stepwise → core Relation

File in src/protocols/stepwise	Includes file in src/core
monte_carlo / mover / AddMover.cc	kinematics / FoldTree.hh
monte_carlo / mover / AddMover.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / AddMover.cc	kinematics / Jump.hh
monte_carlo / mover / AddMover.cc	pose / Pose.hh
monte_carlo / mover / AddMover.cc	conformation / ResidueFactory.hh
monte_carlo / mover / AddMover.cc	chemical / ResidueTypeSet.hh
monte_carlo / mover / AddMover.cc	scoring / ScoreFunction.hh
monte_carlo / mover / AddMover.cc	types.hh
monte_carlo / mover / AddMover.cc	pose / full_model_info / util.hh
monte_carlo / mover / AddMover.cc	chemical / rna / util.hh
monte_carlo / mover / AddMover.cc	pose / variant_util.hh
monte_carlo / mover / AddMover.cc	chemical / VariantType.hh
monte_carlo / mover / AddMover.hh	pose / Pose.fwd.hh
monte_carlo / mover / AddMover.hh	conformation / Residue.fwd.hh
monte_carlo / mover / AddMover.hh	chemical / ResidueTypeSet.fwd.hh
monte_carlo / mover / AddMover.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / mover / AddMover.hh	types.hh
monte_carlo / mover / AddOrDeleteMover.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / AddOrDeleteMover.cc	pose / Pose.hh
monte_carlo / mover / AddOrDeleteMover.cc	types.hh
monte_carlo / mover / AddOrDeleteMover.cc	pose / util.hh
monte_carlo / mover / AddOrDeleteMover.cc	pose / full_model_info / util.hh
monte_carlo / mover / AddOrDeleteMover.cc	chemical / VariantType.hh
monte_carlo / mover / AddOrDeleteMover.hh	pose / Pose.fwd.hh
monte_carlo / mover / AddOrDeleteMover.hh	types.hh
screener / AlignRMSD_Screener.cc	pose / Pose.hh
screener / AlignRMSD_Screener.hh	pose / Pose.fwd.hh
screener / AlignRMSD_Screener.hh	types.hh
screener / AnchorSugarScreener.cc	pose / extra_pose_info_util.hh
screener / AnchorSugarScreener.cc	pose / Pose.hh
screener / AnchorSugarScreener.hh	pose / Pose.fwd.hh
screener / AnchorSugarScreener.hh	types.hh
screener / BaseCentroidScreener.cc	pose / Pose.hh
screener / BaseCentroidScreener.cc	kinematics / Stub.hh
screener / BaseCentroidScreener.hh	pose / Pose.fwd.hh
screener / BaseCentroidScreener.hh	kinematics / Stub.fwd.hh
modeler / rna / bulge / BulgeApplyMover.cc	pose / Pose.hh
modeler / rna / bulge / BulgeApplyMover.cc	scoring / constraints / util.hh
modeler / rna / bulge / BulgeApplyMover.cc	pose / rna / util.hh
modeler / rna / bulge / BulgeUnApplyMover.cc	pose / Pose.hh
modeler / rna / bulge / BulgeUnApplyMover.cc	scoring / constraints / util.hh
modeler / rna / bulge / BulgeUnApplyMover.cc	pose / rna / util.hh
screener / CentroidDistanceScreener.cc	pose / Pose.hh
screener / CentroidDistanceScreener.cc	chemical / rna / util.hh
screener / CentroidDistanceScreener.hh	pose / Pose.fwd.hh
screener / CentroidDistanceScreener.hh	types.hh
modeler / constraint_util.cc	scoring / constraints / Constraint.hh
modeler / constraint_util.cc	scoring / constraints / ConstraintIO.hh
modeler / constraint_util.cc	scoring / constraints / ConstraintSet.hh
modeler / constraint_util.cc	scoring / constraints / CoordinateConstraint.hh
modeler / constraint_util.cc	pose / Pose.hh
modeler / constraint_util.cc	scoring / ScoreFunction.hh
modeler / constraint_util.cc	id / SequenceMapping.hh
modeler / constraint_util.cc	pose / util.hh
modeler / constraint_util.cc	scoring / constraints / util.hh
modeler / constraint_util.hh	scoring / constraints / ConstraintSet.fwd.hh
modeler / constraint_util.hh	pose / Pose.fwd.hh
modeler / constraint_util.hh	scoring / ScoreFunction.fwd.hh
