| apply(core::pose::Pose &pose) override | protocols::glycan_docking::GlycanDockProtocol | virtual |
| clear_counters() | protocols::glycan_docking::GlycanDockProtocol | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::glycan_docking::GlycanDockProtocol | virtual |
| create() | protocols::moves::Mover | virtual |
| current_job_ | protocols::moves::Mover | private |
| current_tag_ | protocols::moves::Mover | private |
| dock_jump_num_ | protocols::glycan_docking::GlycanDockProtocol | private |
| docking_filter(core::pose::Pose const &pose, core::Size const repeat) | protocols::glycan_docking::GlycanDockProtocol | private |
| fresh_instance() const override | protocols::glycan_docking::GlycanDockProtocol | virtual |
| full_pack_freq_ | protocols::glycan_docking::GlycanDockProtocol | private |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_full_packing_frequency() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_interface_packing_distance() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_last_move_status() const | protocols::moves::Mover | |
| get_mc_kt() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_n_repeats() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_n_rigid_body_rounds() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_n_torsion_rounds() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_name() const override | protocols::glycan_docking::GlycanDockProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_partners() const | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_prepack_only() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_ramp_scorefxn() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_rand_glycan_jump_res() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_refine_only() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_scorefunction() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_slide_glycan_into_contact() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_stage1_perturb_glycan_com_rot_mag() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_stage1_perturb_glycan_com_trans_mag() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_stage1_rotate_glycan_about_com() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_stage1_torsion_uniform_pert_mag() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_stage2_rot_mag() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_stage2_trans_mag() | protocols::glycan_docking::GlycanDockProtocol | inline |
| get_type() const | protocols::moves::Mover | inline |
| get_watch_in_pymol() | protocols::glycan_docking::GlycanDockProtocol | inline |
| GlycanDockProtocol() | protocols::glycan_docking::GlycanDockProtocol | |
| GlycanDockProtocol(GlycanDockProtocol const &object_to_copy) | protocols::glycan_docking::GlycanDockProtocol | |
| glycoligand_has_dihedrals_ | protocols::glycan_docking::GlycanDockProtocol | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| info_ | protocols::moves::Mover | private |
| init_options() | protocols::glycan_docking::GlycanDockProtocol | private |
| input_pose_ | protocols::moves::Mover | private |
| intf_pack_dist_ | protocols::glycan_docking::GlycanDockProtocol | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| last_status_ | protocols::moves::Mover | private |
| lock_rings_ | protocols::glycan_docking::GlycanDockProtocol | private |
| mc_kt_ | protocols::glycan_docking::GlycanDockProtocol | private |
| min_tolerance_ | protocols::glycan_docking::GlycanDockProtocol | private |
| min_type_ | protocols::glycan_docking::GlycanDockProtocol | private |
| movable_jump_ | protocols::glycan_docking::GlycanDockProtocol | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::glycan_docking::GlycanDockProtocol | static |
| n_cycles_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_rb_cycles_performed_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_rb_moves_accepted_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_rb_moves_made_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_rb_rounds_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_repeats_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_shear_moves_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_stage2_cycles_performed_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_tor_cycles_performed_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_tor_moves_accepted_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_tor_moves_made_ | protocols::glycan_docking::GlycanDockProtocol | private |
| n_tor_rounds_ | protocols::glycan_docking::GlycanDockProtocol | private |
| name() | protocols::moves::Mover | inlinestatic |
| native_pose_ | protocols::moves::Mover | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override | protocols::glycan_docking::GlycanDockProtocol | virtual |
| partners_ | protocols::glycan_docking::GlycanDockProtocol | private |
| partners_provided_ | protocols::glycan_docking::GlycanDockProtocol | private |
| perform_stage2_docking_and_optimization(core::pose::Pose &pose, protocols::moves::RandomMoverOP stage2_rb_randmover, protocols::moves::RandomMoverOP stage2_tor_randmover, minimization_packing::PackRotamersMoverOP full_packer, minimization_packing::EnergyCutRotamerTrialsMoverOP ecut_packer, minimization_packing::MinMoverOP min_mover, moves::MonteCarloOP mc) | protocols::glycan_docking::GlycanDockProtocol | private |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| prepack_only(core::pose::Pose &pose, protocols::minimization_packing::PackRotamersMoverOP prepack_packer) | protocols::glycan_docking::GlycanDockProtocol | private |
