| ab_sequence_ | protocols::antibody::AntibodyInfo | private |
| add_CDR_to_MoveMap(pose::Pose const &pose, kinematics::MoveMapOP movemap, CDRNameEnum const &cdr_name, bool const &bb_only=false, bool const &include_nb_sc=false, Real const &nb_dist=10.0) const | protocols::antibody::AntibodyInfo | |
| AntibodyInfo(pose::Pose const &pose, bool const &cdr_pdb_numbered=true) | protocols::antibody::AntibodyInfo | |
| AntibodyInfo(pose::Pose const &pose, AntibodyNumberingSchemeEnum const &numbering_scheme, CDRDefinitionEnum const &cdr_definition, bool const &cdr_pdb_numbered=true) | protocols::antibody::AntibodyInfo | |
| 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 |
| Chain_IDs_for_antigen_ | protocols::antibody::AntibodyInfo | private |
| Chain_IDs_for_CDRs_ | protocols::antibody::AntibodyInfo | private |
| current_transform_ | protocols::antibody::AntibodyInfo | private |
| detect_and_set_camelid_CDR_H3_stem_type(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| detect_and_set_regular_CDR_H3_stem_type(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| detect_and_set_regular_CDR_H3_stem_type_new_rule(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| enum_manager_ | protocols::antibody::AntibodyInfo | private |
| framework_info_ | protocols::antibody::AntibodyInfo | private |
| get_AllCDRs_in_loopsop() const | protocols::antibody::AntibodyInfo | |
| get_antibody_enum_manager() const | protocols::antibody::AntibodyInfo | |
| get_antibody_sequence() const | protocols::antibody::AntibodyInfo | |
| get_AntibodyFrameworkInfo() 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_definition_transform(CDRDefinitionEnum const cdr_definition) const | protocols::antibody::AntibodyInfo | private |
| get_CDR_end(CDRNameEnum const &cdr_name, pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_CDR_end(CDRNameEnum const &cdr_name, 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(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, 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, pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_CDR_loop(CDRNameEnum const &cdr_name, pose::Pose const &pose, CDRDefinitionEnum const &transform) const | protocols::antibody::AntibodyInfo | |
| get_CDR_loops(pose::Pose const &pose) 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, Size left_stem=0, Size right_stem=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_sequence_with_stem(CDRNameEnum const &cdr_name, core::pose::Pose const &pose, CDRDefinitionEnum const &transform, Size left_stem=0, Size right_stem=0) const | protocols::antibody::AntibodyInfo | |
| get_CDR_start(CDRNameEnum const &cdr_name, pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_CDR_start(CDRNameEnum const &cdr_name, 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_cluster_enum(std::string const cluster) const | protocols::antibody::AntibodyInfo | |
| get_cluster_length(CDRClusterEnum const cluster) const | protocols::antibody::AntibodyInfo | |
| get_cluster_name(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(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_AllCDRs_LHDock(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_L_HA(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_LA_H(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_FoldTree_LH_A(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| get_landmark_resnum(pose::Pose const &pose, AntibodyNumberingSchemeEnum const scheme, char const chain, Size const pdb_resnum, char const insertion_code=' ') const | protocols::antibody::AntibodyInfo | |
| get_LoopCentral_ScoreFxn(void) | protocols::antibody::AntibodyInfo | privatestatic |
| get_LoopHighRes_ScoreFxn(void) | protocols::antibody::AntibodyInfo | privatestatic |
| get_MoveMap_for_AllCDRsSideChains_and_H3backbone(pose::Pose const &pose, bool const &include_nb_sc=false, Real const &nb_dist=10.0) const | protocols::antibody::AntibodyInfo | |
| get_MoveMap_for_Loops(pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, Real const &nb_dist=10.0) const | protocols::antibody::AntibodyInfo | |
| get_MoveMap_for_LoopsandDock(pose::Pose const &pose, loops::Loops const &the_loops, bool const &bb_only=false, bool const &include_nb_sc=false, 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_pose_has_antigen() const | protocols::antibody::AntibodyInfo | inline |
| get_Predicted_H3BaseType() const | protocols::antibody::AntibodyInfo | |
| get_TaskFactory_AllCDRs(pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| get_TaskFactory_OneCDR(pose::Pose &pose, CDRNameEnum const &cdr_name) const | protocols::antibody::AntibodyInfo | |
| get_total_num_CDRs() const | protocols::antibody::AntibodyInfo | inline |
| H_chain_ | protocols::antibody::AntibodyInfo | private |
| has_cluster_for_cdr(CDRNameEnum const cdr_name) const | protocols::antibody::AntibodyInfo | |
| identify_antibody(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| identify_CDR_from_a_sequence(std::string const &querychain) | protocols::antibody::AntibodyInfo | private |
| init(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| InputPose_has_antigen_ | protocols::antibody::AntibodyInfo | private |
| is_camelid() const | protocols::antibody::AntibodyInfo | inline |
| is_camelid_ | protocols::antibody::AntibodyInfo | private |
| kink_anion_atoms(const pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| kink_anion_residue(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_begin(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_cation_atoms(const pose::Pose &pose) const | protocols::antibody::AntibodyInfo | |
| kink_cation_residue(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_end(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| kink_trp(pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | inline |
| L_chain_ | 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(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| predicted_H3_base_type_ | protocols::antibody::AntibodyInfo | private |
| sequence_map_ | protocols::antibody::AntibodyInfo | private |
| set_default() | protocols::antibody::AntibodyInfo | private |
| setup_CDR_clusters(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | |
| setup_CDRsInfo(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| setup_FrameWorkInfo(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(Size const &jumppoint1, Size const &cutpoint, Size const &jumppoint2, pose::Pose const &pose) const | protocols::antibody::AntibodyInfo | |
| setup_VL_VH_packing_angle(pose::Pose const &pose) | protocols::antibody::AntibodyInfo | private |
| show(std::ostream &out=std::cout) | protocols::antibody::AntibodyInfo | |
| total_cdr_loops_ | protocols::antibody::AntibodyInfo | private |
| vector1_loopsop_having_cdr_ | protocols::antibody::AntibodyInfo | private |
| ~AntibodyInfo() | protocols::antibody::AntibodyInfo | virtual |
1.8.7