modeler / constraint_util.hh	types.hh
sampler / copy_dofs / CopyDofStepWiseSampler.cc	pose / Pose.hh
sampler / copy_dofs / CopyDofStepWiseSampler.hh	pose / Pose.hh
monte_carlo / mover / DeleteMover.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / DeleteMover.cc	pose / Pose.hh
monte_carlo / mover / DeleteMover.cc	conformation / Residue.hh
monte_carlo / mover / DeleteMover.cc	conformation / ResidueFactory.hh
monte_carlo / mover / DeleteMover.cc	chemical / ResidueTypeSet.hh
monte_carlo / mover / DeleteMover.cc	scoring / ScoreFunction.hh
monte_carlo / mover / DeleteMover.cc	pose / full_model_info / SubMotifInfo.hh
monte_carlo / mover / DeleteMover.cc	types.hh
monte_carlo / mover / DeleteMover.cc	pose / full_model_info / util.hh
monte_carlo / mover / DeleteMover.cc	pose / util.hh
monte_carlo / mover / DeleteMover.cc	chemical / VariantType.hh
monte_carlo / mover / DeleteMover.hh	pose / Pose.fwd.hh
monte_carlo / mover / DeleteMover.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / mover / DeleteMover.hh	types.hh
sampler / rigid_body / EulerAngles.hh	types.hh
modeler / rna / rigid_body / FloatingBaseClasses.hh	types.hh
monte_carlo / mover / FromScratchMover.cc	pose / annotated_sequence.hh
monte_carlo / mover / FromScratchMover.cc	chemical / ChemicalManager.hh
monte_carlo / mover / FromScratchMover.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / FromScratchMover.cc	pose / Pose.hh
monte_carlo / mover / FromScratchMover.cc	pose / full_model_info / util.hh
monte_carlo / mover / FromScratchMover.cc	chemical / util.hh
monte_carlo / mover / FromScratchMover.cc	pose / util.hh
monte_carlo / mover / FromScratchMover.hh	pose / Pose.fwd.hh
monte_carlo / mover / FromScratchMover.hh	types.hh
modeler / protein / InputStreamWithResidueInfo.cc	import_pose / pose_stream / ExtendedPoseInputStream.hh
modeler / protein / InputStreamWithResidueInfo.cc	import_pose / pose_stream / PDBPoseInputStream.hh
modeler / protein / InputStreamWithResidueInfo.cc	pose / Pose.hh
modeler / protein / InputStreamWithResidueInfo.cc	import_pose / pose_stream / PoseInputStream.fwd.hh
modeler / protein / InputStreamWithResidueInfo.cc	chemical / ResidueType.hh
modeler / protein / InputStreamWithResidueInfo.cc	scoring / rms_util.hh
modeler / protein / InputStreamWithResidueInfo.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
modeler / protein / InputStreamWithResidueInfo.cc	types.hh
modeler / protein / InputStreamWithResidueInfo.cc	pose / copydofs / util.hh
modeler / protein / InputStreamWithResidueInfo.cc	pose / rna / util.hh
modeler / protein / InputStreamWithResidueInfo.cc	pose / variant_util.hh
modeler / protein / InputStreamWithResidueInfo.hh	pose / Pose.fwd.hh
modeler / protein / InputStreamWithResidueInfo.hh	import_pose / pose_stream / PoseInputStream.fwd.hh
modeler / protein / InputStreamWithResidueInfo.hh	chemical / ResidueTypeSet.fwd.hh
modeler / protein / InputStreamWithResidueInfo.hh	types.hh
sampler / jump / JumpStepWiseSampler.cc	pose / Pose.hh
sampler / jump / JumpStepWiseSampler.hh	kinematics / Jump.hh
sampler / jump / JumpStepWiseSampler.hh	types.hh
modeler / protein / MainChainTorsionSet.cc	io / silent / BinarySilentStruct.hh
modeler / protein / MainChainTorsionSet.cc	types.hh
modeler / protein / MainChainTorsionSet.hh	types.hh
modeler / rna / phosphate / MultiPhosphateSampler.cc	kinematics / FoldTree.hh
modeler / rna / phosphate / MultiPhosphateSampler.cc	pose / full_model_info / FullModelInfo.hh
