| ab_info_ | protocols::antibody::design::AntibodyDesignMover | private |
| accept_log_ | protocols::antibody::design::AntibodyDesignMover | private |
| adapt_graft_ | protocols::antibody::design::AntibodyDesignMover | private |
| add_log_to_pose_ | protocols::antibody::design::AntibodyDesignMover | private |
| additional_outputs_returned_ | protocols::antibody::design::AntibodyDesignMover | private |
| anchored_graft_mover_ | protocols::antibody::design::AntibodyDesignMover | private |
| AntibodyDesignMover() | protocols::antibody::design::AntibodyDesignMover | |
| AntibodyDesignMover(AntibodyDesignMover const &src) | protocols::antibody::design::AntibodyDesignMover | |
| apply(core::pose::Pose &pose) override | protocols::antibody::design::AntibodyDesignMover | virtual |
| apply_to_cdr(core::pose::Pose &pose, CDRNameEnum cdr, core::Size index, bool min_post_graft=true) | protocols::antibody::design::AntibodyDesignMover | private |
| benchmark_ | protocols::antibody::design::AntibodyDesignMover | private |
| cart_min_graft_ | protocols::antibody::design::AntibodyDesignMover | private |
| cdr_dihedral_cst_mover_ | protocols::antibody::design::AntibodyDesignMover | private |
| cdr_graft_design_options_ | protocols::antibody::design::AntibodyDesignMover | private |
| cdr_seq_design_options_ | protocols::antibody::design::AntibodyDesignMover | private |
| cdr_set_ | protocols::antibody::design::AntibodyDesignMover | private |
| cdr_set_options_ | protocols::antibody::design::AntibodyDesignMover | private |
| cdrs_to_design_ | protocols::antibody::design::AntibodyDesignMover | private |
| check_for_top_designs(core::pose::Pose &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::antibody::design::AntibodyDesignMover | virtual |
| cluster_based_CDRDBPose_indexes_ | protocols::antibody::design::AntibodyDesignMover | private |
| create() | protocols::moves::Mover | virtual |
| db_manager_ | protocols::antibody::design::AntibodyDesignMover | private |
| design_enum_manager_ | protocols::antibody::design::AntibodyDesignMover | private |
| design_protocol_ | protocols::antibody::design::AntibodyDesignMover | private |
| dock_cycles_ | protocols::antibody::design::AntibodyDesignMover | private |
| dock_first_cycles_ | protocols::antibody::design::AntibodyDesignMover | private |
| dock_post_graft_ | protocols::antibody::design::AntibodyDesignMover | private |
| dock_second_cycles_ | protocols::antibody::design::AntibodyDesignMover | private |
| enable_adapt_graft_cartesian_ | protocols::antibody::design::AntibodyDesignMover | private |
| epitope_residues_ | protocols::antibody::design::AntibodyDesignMover | private |
| finalize_pose(AntibodyInfoCOP ab_info, core::pose::Pose &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| finalize_setup(core::pose::Pose &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| framework_mutator_ | protocols::antibody::design::AntibodyDesignMover | private |
| fresh_instance() const override | protocols::antibody::design::AntibodyDesignMover | virtual |
| get_additional_output() override | protocols::antibody::design::AntibodyDesignMover | virtual |
| get_cdr_set_index_list() | protocols::antibody::design::AntibodyDesignMover | private |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const override | protocols::antibody::design::AntibodyDesignMover | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| 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_top_designs() | protocols::antibody::design::AntibodyDesignMover | inline |
| get_type() const | protocols::moves::Mover | inline |
| graft_design_override_ | protocols::antibody::design::AntibodyDesignMover | private |
| graft_in_cdr(core::pose::Pose &pose, CDRNameEnum const cdr, CDRDBPose &cdr_pose) | protocols::antibody::design::AntibodyDesignMover | private |
| graft_log_ | protocols::antibody::design::AntibodyDesignMover | private |
| graft_mover_ | protocols::antibody::design::AntibodyDesignMover | private |
| idealize_graft_cdrs_ | protocols::antibody::design::AntibodyDesignMover | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init_ab_info(core::pose::Pose const &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| initialize_cdr_set(core::pose::Pose const &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| inner_cycles_ | protocols::antibody::design::AntibodyDesignMover | private |
| inner_kt_ | protocols::antibody::design::AntibodyDesignMover | private |
| inner_mc_ | protocols::antibody::design::AntibodyDesignMover | private |
| instruction_file_ | protocols::antibody::design::AntibodyDesignMover | private |
