loops → core Relation

File in src/protocols/loops	Includes file in src/core
loop_closure / ccd / ccd_closure.cc	pose / Pose.hh
loop_closure / ccd / ccd_closure.cc	conformation / Residue.hh
loop_closure / ccd / ccd_closure.cc	chemical / ResidueConnection.hh
loop_closure / ccd / ccd_closure.cc	kinematics / Stub.hh
loop_closure / ccd / ccd_closure.cc	types.hh
loop_closure / ccd / ccd_closure.hh	pose / Pose.fwd.hh
loop_closure / ccd / ccd_closure.hh	types.hh
loop_closure / ccd / CCDLoopClosureMover.cc	kinematics / MoveMap.hh
loop_closure / ccd / CCDLoopClosureMover.cc	pose / Pose.hh
loop_closure / ccd / CCDLoopClosureMover.cc	conformation / Residue.hh
loop_closure / ccd / CCDLoopClosureMover.cc	chemical / util.hh
loop_closure / ccd / CCDLoopClosureMover.cc	chemical / VariantType.hh
loop_closure / ccd / CCDLoopClosureMover.hh	kinematics / MoveMap.fwd.hh
loop_closure / ccd / CCDLoopClosureMover.hh	conformation / Residue.fwd.hh
loop_closure / ccd / CCDLoopClosureMover.hh	id / TorsionID.fwd.hh
loop_closure / ccd / CCDLoopClosureMover.hh	types.hh
FoldTreeFromLoopsWrapper.cc	kinematics / FoldTree.hh
FoldTreeFromLoopsWrapper.cc	pose / Pose.hh
loop_mover / IndependentLoopMover.cc	kinematics / FoldTree.hh
loop_mover / IndependentLoopMover.cc	pose / Pose.hh
loop_mover / IndependentLoopMover.cc	scoring / ScoreFunction.hh
loop_mover / IndependentLoopMover.hh	pose / Pose.fwd.hh
loop_mover / IndependentLoopMover.hh	types.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	kinematics / AtomTree.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	kinematics / FoldTree.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	kinematics / jacobian / JacobianStructure.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	kinematics / jacobian / ModuleType1.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	kinematics / MoveMap.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	pose / Pose.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	conformation / Residue.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	chemical / ResidueConnection.hh
loop_closure / jacobi / JacobiLoopClosureMover.cc	kinematics / jacobian / SeriesJacobians.hh
loop_closure / jacobi / JacobiLoopClosureMover.hh	chemical / AtomICoor.hh
loop_closure / jacobi / JacobiLoopClosureMover.hh	id / AtomID.hh
loop_closure / jacobi / JacobiLoopClosureMover.hh	kinematics / MoveMap.fwd.hh
loop_closure / jacobi / JacobiLoopClosureMover.hh	kinematics / RT.fwd.hh
loop_closure / jacobi / JacobiLoopClosureMover.hh	kinematics / jacobian / SeriesJacobians.fwd.hh
loop_closure / kinematic_closure / KinematicMover.cc	chemical / AtomType.hh
loop_closure / kinematic_closure / KinematicMover.cc	conformation / Conformation.hh
loop_closure / kinematic_closure / KinematicMover.cc	id / DOF_ID.hh
loop_closure / kinematic_closure / KinematicMover.cc	pose / Pose.hh
loop_closure / kinematic_closure / KinematicMover.cc	conformation / ppo_torsion_bin.hh
loop_closure / kinematic_closure / KinematicMover.cc	scoring / Ramachandran.hh
loop_closure / kinematic_closure / KinematicMover.cc	conformation / Residue.hh
loop_closure / kinematic_closure / KinematicMover.cc	conformation / ResidueFactory.hh
loop_closure / kinematic_closure / KinematicMover.cc	scoring / ScoreFunction.hh
loop_closure / kinematic_closure / KinematicMover.cc	scoring / ScoringManager.hh
loop_closure / kinematic_closure / KinematicMover.cc	id / TorsionID.hh
loop_closure / kinematic_closure / KinematicMover.cc	conformation / util.hh
loop_closure / kinematic_closure / KinematicMover.hh	chemical / AA.hh
loop_closure / kinematic_closure / KinematicMover.hh	conformation / ppo_torsion_bin.fwd.hh
loop_closure / kinematic_closure / KinematicMover.hh	conformation / Residue.fwd.hh