modeler / rna / phosphate / MultiPhosphateSampler.cc	pose / Pose.hh
modeler / rna / phosphate / MultiPhosphateSampler.cc	conformation / Residue.hh
modeler / rna / phosphate / MultiPhosphateSampler.cc	scoring / ScoreFunction.hh
modeler / rna / phosphate / MultiPhosphateSampler.cc	id / TorsionID.hh
modeler / rna / phosphate / MultiPhosphateSampler.cc	chemical / rna / util.hh
modeler / rna / phosphate / MultiPhosphateSampler.hh	pose / Pose.fwd.hh
modeler / rna / phosphate / MultiPhosphateSampler.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / phosphate / MultiPhosphateSampler.hh	types.hh
modeler / rna / o2prime / O2PrimePacker.cc	pack / task / PackerTask.hh
modeler / rna / o2prime / O2PrimePacker.cc	pack / rotamer_trials.hh
modeler / rna / o2prime / O2PrimePacker.cc	scoring / ScoreFunction.hh
modeler / rna / o2prime / O2PrimePacker.cc	pack / task / TaskFactory.hh
modeler / rna / o2prime / O2PrimePacker.cc	pack / task / operation / TaskOperations.hh
modeler / rna / o2prime / O2PrimePacker.hh	pack / task / PackerTask.fwd.hh
modeler / rna / o2prime / O2PrimePacker.hh	pose / Pose.hh
modeler / rna / o2prime / O2PrimePacker.hh	scoring / ScoreFunction.fwd.hh
modeler / output_util.cc	kinematics / FoldTree.hh
modeler / output_util.cc	kinematics / MoveMap.hh
modeler / output_util.cc	pose / Pose.hh
modeler / output_util.cc	chemical / ResidueType.hh
modeler / output_util.hh	kinematics / MoveMap.fwd.hh
modeler / output_util.hh	pose / Pose.fwd.hh
modeler / output_util.hh	types.hh
screener / PackScreener.cc	pose / Pose.hh
screener / PackScreener.hh	pose / Pose.fwd.hh
screener / PartitionContactScreener.cc	scoring / etable / count_pair / CountPairFactory.hh
screener / PartitionContactScreener.cc	scoring / etable / count_pair / CountPairFunction.hh
screener / PartitionContactScreener.cc	scoring / methods / EnergyMethodOptions.hh
screener / PartitionContactScreener.cc	scoring / etable / Etable.hh
screener / PartitionContactScreener.cc	scoring / etable / EtableEnergy.hh
screener / PartitionContactScreener.cc	pose / Pose.hh
screener / PartitionContactScreener.cc	conformation / Residue.hh
screener / PartitionContactScreener.cc	scoring / ScoringManager.hh
screener / PartitionContactScreener.hh	scoring / methods / EnergyMethodOptions.fwd.hh
screener / PartitionContactScreener.hh	scoring / etable / EtableEnergy.fwd.hh
screener / PartitionContactScreener.hh	pose / Pose.fwd.hh
screener / PartitionContactScreener.hh	types.hh
modeler / rna / phosphate / PhosphateMove.hh	types.hh
modeler / rna / phosphate / PhosphateMover.cc	chemical / AtomType.hh
modeler / rna / phosphate / PhosphateMover.cc	scoring / Energies.hh
modeler / rna / phosphate / PhosphateMover.cc	kinematics / FoldTree.hh
modeler / rna / phosphate / PhosphateMover.cc	pose / Pose.hh
modeler / rna / phosphate / PhosphateMover.cc	conformation / ResidueFactory.hh
modeler / rna / phosphate / PhosphateMover.cc	chemical / ResidueType.hh
modeler / rna / phosphate / PhosphateMover.cc	chemical / rna / RNA_Info.hh
modeler / rna / phosphate / PhosphateMover.cc	chemical / rna / RNA_SamplerUtil.hh
modeler / rna / phosphate / PhosphateMover.cc	scoring / ScoreFunction.hh
modeler / rna / phosphate / PhosphateMover.cc	id / TorsionID.hh
modeler / rna / phosphate / PhosphateMover.cc	chemical / rna / util.hh
modeler / rna / phosphate / PhosphateMover.cc	pose / rna / util.hh
modeler / rna / phosphate / PhosphateMover.cc	pose / variant_util.hh
modeler / rna / phosphate / PhosphateMover.hh	pose / Pose.fwd.hh
