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| static basic::Tracer | TR ("antibody.util") |
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| utility::vector1< bool > | protocols::antibody::get_cdr_bool_from_tag (utility::tag::TagCOP tag, std::string const &name, bool include_cdr4=false) |
| | Geta boolean vector of CDRs from a RosettaScripts tag. Companion function for XSD generation: attributes_for_get_cdr_bool_from_tag. More...
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| void | protocols::antibody::attributes_for_get_cdr_bool_from_tag (utility::tag::AttributeList &attlist, std::string const &tagname, std::string const &Description) |
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| protocols::loops::LoopsOP | protocols::antibody::get_cdr_loops (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, utility::vector1< bool > const &cdrs, core::Size stem_size) |
| | Get a set of loops for a boolean vector of CDRNameEnums including any stem residues. More...
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| core::pack::task::TaskFactoryOP | protocols::antibody::setup_packer_task (core::pose::Pose &pose_in) |
| | Very specific packertask,. More...
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| bool | protocols::antibody::cutpoints_separation (core::pose::Pose &pose, AntibodyInfoOP &antibody_info) |
| | return false if any cdr cutpoint is broken More...
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| Real | protocols::antibody::cutpoint_separation (pose::Pose &pose_in, core::Size cutpoint) |
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| Real | protocols::antibody::global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop) |
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| void | protocols::antibody::align_to_native (core::pose::Pose &pose, core::pose::Pose const &native_pose, AntibodyInfoOP const ab_info, AntibodyInfoOP const native_ab_info, std::string const &request_chain="LH") |
| | align current Fv to native.Fv More...
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| vector1< bool > | protocols::antibody::select_epitope_residues (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, core::Size const interface_distance=10.0) |
| | Get the epitope residues using the InterGroupNeighborsCalculator. More...
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| void | protocols::antibody::check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, CDRNameEnum cdr, core::pose::Pose &pose) |
| | Checks the length of the CDR, fixes AHO numbering for longer CDR loops that don't fit within the numbering scheme. More...
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| void | protocols::antibody::check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, core::pose::Pose &pose) |
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| void | protocols::antibody::simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop) |
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| void | protocols::antibody::simple_fold_tree (pose::Pose &pose_in, core::Size jumppoint1, core::Size cutpoint, core::Size jumppoint2) |
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| std::string | protocols::antibody::setup_LH_A_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose) |
| | Setup LH_A foldtree via docking. Return dock_chains string. More...
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| std::string | protocols::antibody::setup_A_LH_foldtree (AntibodyInfoCOP ab_info, core::pose::Pose &pose) |
| | Setup A_LH foldtree via docking. Return dock_chains string. More...
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| bool | protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule (const pose::Pose &pose_in, loops::Loop &input_loop, bool is_camelid) |
| | tests if a loop has H3 like base charachteristics More...
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| bool | protocols::antibody::CDR_H3_cter_filter (const pose::Pose &pose_in, AntibodyInfoOP ab_info) |
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| bool | protocols::antibody::is_H3_rama_kinked (std::string const &rama) |
| | Very basic kink function based on rama groups. Kink is defined as having AB + DB at the C-terminal stem. This is in the North/Dunbrack CDR definition. Avoid this definition if you can and talk to brain. This is currently used for a quick filtering for design. More...
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| void | protocols::antibody::kink_constrain_antibody_H3 (core::pose::Pose &pose, AntibodyInfoOP const antibody_info) |
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| void | protocols::antibody::kink_constrain_antibody_H3 (core::pose::Pose &pose, core::Size kink_begin) |
| | Apply auto-generated kink constraint. More...
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| void | protocols::antibody::qq_constrain_antibody (core::pose::Pose &pose, core::Size VH_qq_resi, core::Size VL_qq_resi) |
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| PDBLandmarkCOP | protocols::antibody::get_matching_landmark (AntibodyNumbering const &numbering, PDBLandmark const &landmark, AntibodyNumberingSchemeEnum const from_scheme, AntibodyNumberingSchemeEnum const to_scheme) |
| | get the equivalent landmark in a numbering scheme. Set the resnum to zero if not found. More...
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| vector1< Real > | protocols::antibody::get_conserved_residue_list (char chain) |
| | return vector of Chothia-nubmered, conserved residues for grafting and alignment More...
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