| interface_dis_ | protocols::antibody::design::AntibodyDesignMover | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| length_based_CDRDBPose_indexes_ | protocols::antibody::design::AntibodyDesignMover | private |
| light_chain_ | protocols::antibody::design::AntibodyDesignMover | private |
| mc_ | protocols::antibody::design::AntibodyDesignMover | private |
| mc_interface_weight_ | protocols::antibody::design::AntibodyDesignMover | private |
| mc_optimize_dG_ | protocols::antibody::design::AntibodyDesignMover | private |
| mc_total_weight_ | protocols::antibody::design::AntibodyDesignMover | private |
| mintype_ | protocols::antibody::design::AntibodyDesignMover | private |
| modeler_ | protocols::antibody::design::AntibodyDesignMover | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::antibody::design::AntibodyDesignMover | static |
| mutate_framework_for_cluster_ | protocols::antibody::design::AntibodyDesignMover | private |
| name() | protocols::moves::Mover | inlinestatic |
| neighbor_dis_ | protocols::antibody::design::AntibodyDesignMover | private |
| num_top_designs_ | protocols::antibody::design::AntibodyDesignMover | private |
| outer_cycles_ | protocols::antibody::design::AntibodyDesignMover | private |
| outer_kt_ | protocols::antibody::design::AntibodyDesignMover | private |
| overhang_ | protocols::antibody::design::AntibodyDesignMover | private |
| paratope_cdrs_ | protocols::antibody::design::AntibodyDesignMover | private |
| paratope_cst_mover_ | protocols::antibody::design::AntibodyDesignMover | private |
| paratope_epitope_cst_mover_ | protocols::antibody::design::AntibodyDesignMover | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) override | protocols::antibody::design::AntibodyDesignMover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| primary_cdrs_ | protocols::antibody::design::AntibodyDesignMover | private |
| print_str_vec(std::string const name, utility::vector1< std::string > const &vec, std::ostream &output=std::cout) const | protocols::antibody::design::AntibodyDesignMover | private |
| print_tracer_info_ | protocols::antibody::design::AntibodyDesignMover | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const override | protocols::antibody::design::AntibodyDesignMover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::antibody::design::AntibodyDesignMover | static |
| rb_min_post_graft_ | protocols::antibody::design::AntibodyDesignMover | private |
| read_command_line_options() | protocols::antibody::design::AntibodyDesignMover | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| relax_cycles_ | protocols::antibody::design::AntibodyDesignMover | private |
| remove_antigen_ | protocols::antibody::design::AntibodyDesignMover | private |
| reset_status() | protocols::moves::Mover | |
| run_basic_mc_algorithm(core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design, AntibodyDesignProtocolEnum mc_algorithm) | protocols::antibody::design::AntibodyDesignMover | private |
| run_deterministic_graft_algorithm(core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design) | protocols::antibody::design::AntibodyDesignMover | private |
| run_final_AIM_ | protocols::antibody::design::AntibodyDesignMover | private |
| run_final_IAM(bool run_IAM) | protocols::antibody::design::AntibodyDesignMover | private |
| run_graft(core::pose::Pose &pose, core::pose::Pose const &grafting_pose, CDRNameEnum const cdr, clusters::CDRClusterEnum const cluster, protocols::grafting::AnchoredGraftMoverOP grafter) | protocols::antibody::design::AntibodyDesignMover | private |
| run_optimization_cycle(core::pose::Pose &pose, protocols::moves::MonteCarlo &mc, CDRNameEnum cdr) | protocols::antibody::design::AntibodyDesignMover | private |
| scorefxn_ | protocols::antibody::design::AntibodyDesignMover | private |
| scorefxn_cart_graft_ | protocols::antibody::design::AntibodyDesignMover | private |
| scorefxn_min_ | protocols::antibody::design::AntibodyDesignMover | private |
| seq_design_creator_ | protocols::antibody::design::AntibodyDesignMover | private |
| seq_design_override_ | protocols::antibody::design::AntibodyDesignMover | private |
| set_cdr_set_options(AntibodyCDRSetOptions cdr_set_options) | protocols::antibody::design::AntibodyDesignMover | |
| 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::antibody::design::AntibodyDesignMover | |
| set_design_protocol(AntibodyDesignProtocolEnum design_protocol) | protocols::antibody::design::AntibodyDesignMover | |
| set_dock_first_cycles(core::Size dock_first_cycles) | protocols::antibody::design::AntibodyDesignMover | |