modeler / rna / phosphate / PhosphateMover.hh	chemical / rna / RNA_FittedTorsionInfo.hh
modeler / rna / phosphate / PhosphateMover.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / phosphate / PhosphateMover.hh	types.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	id / AtomID.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	scoring / hbonds / HBondDatabase.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	scoring / hbonds / HBondOptions.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	scoring / hbonds / hbonds_geom.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	id / NamedAtomID.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	pose / PDBInfo.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	conformation / Residue.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	conformation / ResidueFactory.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	chemical / ResidueType.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	chemical / rna / RNA_Info.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	kinematics / Stub.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	scoring / hbonds / types.hh
modeler / polar_hydrogens / PolarHydrogenPacker.cc	pose / variant_util.hh
modeler / polar_hydrogens / PolarHydrogenPacker.hh	scoring / hbonds / HBEvalTuple.hh
modeler / polar_hydrogens / PolarHydrogenPacker.hh	scoring / hbonds / HBondDatabase.fwd.hh
modeler / polar_hydrogens / PolarHydrogenPacker.hh	scoring / hbonds / HBondOptions.fwd.hh
modeler / polar_hydrogens / PolarHydrogenPacker.hh	kinematics / Stub.fwd.hh
modeler / polar_hydrogens / PolarHydrogenPacker.hh	types.hh
screener / PoseSelectionScreener.cc	pose / Pose.hh
screener / PoseSelectionScreener.cc	scoring / ScoreFunction.hh
screener / PoseSelectionScreener.hh	pose / Pose.fwd.hh
screener / PoseSelectionScreener.hh	scoring / ScoreFunction.fwd.hh
screener / PoseSelectionScreener.hh	types.hh
modeler / precomputed / PrecomputedLibraryMover.cc	conformation / Conformation.hh
modeler / precomputed / PrecomputedLibraryMover.cc	kinematics / FoldTree.hh
modeler / precomputed / PrecomputedLibraryMover.cc	pose / full_model_info / FullModelInfo.hh
modeler / precomputed / PrecomputedLibraryMover.cc	pose / Pose.hh
modeler / precomputed / PrecomputedLibraryMover.cc	conformation / Residue.hh
modeler / precomputed / PrecomputedLibraryMover.cc	io / silent / SilentFileData.hh
modeler / precomputed / PrecomputedLibraryMover.cc	io / silent / SilentFileOptions.hh
modeler / precomputed / PrecomputedLibraryMover.cc	io / silent / SilentStruct.hh
modeler / precomputed / PrecomputedLibraryMover.cc	pose / full_model_info / util.hh
modeler / precomputed / PrecomputedLibraryMover.cc	pose / util.hh
modeler / precomputed / PrecomputedLibraryMover.hh	pose / Pose.fwd.hh
modeler / precomputed / PrecomputedLibraryMover.hh	io / silent / SilentFileData.fwd.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	scoring / Energies.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	scoring / methods / EnergyMethodOptions.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	scoring / etable / Etable.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	scoring / etable / EtableEnergy.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	pose / Pose.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	scoring / ScoreFunction.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	scoring / ScoringManager.hh
modeler / protein / checker / ProteinAtrRepChecker.cc	pose / util.hh
