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util.hh File Reference

Utility functions for the Antibody namespace. More...

#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/antibody/AntibodyInfo.fwd.hh>
#include <protocols/antibody/AntibodyEnum.hh>
#include <protocols/antibody/AntibodyNumberingParser.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/tag/XMLSchemaGeneration.fwd.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::antibody
 

Functions

utility::vector1< boolprotocols::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...
 
void protocols::antibody::attributes_for_get_cdr_bool_from_tag (utility::tag::AttributeList &attlist, std::string const &tagname, std::string const &Description)
 
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...
 
Real protocols::antibody::global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop)
 
bool protocols::antibody::cutpoints_separation (core::pose::Pose &pose, AntibodyInfoOP &antibody_info)
 return false if any cdr cutpoint is broken More...
 
Real protocols::antibody::cutpoint_separation (pose::Pose &pose_in, core::Size cutpoint)
 
vector1< boolprotocols::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...
 
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...
 
void protocols::antibody::check_fix_aho_cdr_numbering (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
 
void protocols::antibody::simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop)
 
void protocols::antibody::simple_fold_tree (pose::Pose &pose_in, core::Size jumppoint1, core::Size cutpoint, core::Size jumppoint2)
 
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...
 
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...
 
core::pack::task::TaskFactoryOP protocols::antibody::setup_packer_task (core::pose::Pose &pose_in)
 Very specific packertask,. More...
 
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...
 
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...
 
bool protocols::antibody::CDR_H3_cter_filter (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
 
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...
 
void protocols::antibody::kink_constrain_antibody_H3 (core::pose::Pose &pose, core::Size kink_begin)
 Apply auto-generated kink constraint. More...
 
void protocols::antibody::kink_constrain_antibody_H3 (core::pose::Pose &pose, AntibodyInfoOP const antibody_info)
 
void protocols::antibody::qq_constrain_antibody (core::pose::Pose &pose, core::Size VH_qq_resi, core::Size VL_qq_resi)
 
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...
 
vector1< Realprotocols::antibody::get_conserved_residue_list (char chain)
 return vector of Chothia-nubmered, conserved residues for grafting and alignment More...
 

Detailed Description

Utility functions for the Antibody namespace.

Author
Jianqing Xu (xubes.nosp@m.t@gm.nosp@m.ail.c.nosp@m.om)
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)