loop_closure / kinematic_closure / KinematicMover.hh	scoring / ScoreFunction.fwd.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	chemical / AA.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	kinematics / AtomTree.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	kinematics / MoveMap.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	pose / Pose.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	conformation / ppo_torsion_bin.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	scoring / Ramachandran.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	scoring / Ramachandran2B.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	conformation / Residue.hh
loop_closure / kinematic_closure / KinematicPerturber.cc	scoring / ScoringManager.hh
loop_closure / kinematic_closure / KinematicPerturber.hh	chemical / AA.hh
loop_closure / kinematic_closure / KinematicPerturber.hh	kinematics / MoveMap.fwd.hh
loop_closure / kinematic_closure / KinematicPerturber.hh	pose / Pose.fwd.hh
loop_closure / kinematic_closure / KinematicPerturber.hh	conformation / ppo_torsion_bin.hh
loop_closure / kinematic_closure / KinematicPerturber.hh	scoring / Ramachandran.fwd.hh
loop_closure / kinematic_closure / KinematicPerturber.hh	scoring / Ramachandran2B.fwd.hh
loop_closure / kinematic_closure / KinematicPerturber.hh	types.hh
loop_closure / kinematic_closure / KinematicWrapper.cc	kinematics / MoveMap.hh
loop_closure / kinematic_closure / KinematicWrapper.cc	types.hh
loop_closure / kinematic_closure / KinematicWrapper.hh	kinematics / MoveMap.fwd.hh
loop_closure / kinematic_closure / KinematicWrapper.hh	pose / Pose.fwd.hh
loop_closure / kinematic_closure / KinematicWrapper.hh	types.hh
Loop.cc	kinematics / MoveMap.hh
Loop.cc	pose / Pose.hh
Loop.cc	conformation / Residue.hh
Loop.fwd.hh	types.hh
Loop.hh	kinematics / MoveMap.fwd.hh
Loop.hh	pose / Pose.fwd.hh
Loop.hh	id / types.hh
Loop.hh	types.hh
loop_closure / ccd / LoopClosure.cc	fragment / BBTorsionSRFD.hh
loop_closure / ccd / LoopClosure.cc	fragment / FragData.hh
loop_closure / ccd / LoopClosure.cc	fragment / FragSet.hh
loop_closure / ccd / LoopClosure.cc	fragment / Frame.hh
loop_closure / ccd / LoopClosure.cc	kinematics / MoveMap.hh
loop_closure / ccd / LoopClosure.cc	pose / Pose.hh
loop_closure / ccd / LoopClosure.cc	scoring / ScoreFunction.hh
loop_closure / ccd / LoopClosure.hh	fragment / FragSet.fwd.hh
loop_closure / ccd / LoopClosure.hh	fragment / Frame.hh
loop_closure / ccd / LoopClosure.hh	kinematics / MoveMap.fwd.hh
loop_closure / ccd / LoopClosure.hh	pose / Pose.fwd.hh
loop_closure / ccd / LoopClosure.hh	scoring / ScoreFunction.fwd.hh
loop_closure / ccd / LoopClosure.hh	types.hh
loop_mover / LoopCM.cc	environment / DofPassport.hh
loop_mover / LoopCM.cc	environment / LocalPosition.hh
loop_mover / LoopCM.cc	kinematics / MoveMap.hh
loop_mover / LoopCM.cc	select / residue_selector / ResidueSelector.hh
loop_mover / LoopCM.hh	select / residue_selector / ResidueSelector.hh
loopfinder.cc	id / AtomID.hh
loopfinder.cc	conformation / Conformation.hh
loopfinder.cc	scoring / dssp / Dssp.hh
loopfinder.cc	pose / Pose.hh
loopfinder.cc	conformation / Residue.hh
loopfinder.hh	pose / Pose.fwd.hh
loop_mover / LoopMover.cc	pose / datacache / cacheable_observers.hh
loop_mover / LoopMover.cc	pose / datacache / CacheableObserverType.hh
loop_mover / LoopMover.cc	fragment / FragSet.hh
loop_mover / LoopMover.cc	kinematics / MoveMap.hh
loop_mover / LoopMover.cc	pose / datacache / ObserverCache.hh
loop_mover / LoopMover.cc	pose / Pose.hh
loop_mover / LoopMover.cc	conformation / ppo_torsion_bin.hh
loop_mover / LoopMover.cc	scoring / ScoreFunction.hh
loop_mover / LoopMover.hh	fragment / FragSet.fwd.hh
loop_mover / LoopMover.hh	kinematics / MoveMap.fwd.hh
loop_mover / LoopMover.hh	pose / Pose.fwd.hh
loop_mover / LoopMover.hh	conformation / ppo_torsion_bin.fwd.hh
loop_mover / LoopMover.hh	scoring / ScoreFunction.fwd.hh
loop_mover / LoopMover.hh	types.hh
loop_mover / refine / LoopMover_Backrub.cc	pack / pack_rotamers.hh