modeler / protein / checker / ProteinAtrRepChecker.hh	pose / Pose.hh
modeler / protein / checker / ProteinAtrRepChecker.hh	scoring / ScoreFunction.fwd.hh
legacy / screener / ProteinAtrRepScreener.cc	pose / Pose.hh
legacy / screener / ProteinAtrRepScreener.hh	pose / Pose.fwd.hh
sampler / protein / ProteinBetaAntiParallelStepWiseSampler.cc	kinematics / FoldTree.hh
sampler / protein / ProteinBetaAntiParallelStepWiseSampler.cc	kinematics / Jump.hh
sampler / protein / ProteinBetaAntiParallelStepWiseSampler.cc	pose / Pose.hh
sampler / protein / ProteinFragmentStepWiseSampler.cc	fragment / ConstantLengthFragSet.hh
sampler / protein / ProteinFragmentStepWiseSampler.cc	fragment / FragSet.hh
sampler / protein / ProteinFragmentStepWiseSampler.cc	fragment / Frame.hh
sampler / protein / ProteinFragmentStepWiseSampler.cc	fragment / FrameList.hh
sampler / protein / ProteinFragmentStepWiseSampler.cc	fragment / util.hh
sampler / protein / ProteinFragmentStepWiseSampler.hh	fragment / Frame.fwd.hh
sampler / protein / ProteinFragmentStepWiseSampler.hh	pose / Pose.fwd.hh
sampler / protein / ProteinFragmentStepWiseSampler.hh	types.hh
sampler / protein / ProteinMainChainStepWiseSampler.cc	pose / Pose.hh
sampler / protein / ProteinMainChainStepWiseSampler.cc	id / TorsionID.hh
sampler / protein / ProteinMainChainStepWiseSampler.hh	id / TorsionID.fwd.hh
sampler / protein / ProteinMainChainStepWiseSampler.hh	types.hh
monte_carlo / mover / ResampleMover.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / ResampleMover.cc	pose / Pose.hh
monte_carlo / mover / ResampleMover.cc	scoring / ScoreFunction.hh
monte_carlo / mover / ResampleMover.cc	pose / full_model_info / util.hh
monte_carlo / mover / ResampleMover.cc	chemical / rna / util.hh
monte_carlo / mover / ResampleMover.hh	pose / Pose.fwd.hh
monte_carlo / mover / ResampleMover.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / mover / ResampleMover.hh	types.hh
sampler / copy_dofs / ResidueAlternativeSet.cc	pose / Pose.hh
sampler / copy_dofs / ResidueAlternativeSet.hh	pose / Pose.fwd.hh
sampler / copy_dofs / ResidueAlternativeSet.hh	types.hh
sampler / copy_dofs / ResidueAlternativeStepWiseSampler.cc	pose / Pose.hh
sampler / copy_dofs / ResidueAlternativeStepWiseSampler.cc	conformation / Residue.hh
sampler / copy_dofs / ResidueAlternativeStepWiseSampler.hh	pose / Pose.hh
sampler / copy_dofs / ResidueAlternativeStepWiseSampler.hh	conformation / Residue.fwd.hh
sampler / copy_dofs / ResidueAlternativeStepWiseSamplerComb.hh	conformation / Residue.fwd.hh
screener / ResidueContactScreener.hh	pose / Pose.fwd.hh
screener / ResidueContactScreener.hh	types.hh
sampler / copy_dofs / ResidueListStepWiseSampler.cc	conformation / Residue.hh
sampler / copy_dofs / ResidueListStepWiseSampler.hh	conformation / Residue.fwd.hh
sampler / rigid_body / RigidBodyStepWiseSampler.cc	kinematics / tree / Atom.hh
sampler / rigid_body / RigidBodyStepWiseSampler.cc	id / AtomID.hh
sampler / rigid_body / RigidBodyStepWiseSampler.cc	kinematics / AtomTree.hh
sampler / rigid_body / RigidBodyStepWiseSampler.cc	kinematics / Jump.hh
sampler / rigid_body / RigidBodyStepWiseSampler.cc	pose / Pose.hh
sampler / rigid_body / RigidBodyStepWiseSampler.cc	kinematics / Stub.hh
sampler / rigid_body / RigidBodyStepWiseSampler.hh	id / AtomID.hh
sampler / rigid_body / RigidBodyStepWiseSampler.hh	kinematics / Jump.hh
sampler / rigid_body / RigidBodyStepWiseSampler.hh	conformation / Residue.hh
sampler / rigid_body / RigidBodyStepWiseSampler.hh	kinematics / Stub.hh
