RemodelLoopMover.cc File Reference

Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++. More...

#include <protocols/forge/remodel/RemodelData.hh>
#include <protocols/forge/remodel/RemodelLoopMover.hh>
#include <protocols/forge/remodel/RemodelGlobalFrame.hh>
#include <protocols/forge/methods/chainbreak_eval.hh>
#include <protocols/forge/methods/fold_tree_functions.hh>
#include <protocols/forge/methods/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/util.hh>
#include <core/io/pdb/file_data.hh>
#include <core/id/TorsionID.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/ConstantLengthFragSet.fwd.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/Frame.fwd.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/symmetry/SetupForSymmetryMover.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/methods/vall_lookback/VallLookbackPotential.hh>
#include <core/scoring/methods/vall_lookback/VallLookbackData.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/VariantType.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/sequence/ABEGOManager.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <basic/Tracer.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/simple_moves/GunnCost.hh>
#include <protocols/simple_moves/SmoothFragmentMover.hh>
#include <protocols/simple_moves/VallLookbackFragMover.hh>
#include <protocols/loops/loop_closure/ccd/CCDLoopClosureMover.hh>
#include <protocols/loops/loops_main.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/simple_moves/symmetry/SetupNCSMover.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/remodel.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/indexed_structure_store.OptionKeys.gen.hh>
#include <protocols/loophash/BackboneDB.hh>
#include <protocols/loophash/LoopHashLibrary.hh>
#include <protocols/loophash/LoopHashLibrary.fwd.hh>
#include <protocols/loophash/LoopHashMap.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/constraints/ResidueTypeLinkingConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <protocols/simple_moves/ConstraintSetMover.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <boost/format.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/foreach.hpp>
#include <algorithm>
#include <set>
#include <sstream>
#include <utility>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.hh>
#include <boost/lexical_cast.hpp>
#include <core/conformation/Conformation.hh>
#include <utility/string_util.hh>

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

Functions
static thread_local basic::Tracer	protocols::forge::remodel::TR ("protocols.forge.remodel.RemodelLoopMover")
bool	protocols::forge::remodel::fast_clash_check (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const check_atids, core::Real const clash_dist_cut)

Detailed Description

Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++.

Author

Possu Huang (possu.nosp@m.@u.w.nosp@m.ashin.nosp@m.gton.nosp@m..edu)

Yih-En Andrew Ban (yab@u.nosp@m..was.nosp@m.hingt.nosp@m.on.e.nosp@m.du)

Possu Huang (possu.nosp@m.@u.w.nosp@m.ashin.nosp@m.gton.nosp@m..edu)