loop_mover / refine / LoopMover_Backrub.cc	pack / task / PackerTask.hh
loop_mover / refine / LoopMover_Backrub.cc	pose / Pose.hh
loop_mover / refine / LoopMover_Backrub.cc	conformation / Residue.hh
loop_mover / refine / LoopMover_Backrub.cc	scoring / ScoreFunction.hh
loop_mover / refine / LoopMover_Backrub.cc	scoring / ScoreFunctionFactory.hh
loop_mover / refine / LoopMover_Backrub.cc	pack / task / TaskFactory.hh
loop_mover / refine / LoopMover_Backrub.cc	pack / task / operation / TaskOperations.hh
loop_mover / refine / LoopMover_Backrub.cc	id / TorsionID.hh
loop_mover / refine / LoopMover_Backrub.hh	kinematics / MoveMap.fwd.hh
loop_mover / refine / LoopMover_Backrub.hh	pose / Pose.fwd.hh
loop_mover / refine / LoopMover_Backrub.hh	scoring / ScoreFunction.fwd.hh
loop_mover / refine / LoopMover_Backrub.hh	pack / task / TaskFactory.hh
loop_mover / refine / LoopMover_Backrub.hh	types.hh
loop_mover / refine / LoopMover_CCD.cc	optimization / AtomTreeMinimizer.hh
loop_mover / perturb / LoopMover_CCD.cc	optimization / AtomTreeMinimizer.hh
loop_mover / refine / LoopMover_CCD.cc	scoring / Energies.hh
loop_mover / perturb / LoopMover_CCD.cc	scoring / Energies.hh
loop_mover / refine / LoopMover_CCD.cc	kinematics / FoldTree.hh
loop_mover / perturb / LoopMover_CCD.cc	kinematics / FoldTree.hh
loop_mover / perturb / LoopMover_CCD.cc	fragment / FragSet.hh
loop_mover / perturb / LoopMover_CCD.cc	optimization / MinimizerOptions.hh
loop_mover / refine / LoopMover_CCD.cc	kinematics / MoveMap.hh
loop_mover / perturb / LoopMover_CCD.cc	kinematics / MoveMap.hh
loop_mover / refine / LoopMover_CCD.cc	select / movemap / MoveMapFactory.hh
loop_mover / refine / LoopMover_CCD.cc	pack / task / operation / NoRepackDisulfides.hh
loop_mover / refine / LoopMover_CCD.cc	pack / pack_rotamers.hh
loop_mover / refine / LoopMover_CCD.cc	pack / task / PackerTask.hh
loop_mover / refine / LoopMover_CCD.cc	pose / Pose.hh
loop_mover / perturb / LoopMover_CCD.cc	pose / Pose.hh
loop_mover / perturb / LoopMover_CCD.cc	conformation / Residue.hh
loop_mover / refine / LoopMover_CCD.cc	scoring / ScoreFunction.hh
loop_mover / perturb / LoopMover_CCD.cc	scoring / ScoreFunction.hh
loop_mover / refine / LoopMover_CCD.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
loop_mover / perturb / LoopMover_CCD.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
loop_mover / refine / LoopMover_CCD.cc	pack / task / TaskFactory.fwd.hh
loop_mover / perturb / LoopMover_CCD.cc	pack / task / TaskFactory.fwd.hh
loop_mover / refine / LoopMover_CCD.cc	pack / task / TaskFactory.hh
loop_mover / refine / LoopMover_CCD.cc	pack / task / operation / TaskOperations.hh
loop_mover / perturb / LoopMover_CCD.cc	id / TorsionID.hh
loop_mover / refine / LoopMover_CCD.cc	pose / util.hh
loop_mover / refine / LoopMover_CCD.cc	pose / symmetry / util.hh
loop_mover / perturb / LoopMover_CCD.cc	pose / symmetry / util.hh
loop_mover / perturb / LoopMover_CCD.cc	conformation / util.hh
loop_mover / perturb / LoopMover_CCD.cc	pose / variant_util.hh
loop_mover / perturb / LoopMover_CCD.cc	chemical / VariantType.hh
loop_mover / refine / LoopMover_CCD.hh	optimization / AtomTreeMinimizer.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	kinematics / FoldTree.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	fragment / FragSet.fwd.hh
loop_mover / perturb / LoopMover_CCD.hh	fragment / FragSet.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	optimization / MinimizerOptions.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	kinematics / MoveMap.fwd.hh
loop_mover / perturb / LoopMover_CCD.hh	kinematics / MoveMap.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	select / movemap / MoveMapFactory.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	pack / task / PackerTask.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	pose / Pose.fwd.hh