sampler / rigid_body / RigidBodyStepWiseSampler.hh	types.hh
sampler / rigid_body / RigidBodyStepWiseSamplerValueRange.hh	types.hh
sampler / rigid_body / RigidBodyStepWiseSamplerWithResidueAlternatives.cc	pose / Pose.hh
sampler / rigid_body / RigidBodyStepWiseSamplerWithResidueList.hh	conformation / Residue.fwd.hh
sampler / rigid_body / RigidBodyStepWiseSamplerWithResidueList.hh	kinematics / Stub.fwd.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	io / silent / BinarySilentStruct.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	pose / Pose.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	conformation / Residue.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	scoring / rms_util.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	scoring / ScoreFunction.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	io / silent / SilentFileData.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	io / silent / SilentFileOptions.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	io / silent / SilentStruct.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	id / types.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	types.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	pose / full_model_info / util.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	pose / util.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.cc	chemical / VariantType.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.hh	pose / Pose.fwd.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.hh	io / silent / SilentFileData.fwd.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.hh	io / silent / SilentFileOptions.fwd.hh
monte_carlo / rna / RNA_AddDeleteMonteCarlo.hh	types.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	kinematics / tree / Atom.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	id / AtomID.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	kinematics / AtomTree.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	id / DOF_ID.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	kinematics / FoldTree.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	id / NamedAtomID.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	pose / Pose.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	conformation / Residue.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	chemical / ResidueType.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	chemical / rna / RNA_Info.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	scoring / ScoreFunction.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	types.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.cc	chemical / VariantType.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.hh	kinematics / tree / Atom.fwd.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.hh	id / DOF_ID.fwd.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.hh	id / NamedAtomID.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.hh	pose / Pose.fwd.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.hh	scoring / ScoreFunction.hh
legacy / modeler / rna / RNA_AnalyticLoopCloser.hh	types.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	scoring / Energies.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	scoring / methods / EnergyMethodOptions.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	scoring / etable / Etable.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	scoring / etable / EtableEnergy.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	pose / Pose.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	scoring / ScoreFunction.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	scoring / ScoringManager.hh
