| ab_sequence_ | protocols::antibody::AntibodyInfo | private |
| add_CDR_to_MoveMap(core::pose::Pose const &pose, core::kinematics::MoveMapOP movemap, CDRNameEnum const cdr_name, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const | protocols::antibody::AntibodyInfo | |
| all_cdrs_present_ | protocols::antibody::AntibodyInfo | private |
| all_cdrs_present_and_proto_ | protocols::antibody::AntibodyInfo | private |
| AntibodyInfo(core::pose::Pose const &pose, bool const cdr_pdb_numbered=true) | protocols::antibody::AntibodyInfo | |
| AntibodyInfo(core::pose::Pose const &pose, AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const cdr_definition, bool const cdr_pdb_numbered=true) | protocols::antibody::AntibodyInfo | |
| AntibodyInfo(core::pose::Pose const &pose, CDRDefinitionEnum const cdr_definition, bool const cdr_pdb_numbered=true) | protocols::antibody::AntibodyInfo | |
| AntibodyInfo(AntibodyInfo const &src) | protocols::antibody::AntibodyInfo | |
| antigen_present() const | protocols::antibody::AntibodyInfo | inline |
| cdr_cluster_manager_ | protocols::antibody::AntibodyInfo | private |
| cdr_cluster_set_ | protocols::antibody::AntibodyInfo | private |
| cdr_definition_transform_present(CDRDefinitionEnum const cdr_definition) const | protocols::antibody::AntibodyInfo | private |
| cdr_pdb_numbered_ | protocols::antibody::AntibodyInfo | private |
| chains_for_antigen_ | protocols::antibody::AntibodyInfo | private |
| chains_for_cdrs_ | protocols::antibody::AntibodyInfo | private |
| check_cdr_quality(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | private |
| clone() const | protocols::antibody::AntibodyInfo | |
| current_transform_ | protocols::antibody::AntibodyInfo | private |
| detect_and_set_camelid_CDR_H3_stem_type(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| detect_and_set_regular_CDR_H3_stem_type(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| detect_and_set_regular_CDR_H3_stem_type_new_rule(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| enum_manager_ | protocols::antibody::AntibodyInfo | private |
| framework_info_ | protocols::antibody::AntibodyInfo | private |
| get_all_cdrs(bool include_proto_cdr4=false) const | protocols::antibody::AntibodyInfo | |
| get_all_cdrs_present(bool include_proto_cdr4=false) const | protocols::antibody::AntibodyInfo | |
| get_AllCDRs_in_loopsop() const | protocols::antibody::AntibodyInfo | |
| get_antibody_chain_ids(const core::pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| get_antibody_chain_string() const | protocols::antibody::AntibodyInfo | |
| get_antibody_chains() const | protocols::antibody::AntibodyInfo | |
| get_antibody_enum_manager() const | protocols::antibody::AntibodyInfo | |
| get_antibody_numbering_info() const | protocols::antibody::AntibodyInfo | inline |
| get_antibody_sequence() const | protocols::antibody::AntibodyInfo | |
| get_AntibodyFrameworkInfo() const | protocols::antibody::AntibodyInfo | |
| get_antigen_chain_ids(const core::pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| get_antigen_chain_string() const | protocols::antibody::AntibodyInfo | |
| get_antigen_chains() const | protocols::antibody::AntibodyInfo | inline |
| get_CDR_chain(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | inline |
| get_CDR_cluster(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_cdr_cluster_enum_manager() const | protocols::antibody::AntibodyInfo | |
| get_CDR_cluster_set() const | protocols::antibody::AntibodyInfo | |
| get_cdr_definition_transform(CDRDefinitionEnum const cdr_definition) const | protocols::antibody::AntibodyInfo | private |
| get_CDR_end(CDRNameEnum const cdr_name, core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_CDR_end(CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform) const | protocols::antibody::AntibodyInfo | |
| get_CDR_end_PDB_num(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | inline |
| get_cdr_enum_for_cluster(clusters::CDRClusterEnum const cluster) const | protocols::antibody::AntibodyInfo | |
| get_CDR_in_loopsop(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_CDR_length(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_CDR_length(CDRNameEnum const cdr_name, core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_CDR_length(CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const transform) const | protocols::antibody::AntibodyInfo | |
| get_CDR_loop(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_CDR_loop(CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size overhang=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_loop(CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const transform, core::Size overhang=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_loops(core::pose::Pose const &pose, core::Size overhang=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_loops(core::pose::Pose const &pose, const utility::vector1< bool > &cdrs, core::Size overhang=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_name(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_CDR_name_enum(std::string const &cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_CDR_sequence_with_stem(CDRNameEnum const cdr_name, core::Size left_stem=0, core::Size right_stem=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_sequence_with_stem(CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size left_stem=0, core::Size right_stem=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_sequence_with_stem(CDRNameEnum const cdr_name, core::pose::Pose const &pose, core::Size left_stem, core::Size right_stem, CDRDefinitionEnum const &transform) const | protocols::antibody::AntibodyInfo | |
| get_CDR_start(CDRNameEnum const cdr_name, core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_CDR_start(CDRNameEnum const cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform) const | protocols::antibody::AntibodyInfo | |
| get_CDR_start_PDB_num(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | inline |
| get_CDRNameEnum_of_residue(core::pose::Pose const &pose, core::Size resnum, bool de_as_framework=true) const | protocols::antibody::AntibodyInfo | |
| get_cluster_enum(std::string const &cluster) const | protocols::antibody::AntibodyInfo | |
| get_cluster_length(clusters::CDRClusterEnum const cluster) const | protocols::antibody::AntibodyInfo | |
| get_cluster_name(clusters::CDRClusterEnum const cluster) const | protocols::antibody::AntibodyInfo | |