loop_mover / perturb / LoopMover_CCD.hh	pose / Pose.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	scoring / ScoreFunction.fwd.hh
loop_mover / perturb / LoopMover_CCD.hh	scoring / ScoreFunction.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	pack / task / TaskFactory.fwd.hh
loop_mover / perturb / LoopMover_CCD.hh	pack / task / TaskFactory.fwd.hh
loop_mover / refine / LoopMover_CCD.hh	types.hh
loop_mover / perturb / LoopMover_CCD.hh	types.hh
loop_mover / perturb / LoopMover_KIC.cc	scoring / Energies.hh
loop_mover / perturb / LoopMover_KIC.cc	kinematics / FoldTree.hh
loop_mover / refine / LoopMover_KIC.cc	kinematics / MoveMap.hh
loop_mover / perturb / LoopMover_KIC.cc	kinematics / MoveMap.hh
loop_mover / refine / LoopMover_KIC.cc	pack / pack_rotamers.hh
loop_mover / refine / LoopMover_KIC.cc	pack / task / PackerTask.hh
loop_mover / refine / LoopMover_KIC.cc	pose / Pose.hh
loop_mover / perturb / LoopMover_KIC.cc	pose / Pose.hh
loop_mover / refine / LoopMover_KIC.cc	conformation / ppo_torsion_bin.hh
loop_mover / refine / LoopMover_KIC.cc	conformation / Residue.hh
loop_mover / perturb / LoopMover_KIC.cc	conformation / Residue.hh
loop_mover / refine / LoopMover_KIC.cc	pack / rotamer_trials.hh
loop_mover / refine / LoopMover_KIC.cc	scoring / ScoreFunction.hh
loop_mover / perturb / LoopMover_KIC.cc	scoring / ScoreFunction.hh
loop_mover / refine / LoopMover_KIC.cc	pack / task / TaskFactory.hh
loop_mover / refine / LoopMover_KIC.cc	pack / task / operation / TaskOperations.hh
loop_mover / refine / LoopMover_KIC.cc	id / TorsionID.hh
loop_mover / perturb / LoopMover_KIC.cc	id / TorsionID.hh
loop_mover / refine / LoopMover_KIC.cc	pose / symmetry / util.hh
loop_mover / perturb / LoopMover_KIC.cc	pose / symmetry / util.hh
loop_mover / refine / LoopMover_KIC.cc	pose / variant_util.hh
loop_mover / perturb / LoopMover_KIC.cc	pose / variant_util.hh
loop_mover / refine / LoopMover_KIC.cc	chemical / VariantType.hh
loop_mover / perturb / LoopMover_KIC.cc	chemical / VariantType.hh
loop_mover / refine / LoopMover_KIC.hh	kinematics / MoveMap.fwd.hh
loop_mover / perturb / LoopMover_KIC.hh	kinematics / MoveMap.fwd.hh
loop_mover / refine / LoopMover_KIC.hh	pack / task / PackerTask.fwd.hh
loop_mover / perturb / LoopMover_KIC.hh	pack / task / PackerTask.fwd.hh
loop_mover / refine / LoopMover_KIC.hh	pose / Pose.fwd.hh
loop_mover / perturb / LoopMover_KIC.hh	pose / Pose.fwd.hh
loop_mover / refine / LoopMover_KIC.hh	scoring / ScoreFunction.fwd.hh
loop_mover / perturb / LoopMover_KIC.hh	scoring / ScoreFunction.fwd.hh
loop_mover / refine / LoopMover_KIC.hh	pack / task / TaskFactory.fwd.hh
loop_mover / perturb / LoopMover_KIC.hh	pack / task / TaskFactory.fwd.hh
loop_mover / refine / LoopMover_KIC.hh	types.hh
loop_mover / perturb / LoopMover_KIC.hh	types.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	optimization / AtomTreeMinimizer.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	scoring / constraints / ConstraintSet.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	scoring / Energies.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	kinematics / FoldTree.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	fragment / FragSet.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	optimization / MinimizerOptions.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	kinematics / MoveMap.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	pose / Pose.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	conformation / Residue.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	scoring / ScoreFunction.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	conformation / symmetry / SymmetricConformation.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	conformation / symmetry / SymmetryInfo.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	id / TorsionID.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	pose / symmetry / util.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	pose / variant_util.hh
