FoldTreeHybridize.cc File Reference

Align a random jump to template. More...

#include <protocols/hybridization/FoldTreeHybridize.hh>
#include <protocols/hybridization/ChunkTrialMover.hh>
#include <protocols/hybridization/HybridizeFoldtreeDynamic.hh>
#include <protocols/hybridization/util.hh>
#include <protocols/hybridization/AllResiduesChanged.hh>
#include <protocols/hybridization/DomainAssembly.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/chemical/ResidueProperties.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/util/kinematics_util.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/fragment/util.hh>
#include <core/pose/symmetry/util.hh>
#include <protocols/simple_moves/symmetry/SymPackRotamersMover.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/simple_moves/rational_mc/RationalMonteCarlo.hh>
#include <protocols/simple_moves/MutateResidue.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/simple_moves/GunnCost.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/moves/WhileMover.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/util.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/model_quality/maxsub.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/rigid.OptionKeys.gen.hh>
#include <basic/options/keys/jumps.OptionKeys.gen.hh>
#include <basic/options/keys/evaluation.OptionKeys.gen.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/random/DistributionSampler.hh>
#include <numeric/util.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <utility/tag/Tag.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <protocols/jumping/JumpSetup.hh>
#include <protocols/simple_moves/ExtendedPoseMover.hh>
#include <protocols/jumping/SheetBuilder.hh>
#include <protocols/jumping/RandomSheetBuilder.hh>
#include <core/scoring/dssp/StrandPairing.hh>
#include <core/scoring/rms_util.hh>
#include <boost/math/distributions/poisson.hpp>
#include <set>
#include <list>

Classes
class	protocols::hybridization::hConvergenceCheck

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

Typedefs
typedef utility::pointer::shared_ptr < hConvergenceCheck >	protocols::hybridization::hConvergenceCheckOP

Functions
static thread_local basic::Tracer	TR ("protocols.hybridization.FoldTreeHybridize")

Detailed Description

Align a random jump to template.

Author

Yifan Song, David Kim

Function Documentation

static thread_local basic::Tracer TR ( "protocols.hybridization.FoldTreeHybridize"  )

static