modeling_util.cc File Reference

modeling utility functions for protocols/tcr More...

#include <protocols/tcr/modeling_util.hh>
#include <protocols/tcr/util.hh>
#include <protocols/tcr/grafting_util.hh>
#include <protocols/tcr/TCRloopRefine.hh>
#include <protocols/tcr/TCRseqInfo.hh>
#include <protocols/tcr/TCRmodel.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/antibody/util.hh>
#include <protocols/grafting/util.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <protocols/simple_moves/MutateResidue.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/LoopMoverFactory.hh>
#include <protocols/loops/loop_mover/IndependentLoopMover.hh>
#include <protocols/simple_moves/ReturnSidechainMover.hh>
#include <protocols/loops/loop_mover/refine/LoopMover_KIC.hh>
#include <protocols/loops/loop_mover/perturb/LoopMover_KIC.hh>
#include <protocols/relax/loop/LoopRelaxMover.hh>
#include <protocols/loop_modeling/LoopProtocol.hh>
#include <protocols/loop_modeling/types.hh>
#include <protocols/kinematic_closure/KicMover.hh>
#include <protocols/loop_modeling/refiners/RepackingRefiner.hh>
#include <protocols/loop_modeling/refiners/RotamerTrialsRefiner.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>

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

Functions
static basic::Tracer	TR ("protocols.tcr.modeling_util")
void	protocols::tcr::match_template_and_target_sequence (core::pose::Pose const &scafold, std::string const &targetseq, core::pose::Pose &posecopy)
	match template seq with target seq during modeling More...
void	protocols::tcr::orient_tcr_chain (core::pose::Pose &fr_piece, core::pose::Pose const &ori_tmplt_chain, TCRseqInfo::tcrposi const &selepos)
	orient TCR alpha/beta chains based on the orientation templates More...
void	protocols::tcr::refine_tcr_cdr_loops (core::pose::Pose &tcr_pose, protocols::loops::LoopsOP const &cdrloops)
	loop refine function for CDR loop More...
void	protocols::tcr::refine_all_cdr_loops (core::pose::Pose &tcr_pose, TCRseqInfo::tcrposi const &a_posi, TCRseqInfo::tcrposi const &b_posi)
	refine all cdr loops More...
void	protocols::tcr::refine_cdr3_loops (core::pose::Pose &tcr_pose, antibody::grafting::CDR_Bounds const &acdr3, antibody::grafting::CDR_Bounds const &bcdr3)
	loop refine function for CDR3 alpha and CDR3 beta loops More...
void	protocols::tcr::refine_cdr_loop (core::pose::Pose &tcr_pose, antibody::grafting::CDR_Bounds const &cdr)
	loop refine function for CDR alpha/beta loop More...
void	protocols::tcr::remodel_tcr_cdr_loops (core::pose::Pose &tcr_pose, protocols::loops::LoopsOP const &cdr3loops, bool refine)
	loop remodel function for CDR loop More...
void	protocols::tcr::ind_remodel_tcr_cdr_loops (core::pose::Pose &tcr_pose, core::Size const loopstart, core::Size const loopend)
	loop rebuild function More...

Detailed Description

modeling utility functions for protocols/tcr

Author

Ragul (ragul.nosp@m.@umd.nosp@m..edu)

Function Documentation

static basic::Tracer TR ( "protocols.tcr.modeling_util"  )

static