loop_mover / perturb / LoopMover_QuickCCD.cc	chemical / VariantType.hh
loop_mover / perturb / LoopMover_QuickCCD.hh	fragment / FragSet.fwd.hh
loop_mover / perturb / LoopMover_QuickCCD.hh	kinematics / MoveMap.fwd.hh
loop_mover / perturb / LoopMover_QuickCCD.hh	pose / Pose.fwd.hh
loop_mover / perturb / LoopMover_QuickCCD.hh	scoring / ScoreFunction.fwd.hh
loop_mover / perturb / LoopMover_QuickCCD.hh	types.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	optimization / AtomTreeMinimizer.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	conformation / Conformation.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	scoring / constraints / ConstraintSet.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	scoring / Energies.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	kinematics / FoldTree.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	fragment / FragSet.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	optimization / MinimizerOptions.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	kinematics / MoveMap.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	pose / Pose.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	conformation / Residue.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	scoring / ScoreFunction.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	conformation / symmetry / SymmetricConformation.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	conformation / symmetry / SymmetryInfo.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	id / TorsionID.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	pose / symmetry / util.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	pose / variant_util.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.cc	chemical / VariantType.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.hh	kinematics / MoveMap.fwd.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.hh	pose / Pose.fwd.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.hh	scoring / ScoreFunction.fwd.hh
loop_mover / perturb / LoopMover_QuickCCD_Moves.hh	types.hh
loop_mover / perturb / LoopMover_QuickCCD_MovesCreator.hh	types.hh
LoopMoverFactory.hh	pose / Pose.fwd.hh
loop_mover / refine / LoopRefineInnerCycle.cc	kinematics / MoveMap.hh
loop_mover / refine / LoopRefineInnerCycle.cc	pose / Pose.hh
loop_mover / refine / LoopRefineInnerCycle.cc	scoring / ScoreFunction.hh
loop_mover / refine / LoopRefineInnerCycle.cc	pack / task / TaskFactory.hh
loop_mover / refine / LoopRefineInnerCycle.hh	kinematics / MoveMap.fwd.hh
loop_mover / refine / LoopRefineInnerCycle.hh	scoring / ScoreFunction.fwd.hh
loop_mover / refine / LoopRefineInnerCycle.hh	pack / task / TaskFactory.fwd.hh
loop_mover / refine / LoopRefineInnerCycleContainer.cc	pose / Pose.hh
loop_mover / refine / LoopRefineInnerCycleContainer.cc	scoring / ScoreFunction.hh
loop_mover / refine / LoopRefineInnerCycleContainer.cc	pack / task / TaskFactory.hh
loop_mover / refine / LoopRefineInnerCycleFactory.cc	scoring / ScoreFunction.hh
loop_mover / refine / LoopRefineInnerCycleFactory.cc	pack / task / TaskFactory.hh
loop_mover / refine / LoopRefineInnerCycleFactory.hh	scoring / ScoreFunction.fwd.hh
loop_mover / refine / LoopRefineInnerCycleFactory.hh	pack / task / TaskFactory.fwd.hh
looprelax_protocols.cc	id / AtomID.hh
looprelax_protocols.cc	optimization / AtomTreeMinimizer.hh
looprelax_protocols.cc	conformation / Conformation.hh
looprelax_protocols.cc	scoring / constraints / ConstraintSet.hh
looprelax_protocols.cc	scoring / constraints / CoordinateConstraint.hh
looprelax_protocols.cc	scoring / Energies.fwd.hh
looprelax_protocols.cc	scoring / Energies.hh
looprelax_protocols.cc	scoring / EnergyMap.hh
looprelax_protocols.cc	kinematics / FoldTree.hh
