| ab_dock_chains_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| ab_info_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| AntibodyDesignModeler(AntibodyInfoOP ab_info) | protocols::antibody::design::AntibodyDesignModeler | |
| antigen_interface_tf_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| apply_LH_A_foldtree(core::pose::Pose &pose) const | protocols::antibody::design::AntibodyDesignModeler | protected |
| cdrs_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| cmd_line_operation_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| dock_A_LH_high_res(Pose &pose, int first_cycle=4, int second_cycle=45) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_A_LH_low_res(Pose &pose, bool pack_interface=false) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_H_L_high_res(Pose &pose, int first_cycle=4, int second_cycle=45) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_H_L_low_res(Pose &pose, bool pack_interface=false) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_high_res(core::pose::Pose &pose, std::string dock_chains, int first_cycle=4, int second_cycle=45) const | protocols::antibody::design::AntibodyDesignModeler | protected |
| dock_L_H_high_res(Pose &pose, int first_cycle=4, int second_cycle=45) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_L_H_low_res(Pose &pose, bool pack_interface=false) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_LH_A_high_res(Pose &pose, int first_cycle=4, int second_cycle=45) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_LH_A_low_res(Pose &pose, bool pack_interface=false) const | protocols::antibody::design::AntibodyDesignModeler | |
| dock_low_res(core::pose::Pose &pose, std::string dock_chains, bool pack_interface=false) const | protocols::antibody::design::AntibodyDesignModeler | protected |
| docking_scorefxn_high_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| extend_CDR(Pose &pose, CDRNameEnum cdr) const | protocols::antibody::design::AntibodyDesignModeler | |
| get_ab_dock_chains() | protocols::antibody::design::AntibodyDesignModeler | |
| get_cdr_loops(Pose &pose) const | protocols::antibody::design::AntibodyDesignModeler | protected |
| interface_dis_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| loops_operation_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| minimize_cdrs(Pose &pose, bool min_interface=false, std::string dock_chains="L_H") const | protocols::antibody::design::AntibodyDesignModeler | |
| minimize_cdrs_and_neighbor_sc(Pose &pose, bool min_interface=false, std::string dock_chains="L_H") const | protocols::antibody::design::AntibodyDesignModeler | |
| minimize_interface(Pose &pose, std::string dock_chains, bool min_interface_sc=true) const | protocols::antibody::design::AntibodyDesignModeler | |
| neighbor_dis_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| read_command_line_options() | protocols::antibody::design::AntibodyDesignModeler | protected |
| relax_cdrs(Pose &pose, bool centroid_mode, bool starting_coordinate_constraints=false, bool min_interface=false, std::string dock_chains="L_H") const | protocols::antibody::design::AntibodyDesignModeler | |
| relax_cdrs_and_neighbor_sc(Pose &pose, bool starting_coordinate_constraints=false, bool min_interface=false, std::string dock_chains="L_H") const | protocols::antibody::design::AntibodyDesignModeler | |
| relax_interface(Pose &pose, std::string dock_chains, bool min_interface_sc=true) const | protocols::antibody::design::AntibodyDesignModeler | |
| repack_antibody_interface(Pose &pose) const | protocols::antibody::design::AntibodyDesignModeler | |
| repack_antigen_ab_interface(Pose &pose) const | protocols::antibody::design::AntibodyDesignModeler | |
| repack_antigen_interface(Pose &pose) const | protocols::antibody::design::AntibodyDesignModeler | |
| repack_CDRs(Pose &pose) | protocols::antibody::design::AntibodyDesignModeler | |
| repack_CDRs_and_neighbors(Pose &pose) | protocols::antibody::design::AntibodyDesignModeler | |
| restrict_design_operation_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| scorefxn_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| set_ab_dock_chains(std::string ab_dock_chains) | protocols::antibody::design::AntibodyDesignModeler | |
| set_cdr(CDRNameEnum const cdr, bool setting) | protocols::antibody::design::AntibodyDesignModeler | |
| set_cdr_only(CDRNameEnum const cdr, bool setting) | protocols::antibody::design::AntibodyDesignModeler | |
| set_cdr_range(CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool setting) | protocols::antibody::design::AntibodyDesignModeler | |
| set_interface_detection_dis(core::Real interface_distance) | protocols::antibody::design::AntibodyDesignModeler | |
| set_neighbor_detection_dis(core::Real neighbor_distance) | protocols::antibody::design::AntibodyDesignModeler | |
| set_scorefunction(ScoreFunctionCOP scorefxn) | protocols::antibody::design::AntibodyDesignModeler | |
| tf_ | protocols::antibody::design::AntibodyDesignModeler | protected |
| ~AntibodyDesignModeler() | protocols::antibody::design::AntibodyDesignModeler | virtual |
1.8.7