modeler / rna / checker / RNA_AtrRepChecker.cc	pose / variant_util.hh
modeler / rna / checker / RNA_AtrRepChecker.hh	scoring / methods / EnergyMethodOptions.fwd.hh
modeler / rna / checker / RNA_AtrRepChecker.hh	pose / Pose.hh
modeler / rna / checker / RNA_AtrRepChecker.hh	scoring / ScoreFunction.fwd.hh
legacy / screener / RNA_AtrRepScreener.cc	pose / Pose.hh
legacy / screener / RNA_AtrRepScreener.hh	pose / Pose.fwd.hh
modeler / rna / checker / RNA_BaseCentroidChecker.cc	kinematics / FoldTree.hh
modeler / rna / checker / RNA_BaseCentroidChecker.cc	pose / Pose.hh
modeler / rna / checker / RNA_BaseCentroidChecker.cc	conformation / Residue.hh
modeler / rna / checker / RNA_BaseCentroidChecker.cc	scoring / rna / RNA_CentroidInfo.hh
modeler / rna / checker / RNA_BaseCentroidChecker.cc	kinematics / Stub.hh
modeler / rna / checker / RNA_BaseCentroidChecker.cc	id / TorsionID.hh
modeler / rna / checker / RNA_BaseCentroidChecker.hh	pose / Pose.fwd.hh
modeler / rna / checker / RNA_BaseCentroidChecker.hh	scoring / rna / RNA_CentroidInfo.fwd.hh
modeler / rna / checker / RNA_BaseCentroidChecker.hh	kinematics / Stub.hh
modeler / rna / checker / RNA_BaseCentroidChecker.hh	types.hh
modeler / rna / checker / RNA_BaseCentroidChecker.hh	chemical / rna / util.hh
modeler / rna / checker / RNA_ChainClosableGeometryChecker.cc	pose / Pose.hh
modeler / rna / checker / RNA_ChainClosableGeometryChecker.cc	conformation / Residue.hh
modeler / rna / checker / RNA_ChainClosableGeometryChecker.cc	kinematics / Stub.hh
modeler / rna / checker / RNA_ChainClosableGeometryChecker.hh	pose / Pose.fwd.hh
modeler / rna / checker / RNA_ChainClosableGeometryChecker.hh	conformation / Residue.fwd.hh
modeler / rna / checker / RNA_ChainClosableGeometryChecker.hh	kinematics / Stub.fwd.hh
modeler / rna / checker / RNA_ChainClosableGeometryChecker.hh	types.hh
screener / RNA_ChainClosableGeometryResidueBasedScreener.hh	conformation / Residue.hh
screener / RNA_ChainClosableGeometryScreener.cc	pose / Pose.hh
screener / RNA_ChainClosableGeometryScreener.hh	pose / Pose.fwd.hh
screener / RNA_ChainClosableGeometryStubBasedScreener.cc	pose / Pose.hh
screener / RNA_ChainClosableGeometryStubBasedScreener.cc	conformation / Residue.hh
screener / RNA_ChainClosableGeometryStubBasedScreener.cc	kinematics / Stub.hh
screener / RNA_ChainClosableGeometryStubBasedScreener.hh	pose / Pose.fwd.hh
screener / RNA_ChainClosableGeometryStubBasedScreener.hh	conformation / Residue.fwd.hh
screener / RNA_ChainClosableGeometryStubBasedScreener.hh	kinematics / Stub.fwd.hh
modeler / rna / checker / RNA_ChainClosureChecker.cc	scoring / Energies.hh
modeler / rna / checker / RNA_ChainClosureChecker.cc	conformation / Residue.hh
modeler / rna / checker / RNA_ChainClosureChecker.cc	scoring / ScoreFunction.hh
modeler / rna / checker / RNA_ChainClosureChecker.cc	scoring / ScoreType.hh
modeler / rna / checker / RNA_ChainClosureChecker.cc	id / TorsionID.hh
modeler / rna / checker / RNA_ChainClosureChecker.cc	chemical / VariantType.hh
modeler / rna / checker / RNA_ChainClosureChecker.hh	pose / Pose.hh
modeler / rna / checker / RNA_ChainClosureChecker.hh	scoring / ScoreFunction.fwd.hh
screener / RNA_ChainClosureScreener.cc	pose / Pose.hh
screener / RNA_ChainClosureScreener.hh	pose / Pose.fwd.hh