looprelax_protocols.cc	fragment / FragSet.hh
looprelax_protocols.cc	scoring / func / Func.hh
looprelax_protocols.cc	scoring / func / HarmonicFunc.hh
looprelax_protocols.cc	optimization / MinimizerOptions.hh
looprelax_protocols.cc	kinematics / MoveMap.fwd.hh
looprelax_protocols.cc	kinematics / MoveMap.hh
looprelax_protocols.cc	pack / task / PackerTask.hh
looprelax_protocols.cc	pose / Pose.hh
looprelax_protocols.cc	chemical / ResidueType.hh
looprelax_protocols.cc	scoring / ScoreFunction.hh
looprelax_protocols.cc	pack / task / TaskFactory.hh
looprelax_protocols.cc	types.hh
looprelax_protocols.cc	pose / variant_util.hh
looprelax_protocols.cc	chemical / VariantType.hh
looprelax_protocols.hh	fragment / FragSet.fwd.hh
looprelax_protocols.hh	pose / Pose.fwd.hh
looprelax_protocols.hh	scoring / ScoreFunction.fwd.hh
looprelax_protocols.hh	types.hh
Loops.cc	kinematics / FoldTree.hh
Loops.cc	id / NamedAtomID.hh
Loops.cc	pose / Pose.hh
Loops.cc	types.hh
Loops.hh	kinematics / MoveMap.fwd.hh
Loops.hh	pose / Pose.fwd.hh
Loops.hh	id / types.hh
Loops.hh	types.hh
loops_main.cc	fragment / BBTorsionSRFD.hh
loops_main.cc	conformation / Conformation.hh
loops_main.cc	fragment / ConstantLengthFragSet.hh
loops_main.cc	scoring / constraints / ConstraintSet.hh
loops_main.cc	scoring / Energies.hh
loops_main.cc	pose / extra_pose_info_util.hh
loops_main.cc	kinematics / FoldTree.hh
loops_main.cc	fragment / FragData.hh
loops_main.cc	fragment / FragmentIO.hh
loops_main.cc	import_pose / import_pose.hh
loops_main.cc	kinematics / MoveMap.hh
loops_main.cc	pose / Pose.hh
loops_main.cc	conformation / ResidueFactory.hh
loops_main.cc	chemical / ResidueTypeSet.hh
loops_main.cc	scoring / rms_util.hh
loops_main.cc	id / SequenceMapping.hh
loops_main.cc	scoring / TenANeighborGraph.hh
loops_main.cc	id / TorsionID.hh
loops_main.cc	types.hh
loops_main.cc	select / util.hh
loops_main.cc	pose / symmetry / util.hh
loops_main.cc	fragment / util.hh
loops_main.cc	conformation / util.hh
loops_main.cc	conformation / symmetry / util.hh
loops_main.cc	pose / util.tmpl.hh
loops_main.cc	pose / variant_util.hh
loops_main.cc	chemical / VariantType.hh
loops_main.hh	kinematics / FoldTree.fwd.hh
loops_main.hh	fragment / FragSet.fwd.hh
loops_main.hh	kinematics / MoveMap.fwd.hh
loops_main.hh	pose / Pose.fwd.hh
loops_main.hh	id / SequenceMapping.fwd.hh
loops_main.hh	types.hh
loops_definers / LoopsDatabaseDefiner.hh	pose / Pose.fwd.hh
loops_definers / LoopsDatabaseDefinerCreator.hh	types.hh
loops_definers / LoopsDefiner.hh	pose / Pose.fwd.hh
loops_definers / LoopsDefinerCreator.hh	types.hh
loops_definers / LoopsDefinerFactory.hh	pose / Pose.fwd.hh
loops_definers / LoopsDefinerLoader.cc	pose / Pose.hh
loops_definers / LoopsExplicitDefiner.cc	pose / Pose.hh
loops_definers / LoopsExplicitDefiner.hh	pose / Pose.fwd.hh
loops_definers / LoopsExplicitDefinerCreator.hh	types.hh
loops_definers / LoopsFileDefiner.hh	pose / Pose.fwd.hh
loops_definers / LoopsFileDefinerCreator.hh	types.hh
LoopsFileFallbackConfiguration.cc	types.hh
LoopsFileIO.cc	pose / PDBInfo.hh
LoopsFileIO.cc	pose / Pose.hh
LoopsFileIO.hh	pose / Pose.fwd.hh
LoopsFileIO.hh	pose / ResidueIndexDescription.hh
loops_definers / LoopsStringDefiner.cc	pose / Pose.hh
loops_definers / LoopsStringDefiner.hh	pose / Pose.fwd.hh
loops_definers / LoopsStringDefinerCreator.hh	types.hh
make_loops.cc	chemical / AA.hh
make_loops.cc	conformation / Conformation.hh
make_loops.cc	pose / PDBInfo.hh
make_loops.cc	pose / Pose.hh
make_loops.hh	pose / Pose.fwd.hh
make_loops.hh	types.hh
loop_closure / ccd / RamaCheck.cc	pose / Pose.hh
loop_closure / ccd / RamaCheck.cc	scoring / Ramachandran.hh
loop_closure / ccd / RamaCheck.cc	scoring / Ramachandran2B.hh
loop_closure / ccd / RamaCheck.cc	conformation / Residue.hh
loop_closure / ccd / RamaCheck.cc	scoring / ScoringManager.hh
loop_closure / ccd / RamaCheck.cc	id / TorsionID.hh