| set_dock_post_graft(bool dock_post_graft) | protocols::antibody::design::AntibodyDesignMover | |
| set_dock_rounds(core::Size dock_rounds) | protocols::antibody::design::AntibodyDesignMover | |
| set_dock_second_cycles(core::Size dock_second_cycles) | protocols::antibody::design::AntibodyDesignMover | |
| set_epitope_residues(utility::vector1< PDBNumbering > epitope_residues) | protocols::antibody::design::AntibodyDesignMover | |
| set_graft_design_cdrs(utility::vector1< CDRNameEnum > graft_design_cdrs) | protocols::antibody::design::AntibodyDesignMover | |
| set_graft_design_options(AntibodyCDRGraftDesignOptions graft_design_options) | protocols::antibody::design::AntibodyDesignMover | |
| set_inner_cycles(core::Size inner_cycles) | protocols::antibody::design::AntibodyDesignMover | |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_instruction_file(std::string instruction_file) | protocols::antibody::design::AntibodyDesignMover | |
| set_interface_dis(core::Real interface_dis) | protocols::antibody::design::AntibodyDesignMover | |
| set_keep_top_designs(core::Size top_designs) | protocols::antibody::design::AntibodyDesignMover | |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_light_chain(std::string const &light_chain) | protocols::antibody::design::AntibodyDesignMover | |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_neighbor_dis(core::Real neighbor_dis) | protocols::antibody::design::AntibodyDesignMover | |
| set_outer_cycles(core::Size outer_cycles) | protocols::antibody::design::AntibodyDesignMover | |
| set_paratope_cdrs(utility::vector1< bool > const &cdrs) | protocols::antibody::design::AntibodyDesignMover | |
| set_primary_cdrs(utility::vector1< CDRNameEnum > primary_cdrs) | protocols::antibody::design::AntibodyDesignMover | |
| set_random_start(bool const random_start) | protocols::antibody::design::AntibodyDesignMover | |
| set_relax_cycles(core::Size relax_cycles) | protocols::antibody::design::AntibodyDesignMover | |
| set_scorefunction(core::scoring::ScoreFunctionOP scorefxn) | protocols::antibody::design::AntibodyDesignMover | |
| set_scorefunction_min(core::scoring::ScoreFunctionOP min_scorefxn) | protocols::antibody::design::AntibodyDesignMover | |
| set_seq_design_cdrs(utility::vector1< CDRNameEnum > seq_design_cdrs) | protocols::antibody::design::AntibodyDesignMover | |
| set_seq_design_options(AntibodyCDRSeqDesignOptions seq_design_options) | protocols::antibody::design::AntibodyDesignMover | |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_use_epitope_constraints(bool use_epitope_csts) | protocols::antibody::design::AntibodyDesignMover | |
| setup_cart_minimizer() | protocols::antibody::design::AntibodyDesignMover | private |
| setup_cdr_pose_sampling_strategies() | protocols::antibody::design::AntibodyDesignMover | private |
| setup_default_graft_settings() | protocols::antibody::design::AntibodyDesignMover | private |
| setup_epitope_residues(core::pose::Pose const &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| setup_modeler() | protocols::antibody::design::AntibodyDesignMover | private |
| setup_native_clusters(core::pose::Pose &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| setup_native_sequence(core::pose::Pose &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| setup_options_classes() | protocols::antibody::design::AntibodyDesignMover | private |
| setup_paratope_epitope_constraints(core::pose::Pose &pose) | protocols::antibody::design::AntibodyDesignMover | private |
| setup_random_start_pose(core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design) | protocols::antibody::design::AntibodyDesignMover | private |
| setup_scorefxn() | protocols::antibody::design::AntibodyDesignMover | private |
| show(std::ostream &output=std::cout) const override | protocols::antibody::design::AntibodyDesignMover | virtual |
| stats_cutoff_ | protocols::antibody::design::AntibodyDesignMover | private |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| top_designs_ | protocols::antibody::design::AntibodyDesignMover | private |
| top_scores_ | protocols::antibody::design::AntibodyDesignMover | private |
| total_permutations_ | protocols::antibody::design::AntibodyDesignMover | private |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| use_epitope_constraints_ | protocols::antibody::design::AntibodyDesignMover | private |
| use_light_chain_type_ | protocols::antibody::design::AntibodyDesignMover | private |
| ~AntibodyDesignMover() override | protocols::antibody::design::AntibodyDesignMover | |
1.8.7