| prepack_only_ | protocols::glycan_docking::GlycanDockProtocol | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::glycan_docking::GlycanDockProtocol | static |
| ramp_score_weight(core::scoring::ScoreType const score_type, core::Real const target_weight, core::Size const current_cycle, core::Size const n_cycles) | protocols::glycan_docking::GlycanDockProtocol | private |
| ramp_scorefxn_ | protocols::glycan_docking::GlycanDockProtocol | private |
| rand_glyc_jump_res_ | protocols::glycan_docking::GlycanDockProtocol | private |
| record_pose_metrics(core::pose::Pose &pose, utility::vector1< bool > const &glycolig_subset, core::pose::Pose const &ref_pose, utility::vector1< bool > const &ref_glycolig_subset) | protocols::glycan_docking::GlycanDockProtocol | private |
| record_protocol_info(core::pose::Pose &pose) | protocols::glycan_docking::GlycanDockProtocol | private |
| refine_only_ | protocols::glycan_docking::GlycanDockProtocol | private |
| register_options() | protocols::glycan_docking::GlycanDockProtocol | private |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| reset_status() | protocols::moves::Mover | |
| rt_energycut_ | protocols::glycan_docking::GlycanDockProtocol | private |
| scorefxn_ | protocols::glycan_docking::GlycanDockProtocol | private |
| set_cmd_line_defaults() | protocols::glycan_docking::GlycanDockProtocol | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_defaults() | protocols::glycan_docking::GlycanDockProtocol | private |
| set_full_packing_frequency(core::Size const full_pack_freq) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_interface_packing_distance(core::Real const intf_pack_dist) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_mc_kt(core::Real const mc_kt) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_n_repeats(core::Size const &n_repeats) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_n_rigid_body_rounds(core::Size const rb_rounds) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_n_torsion_rounds(core::Size const tor_rounds) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_partners(std::string const &p) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_prepack_only(bool const prepack_only) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_ramp_scorefxn(bool const ramp_sf) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_rand_glycan_jump_res(bool const rand_glyc_jump) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_refine_only(bool const refine_only) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_scorefunction(core::scoring::ScoreFunctionOP const &in_sf) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_slide_glycan_into_contact(bool const slide) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_stage1_perturb_glycan_com_rot_mag(core::Real const rot_mag) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_stage1_perturb_glycan_com_trans_mag(core::Real const trans_mag) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_stage1_rotate_glycan_about_com(bool const sg1) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_stage1_torsion_uniform_pert_mag(core::Real const pert_mag) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_stage2_rot_mag(core::Real const rot_mag) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_stage2_trans_mag(core::Real const trans_mag) | protocols::glycan_docking::GlycanDockProtocol | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_watch_in_pymol(bool const pymol) | protocols::glycan_docking::GlycanDockProtocol | inline |
| setup_docking_foldtree(core::pose::Pose &pose, core::pose::Pose &ref_pose) | protocols::glycan_docking::GlycanDockProtocol | private |
| setup_scorefxn(core::pose::Pose &pose) | protocols::glycan_docking::GlycanDockProtocol | private |
| show(std::ostream &output) const override | protocols::glycan_docking::GlycanDockProtocol | virtual |
| show() const | protocols::glycan_docking::GlycanDockProtocol | |
| slide_glyc_into_contact_ | protocols::glycan_docking::GlycanDockProtocol | private |
| stage1_rot_mag_ | protocols::glycan_docking::GlycanDockProtocol | private |
| stage1_rotate_glyc_about_com_ | protocols::glycan_docking::GlycanDockProtocol | private |
| stage1_torsion_uniform_pert_mag_ | protocols::glycan_docking::GlycanDockProtocol | private |
| stage1_trans_mag_ | protocols::glycan_docking::GlycanDockProtocol | private |
| stage2_rot_mag_ | protocols::glycan_docking::GlycanDockProtocol | private |
| stage2_trans_mag_ | protocols::glycan_docking::GlycanDockProtocol | private |
| starting_ramp_down_atr_factor_ | protocols::glycan_docking::GlycanDockProtocol | private |
| starting_ramp_up_rep_factor_ | protocols::glycan_docking::GlycanDockProtocol | private |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| target_atr_ | protocols::glycan_docking::GlycanDockProtocol | private |
| target_rep_ | protocols::glycan_docking::GlycanDockProtocol | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| type_ | protocols::moves::Mover | private |
| watch_in_pymol_ | protocols::glycan_docking::GlycanDockProtocol | private |
| ~GlycanDockProtocol() override | protocols::glycan_docking::GlycanDockProtocol | |
