FragmentExtension.cc File Reference

#include <protocols/loop_grower/FragmentExtensionCreator.hh>
#include <protocols/loop_grower/FragmentExtension.hh>
#include <protocols/loop_grower/FragmentExtension.fwd.hh>
#include <protocols/loop_grower/LoopGrower.hh>
#include <fstream>
#include <iostream>
#include <protocols/hybridization/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <protocols/relax/util.hh>
#include <protocols/simple_moves/ReturnSidechainMover.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/symmetry/SetupNCSMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/comparative_modeling/coord_util.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loops.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/electron_density/ElectronDensity.hh>
#include <core/scoring/Energies.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SWAligner.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/selection.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/VariantType.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/id/AtomID.hh>
#include <core/pose/variant_util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/func/ScalarWeightedFunc.hh>
#include <core/scoring/func/SOGFunc.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/func/USOGFunc.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/conformation/util.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/pose/symmetry/util.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <protocols/symmetry/SetupForSymmetryMover.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/graph/Graph.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/WeightedSampler.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.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/citation_manager/CitationCollection.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <utility/tag/Tag.hh>
#include <utility/string_util.hh>
#include <basic/Tracer.hh>
#include <boost/unordered/unordered_map.hpp>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>

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

Functions
static basic::Tracer	protocols::loop_grower::TR ("protocols.loop_grower.FragmentExtension")
std::string	protocols::loop_grower::fragext_subelement_ct_name (std::string const &name)

Detailed Description

Author

Brandon Frenz

Frank DiMaio