(pose::PoseOP native_pose) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_o2prime_trials(bool const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_rmsd_cutoff(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_score_cutoff(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_score_function(core::scoring::ScoreFunctionOP setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_silent_file_data(core::io::silent::SilentFileDataOP sfd) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_steric_dist_cutoff(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_translation_sample(Real const box_size, Real const xyz_increment) | protocols::stepwise::sampling::legacy::RigidBodySampler | |
| set_x_increment(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_x_max(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_x_min(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_y_increment(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_y_max(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_y_min(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_z_increment(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_z_max(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| set_z_min(Real const setting) | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| setup_heavy_atoms(pose::Pose const &pose, utility::vector1< Vector > &pose_atoms, utility::vector1< Size > const &subset_res) | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| sfd_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| silent_file_data() | protocols::stepwise::sampling::legacy::RigidBodySampler | inline |
| STERIC_DIST_CUTOFF_squared_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| x_increment_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| x_max_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| x_min_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| y_increment_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| y_max_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| y_min_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| z_increment_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| z_max_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| z_min_ | protocols::stepwise::sampling::legacy::RigidBodySampler | private |
| ~RigidBodySampler() | protocols::stepwise::sampling::legacy::RigidBodySampler | virtual |
1.8.7