loop_closure / ccd / RamaCheck.hh	pose / Pose.fwd.hh
loop_closure / ccd / RamaCheck.hh	scoring / Ramachandran.fwd.hh
loop_closure / ccd / RamaCheck.hh	scoring / Ramachandran2B.fwd.hh
loop_closure / ccd / RamaCheck.hh	id / TorsionID.fwd.hh
loop_closure / ccd / RamaCheck.hh	types.hh
loop_mover / refine / RepackTrial.cc	pack / pack_rotamers.hh
loop_mover / refine / RepackTrial.cc	pack / task / PackerTask.hh
loop_mover / refine / RepackTrial.cc	scoring / ScoreFunction.hh
loop_mover / refine / RepackTrial.cc	pack / task / TaskFactory.hh
loop_mover / refine / RepackTrial.hh	optimization / AtomTreeMinimizer.fwd.hh
loop_mover / refine / RepackTrial.hh	pack / task / PackerTask.fwd.hh
loop_mover / refine / ShearMinCCDTrial.cc	optimization / AtomTreeMinimizer.hh
loop_mover / refine / ShearMinCCDTrial.cc	optimization / Minimizer.hh
loop_mover / refine / ShearMinCCDTrial.cc	kinematics / MoveMap.hh
loop_mover / refine / ShearMinCCDTrial.cc	pose / Pose.hh
loop_mover / refine / ShearMinCCDTrial.cc	pack / rotamer_trials.hh
loop_mover / refine / ShearMinCCDTrial.cc	scoring / ScoreFunction.hh
loop_mover / refine / ShearMinCCDTrial.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
loop_mover / refine / ShearMinCCDTrial.cc	pack / task / TaskFactory.hh
loop_mover / refine / ShearMinCCDTrial.cc	pose / symmetry / util.hh
loop_mover / refine / ShearMinCCDTrial.hh	optimization / AtomTreeMinimizer.fwd.hh
loop_mover / refine / ShearMinCCDTrial.hh	optimization / MinimizerOptions.fwd.hh
loop_closure / ccd / ShortLoopClosure.cc	pose / annotated_sequence.hh
loop_closure / ccd / ShortLoopClosure.cc	chemical / ChemicalManager.hh
loop_closure / ccd / ShortLoopClosure.cc	kinematics / FoldTree.hh
loop_closure / ccd / ShortLoopClosure.cc	fragment / FragSet.hh
loop_closure / ccd / ShortLoopClosure.cc	fragment / Frame.hh
loop_closure / ccd / ShortLoopClosure.cc	fragment / FrameList.hh
loop_closure / ccd / ShortLoopClosure.cc	kinematics / MoveMap.hh
loop_closure / ccd / ShortLoopClosure.cc	pose / Pose.hh
loop_closure / ccd / ShortLoopClosure.cc	scoring / ScoreFunction.hh
loop_closure / ccd / ShortLoopClosure.cc	scoring / ScoreType.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / BBTorsionSRFD.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	scoring / Energies.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	pose / extra_pose_info_util.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	kinematics / FoldTree.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / FragCache.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / FragData.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / FragSet.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / Frame.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / FrameIterator.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / FrameIteratorWorker_.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / FrameList.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	kinematics / MoveMap.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	pose / Pose.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	scoring / rms_util.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	scoring / ScoreFunction.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	scoring / ScoreFunctionFactory.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	fragment / SecondaryStructure.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	io / silent / SilentFileData.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	io / silent / SilentFileOptions.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	io / silent / SilentStruct.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	io / silent / SilentStructFactory.hh
