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GlycopeptideDockingLowResRefinement.cc File Reference
#include <protocols/glycopeptide_docking/GlycopeptideDockingLowResRefinement.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/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/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/task_operations/RestrictResiduesToRepackingOperation.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/PyMOLMover.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/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.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.GlycopeptideDockingLowResRefinement")
 
std::ostream & protocols::glycopeptide_docking::operator<< (std::ostream &os, GlycopeptideDockingLowResRefinement const &mover)
 

Detailed Description

Low resolution refinement of glycosyltransferase peptide/glycopeptide substrate complex. This protocol allows enhanced sampling of the peptide/glycopeptide dofs in the low resolution mode with simulated annealing. Current protocol was only tested for monosaccharides. It does not treat the glycan-branch in a special manner. This behavior will change as the protocol is developed in future versions for higher glycans. Protocol similar to low 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.GlycopeptideDockingLowResRefinement"  )
static