| get_current_AntibodyNumberingScheme() const | protocols::antibody::AntibodyInfo | |
| get_current_CDRDefinition() const | protocols::antibody::AntibodyInfo | |
| get_Dock_ScoreFxn(void) | protocols::antibody::AntibodyInfo | privatestatic |
| get_FoldTree_AllCDRs(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_AllCDRs_LHDock(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_L_HA(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_LA_H(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_LH_A(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_H3_kink_type() const | protocols::antibody::AntibodyInfo | |
| get_H3_kink_type_name() const | protocols::antibody::AntibodyInfo | |
| get_landmark_resnum(core::pose::Pose const &pose, AntibodyNumberingSchemeEnum const scheme, char const chain, core::Size const pdb_resnum, char const insertion_code=' ', bool fail_on_missing_resnum=true) const | protocols::antibody::AntibodyInfo | |
| get_light_chain_type() const | protocols::antibody::AntibodyInfo | inline |
| get_light_chain_type_enum() const | protocols::antibody::AntibodyInfo | inline |
| get_LoopCentral_ScoreFxn(void) | protocols::antibody::AntibodyInfo | privatestatic |
| get_LoopHighRes_ScoreFxn(void) | protocols::antibody::AntibodyInfo | privatestatic |
| get_MoveMap_for_AllCDRsSideChains_and_H3backbone(core::pose::Pose const &pose, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const | protocols::antibody::AntibodyInfo | |
| get_MoveMap_for_Loops(core::pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const | protocols::antibody::AntibodyInfo | |
| get_MoveMap_for_LoopsandDock(core::pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, core::Real const &nb_dist=10.0) const | protocols::antibody::AntibodyInfo | |
| get_numbering_scheme_landmarks(AntibodyNumberingSchemeEnum const numbering_scheme) const | protocols::antibody::AntibodyInfo | private |
| get_Pack_ScoreFxn(void) | protocols::antibody::AntibodyInfo | privatestatic |
| get_PackingAngleResidues() const | protocols::antibody::AntibodyInfo | inline |
| get_region_of_residue(core::pose::Pose const &pose, core::Size resnum, bool de_as_framework=true) const | protocols::antibody::AntibodyInfo | |
| get_TaskFactory_AllCDRs(core::pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| get_TaskFactory_OneCDR(core::pose::Pose &pose, CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_total_num_CDRs(bool include_proto_cdr4=false) const | protocols::antibody::AntibodyInfo | |
| H_chain_ | protocols::antibody::AntibodyInfo | private |
| has_antigen_ | protocols::antibody::AntibodyInfo | private |
| has_CDR(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| has_cluster_for_cdr(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| identify_antibody(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| identify_CDR_from_a_sequence(std::string const &querychain) | protocols::antibody::AntibodyInfo | private |
| identify_light_chain(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| init(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| is_camelid() const | protocols::antibody::AntibodyInfo | inline |
| is_camelid_ | protocols::antibody::AntibodyInfo | private |
| kink_anion_atoms(const core::pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| kink_anion_residue(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_begin(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_cation_atoms(const core::pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| kink_cation_residue(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_end(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_trp(core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| L_chain_ | protocols::antibody::AntibodyInfo | private |
| light_chain_type_ | protocols::antibody::AntibodyInfo | private |
| loopsop_having_allcdrs_ | protocols::antibody::AntibodyInfo | private |
| numbering_info_ | protocols::antibody::AntibodyInfo | private |
| numbering_parser_ | protocols::antibody::AntibodyInfo | private |
| numbering_scheme_transform_present(AntibodyNumberingSchemeEnum const numbering_scheme) const | protocols::antibody::AntibodyInfo | private |
| operator<<(std::ostream &out, const AntibodyInfo &ab_info) | protocols::antibody::AntibodyInfo | friend |
| packing_angle_numbering_ | protocols::antibody::AntibodyInfo | private |
| packing_angle_residues_ | protocols::antibody::AntibodyInfo | private |
| predict_H3_base_type(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| predicted_H3_base_type_ | protocols::antibody::AntibodyInfo | private |
| qq_heavy_residue(const core::pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| qq_light_residue(const core::pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| sequence_map_ | protocols::antibody::AntibodyInfo | private |
| set_CDR_cluster(CDRNameEnum cdr, clusters::CDRClusterCOP cluster) | protocols::antibody::AntibodyInfo | |
| set_default() | protocols::antibody::AntibodyInfo | private |
| set_light_chain_type(LightChainTypeEnum light_chain) | protocols::antibody::AntibodyInfo | |
| setup_CDR_cluster(core::pose::Pose const &pose, CDRNameEnum cdr, bool attempt_set_from_pose=false) | protocols::antibody::AntibodyInfo | |
| setup_CDR_clusters(core::pose::Pose const &pose, bool attempt_set_from_pose=false) | protocols::antibody::AntibodyInfo | |
| setup_CDR_clusters(core::pose::Pose const &pose, utility::vector1< bool > const &cdrs, bool attempt_set_from_pose=false) | protocols::antibody::AntibodyInfo | |
| setup_CDRsInfo(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| setup_FrameWorkInfo(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| setup_numbering_info_for_scheme(AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const cdr_definition) | protocols::antibody::AntibodyInfo | private |
| setup_simple_fold_tree(core::Size const &jumppoint1, core::Size const &cutpoint, core::Size const &jumppoint2, core::pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| setup_VL_VH_packing_angle(core::pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| show(std::ostream &out=std::cout) const | protocols::antibody::AntibodyInfo | |
| total_cdr_loops_ | protocols::antibody::AntibodyInfo | private |
| vector1_loopsop_having_cdr_ | protocols::antibody::AntibodyInfo | private |
| ~AntibodyInfo() override | protocols::antibody::AntibodyInfo | |
1.8.7