| ab_info_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| add_extra_restrict_operations(core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose) const | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| AntibodySeqDesignTFCreator(AntibodyInfoCOP ab_info, bool force_north_paper_db=false) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| AntibodySeqDesignTFCreator(AntibodyInfoCOP ab_info, utility::vector1< CDRSeqDesignOptionsOP > const design_options, bool force_north_paper_db=false, core::Size stem_size=2) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| cdr_design_options_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| clone() const | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| design_antigen(bool antigen_design) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| design_antigen_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| design_framework(bool framework_design) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| design_framework_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| design_framework_conservative_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| design_framework_conserved_res_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| design_h3_stem_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| design_proline(bool const setting) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| design_proline_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| disable_design_for_non_designing_cdrs(core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| disable_disallowed_aa(core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose) const | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| disable_proline_design(core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose) const | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| force_north_paper_db_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| generate_task_op_all_cdr_design(core::pose::Pose const &pose, bool design_neighbors=true) const | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| generate_task_op_cdr_design(core::pose::Pose const &pose, bool design_neighbors=true) const | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| generate_task_op_cdr_design(core::pose::Pose const &pose, utility::vector1< bool > cdrs, bool design_neighbors=true) const | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| generate_task_op_cdr_profiles(core::pose::Pose const &pose) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| generate_tf_seq_design(core::pose::Pose const &pose, bool disable_non_designing_cdrs=false) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| generate_tf_seq_design_graft_design(core::pose::Pose const &pose, CDRNameEnum cdr, utility::vector1< bool >const &neighbor_cdr_min) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| get_cdr_design_options() | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| get_cdr_design_options(CDRNameEnum cdr) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| get_design_cdr_loops(core::pose::Pose const &pose, core::Size stem_size=0) const | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| get_design_cdr_loops_with_stem(core::pose::Pose const &pose) const | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| get_framework_conservative_op(core::pose::Pose const &pose) | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| get_general_loop_task_op(protocols::loops::LoopsOP loops, bool design_neighbors=true) const | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| neighbor_detection_dis(core::Real const neighbor_distance) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| neighbor_dis_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| no_data_cdrs_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| no_probability_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| prob_cutoff_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| profile_picking_rounds_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| read_command_line_options() | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| set_cdr_design_options(CDRNameEnum cdr, CDRSeqDesignOptionsCOP design_options) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| set_cdr_design_options(utility::vector1< CDRSeqDesignOptionsOP > const design_options) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| set_design_framework_conservative(bool design_framework_conservative) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| set_design_framework_conserved_res(bool design_framework_conserved_res) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| set_design_H3_stem(bool design_H3_stem) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| set_no_probability(bool no_probability) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| set_probability_data_cutoff(core::Size const cutoff) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| set_zero_prob_weight_at(core::Real const weight) | protocols::antibody::design::AntibodySeqDesignTFCreator | |
| setup_default_options() | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| stem_size_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| use_outliers_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
| zero_prob_weight_ | protocols::antibody::design::AntibodySeqDesignTFCreator | private |
1.8.7