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AntibodyUtil.cc File Reference
#include <protocols/antibody2/AntibodyUtil.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <core/id/AtomID_Map.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <core/pose/util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/import_pose/import_pose.hh>
#include <iostream>
#include <fstream>
#include <numeric/xyz.functions.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/PCA.hh>
#include <core/pack/rotamer_set/UnboundRotamersOperation.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <core/pack/task/operation/OperateOnCertainResidues.hh>
#include <core/pack/task/operation/OptH.hh>
#include <core/pack/task/operation/ResFilters.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <protocols/toolbox/task_operations/RestrictToInterface.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/dunbrack/RotamerConstraint.hh>
#include <core/scoring/rms_util.tmpl.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::antibody2
 

Constant Groups

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::antibody2
 

Functions

static basic::Tracer TR ("antibody2.AntibodyUtil")
 
void protocols::antibody2::simple_one_loop_fold_tree (pose::Pose &pose_in, loops::Loop const &loop)
 
void protocols::antibody2::simple_fold_tree (pose::Pose &pose_in, Size jumppoint1, Size cutpoint, Size jumppoint2)
 
bool protocols::antibody2::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::antibody2::CDR_H3_cter_filter (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
 
core::pack::task::TaskFactoryOP protocols::antibody2::setup_packer_task (pose::Pose &pose_in)
 
bool protocols::antibody2::cutpoints_separation (core::pose::Pose &pose, AntibodyInfoOP &antibody_info)
 return false if any cdr cutpoint is broken More...
 
Real protocols::antibody2::cutpoint_separation (pose::Pose &pose_in, Size cutpoint)
 
Real protocols::antibody2::global_loop_rmsd (const pose::Pose &pose_in, const pose::Pose &native_pose, loops::LoopsOP current_loop)
 
Real protocols::antibody2::vl_vh_packing_angle (const pose::Pose &pose_in, AntibodyInfoOP ab_info)
 
void protocols::antibody2::align_to_native (core::pose::Pose &pose, core::pose::Pose &native_pose, AntibodyInfoOP ab_info, AntibodyInfoOP native_ab_info)
 align current Fv to native.Fv More...
 

Detailed Description

Author
Jianqing Xu (xubes.nosp@m.t@gm.nosp@m.ail.c.nosp@m.om)

Function Documentation

static basic::Tracer TR ( "antibody2.AntibodyUtil"  )
static