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GlycopeptideDockingHighResRefinement.cc File Reference
#include <protocols/glycopeptide_docking/GlycopeptideDockingHighResRefinement.hh>
#include <protocols/glycopeptide_docking/GlycopeptideDockingFlags.hh>
#include <protocols/glycopeptide_docking/utils.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/simple_task_operations/RestrictToInterface.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/docking/DockingInitialPerturbation.hh>
#include <protocols/docking/util.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/task_operations/RestrictResiduesToRepackingOperation.hh>
#include <protocols/moves/TrialMover.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreType.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/pack/task/operation/OperateOnResidueSubset.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/select/residue_selector/ResidueSpanSelector.hh>
#include <core/select/residue_selector/NotResidueSelector.hh>
#include <core/select/residue_selector/GlycanResidueSelector.hh>
#include <numeric/random/random.hh>
#include <numeric/xyzVector.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/carbohydrates.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <utility/tag/Tag.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>
#include <string>
#include <list>
#include <cmath>

Namespaces

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

Functions

static basic::Tracer TR ("protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement")
 
std::ostream & protocols::glycopeptide_docking::operator<< (std::ostream &os, GlycopeptideDockingHighResRefinement const &mover)
 

Detailed Description

High resolution refinement of glycosyltransferase peptide/glycopeptide substrate complex. This protocol applies MCM sampling in torsional and rigid body space with sidechain repacking of the substrate and substrate-enzyme interface. The attractive and repulsive terms are ramped down and up respectively to allow softer potential at the beginning of the run. Protocol similar to high resolution refinement of flexpepdock.

Author
Yashes Srinivasan (yashe.nosp@m.ss@g.nosp@m.mail..nosp@m.com), Sai Pooja Mahajan (saipo.nosp@m.oja@.nosp@m.gmail.nosp@m..com)

Function Documentation

static basic::Tracer TR ( "protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement"  )
static