loop_closure / ccd / SlidingWindowLoopClosure.cc	pose / util.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	fragment / FragID.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	fragment / FragSet.fwd.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	kinematics / MoveMap.fwd.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	fragment / OrderedFragSet.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	pose / Pose.fwd.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	scoring / ScoreFunction.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	fragment / SecondaryStructure.hh
loop_closure / ccd / SlidingWindowLoopClosure.hh	types.hh
loop_mover / refine / SmallMinCCDTrial.cc	optimization / AtomTreeMinimizer.hh
loop_mover / refine / SmallMinCCDTrial.cc	scoring / Energies.hh
loop_mover / refine / SmallMinCCDTrial.cc	optimization / MinimizerOptions.hh
loop_mover / refine / SmallMinCCDTrial.cc	kinematics / MoveMap.hh
loop_mover / refine / SmallMinCCDTrial.cc	pack / task / PackerTask.hh
loop_mover / refine / SmallMinCCDTrial.cc	pose / Pose.hh
loop_mover / refine / SmallMinCCDTrial.cc	pack / rotamer_trials.hh
loop_mover / refine / SmallMinCCDTrial.cc	scoring / ScoreFunction.hh
loop_mover / refine / SmallMinCCDTrial.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
loop_mover / refine / SmallMinCCDTrial.cc	pack / task / TaskFactory.hh
loop_mover / refine / SmallMinCCDTrial.cc	pose / symmetry / util.hh
loop_mover / refine / SmallMinCCDTrial.hh	optimization / AtomTreeMinimizer.fwd.hh
loop_mover / refine / SmallMinCCDTrial.hh	optimization / MinimizerOptions.fwd.hh
loop_mover / refine / SmallMinCCDTrial.hh	pack / task / PackerTask.fwd.hh
util.cc	id / AtomID.hh
util.cc	id / AtomID_Map.hh
util.cc	scoring / constraints / CoordinateConstraint.hh
util.cc	pose / extra_pose_info_util.hh
util.cc	kinematics / FoldTree.hh
util.cc	fragment / FragSet.hh
util.cc	fragment / Frame.hh
util.cc	fragment / FrameList.hh
util.cc	scoring / func / HarmonicFunc.hh
util.cc	kinematics / MoveMap.hh
util.cc	pose / PDBInfo.hh
loops_definers / util.cc	pose / Pose.hh
util.cc	pose / Pose.hh
util.cc	conformation / Residue.hh
util.cc	conformation / ResidueFactory.hh
util.cc	chemical / ResidueType.hh
util.cc	chemical / ResidueTypeSet.hh
util.cc	scoring / rms_util.hh
util.cc	scoring / ScoreFunction.hh
util.cc	scoring / ScoreFunctionFactory.hh
util.cc	fragment / SecondaryStructure.hh
util.cc	pose / selection.hh
util.cc	conformation / symmetry / SymmetricConformation.hh
util.cc	conformation / symmetry / SymmetryInfo.hh
util.cc	pose / util.hh
util.cc	conformation / util.hh
util.cc	pose / symmetry / util.hh
util.cc	pose / util.tmpl.hh
util.hh	fragment / FragSet.fwd.hh
loops_definers / util.hh	pose / Pose.fwd.hh
util.hh	pose / Pose.fwd.hh
util.hh	scoring / ScoreFunction.fwd.hh
util.hh	fragment / SecondaryStructure.fwd.hh
util.hh	types.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	fragment / BBTorsionSRFD.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	kinematics / FoldTree.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	fragment / FragData.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	fragment / FragSet.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	fragment / Frame.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	fragment / FrameList.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	kinematics / MoveMap.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	pose / Pose.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.cc	scoring / ScoreFunction.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.hh	fragment / FragSet.fwd.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.hh	kinematics / MoveMap.fwd.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.hh	fragment / OrderedFragSet.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.hh	pose / Pose.fwd.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.hh	scoring / ScoreFunction.fwd.hh
loop_closure / ccd / WidthFirstSlidingWindowLoopClosure.hh	types.hh