sampler / rna / RNA_ChiStepWiseSampler.cc	chemical / rna / RNA_SamplerUtil.hh
sampler / rna / RNA_ChiStepWiseSampler.cc	id / TorsionID.hh
sampler / rna / RNA_ChiStepWiseSampler.cc	chemical / rna / util.hh
sampler / rna / RNA_ChiStepWiseSampler.hh	chemical / rna / RNA_FittedTorsionInfo.hh
sampler / rna / RNA_ChiStepWiseSampler.hh	chemical / rna / util.hh
sampler / rna / RNA_KIC_Sampler.cc	pose / Pose.hh
sampler / rna / RNA_KIC_Sampler.cc	chemical / rna / RNA_SamplerUtil.hh
sampler / rna / RNA_KIC_Sampler.cc	pose / rna / RNA_SuiteName.hh
sampler / rna / RNA_KIC_Sampler.cc	id / TorsionID.hh
sampler / rna / RNA_KIC_Sampler.cc	pose / rna / util.hh
sampler / rna / RNA_KIC_Sampler.hh	chemical / rna / util.hh
sampler / rna / RNA_KinematicCloser.cc	id / AtomID.hh
sampler / rna / RNA_KinematicCloser.cc	kinematics / AtomTree.hh
sampler / rna / RNA_KinematicCloser.cc	id / DOF_ID.hh
sampler / rna / RNA_KinematicCloser.cc	id / NamedAtomID.hh
sampler / rna / RNA_KinematicCloser.cc	pose / Pose.hh
sampler / rna / RNA_KinematicCloser.cc	conformation / Residue.hh
sampler / rna / RNA_KinematicCloser.cc	chemical / ResidueType.hh
sampler / rna / RNA_KinematicCloser.cc	chemical / rna / RNA_Info.hh
sampler / rna / RNA_KinematicCloser.cc	types.hh
sampler / rna / RNA_KinematicCloser.hh	id / DOF_ID.fwd.hh
sampler / rna / RNA_KinematicCloser.hh	id / NamedAtomID.fwd.hh
sampler / rna / RNA_NucleosideStepWiseSampler.cc	id / TorsionID.hh
sampler / rna / RNA_NucleosideStepWiseSampler.cc	chemical / rna / util.hh
sampler / rna / RNA_NucleosideStepWiseSampler.hh	chemical / rna / RNA_FittedTorsionInfo.fwd.hh
sampler / rna / RNA_NucleosideStepWiseSampler.hh	chemical / rna / util.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	scoring / Energies.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	scoring / EnergyGraph.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	pose / Pose.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	scoring / ScoreFunction.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	id / TorsionID.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	types.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	pose / full_model_info / util.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	pose / util.hh
monte_carlo / rna / RNA_O2PrimeMover.cc	chemical / VariantType.hh
monte_carlo / rna / RNA_O2PrimeMover.hh	pose / Pose.fwd.hh
monte_carlo / rna / RNA_O2PrimeMover.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / rna / RNA_O2PrimeMover.hh	types.hh
sampler / rna / RNA_SugarStepWiseSampler.cc	pose / Pose.hh
sampler / rna / RNA_SugarStepWiseSampler.cc	conformation / Residue.hh
sampler / rna / RNA_SugarStepWiseSampler.cc	chemical / rna / RNA_FittedTorsionInfo.hh
sampler / rna / RNA_SugarStepWiseSampler.cc	pose / rna / RNA_IdealCoord.hh
sampler / rna / RNA_SugarStepWiseSampler.cc	id / TorsionID.hh
sampler / rna / RNA_SugarStepWiseSampler.cc	pose / rna / util.hh
sampler / rna / RNA_SugarStepWiseSampler.hh	id / DOF_ID_Map.hh
sampler / rna / RNA_SugarStepWiseSampler.hh	chemical / rna / util.hh
sampler / rna / RNA_SuiteStepWiseSampler.cc	chemical / rna / RNA_FittedTorsionInfo.hh
sampler / rna / RNA_SuiteStepWiseSampler.cc	chemical / rna / RNA_SamplerUtil.hh
sampler / rna / RNA_SuiteStepWiseSampler.cc	id / TorsionID.hh
sampler / rna / RNA_SuiteStepWiseSampler.cc	pose / rna / util.hh
sampler / rna / RNA_SuiteStepWiseSampler.hh	chemical / rna / RNA_FittedTorsionInfo.fwd.hh
sampler / rna / RNA_SuiteStepWiseSampler.hh	chemical / rna / util.hh
monte_carlo / rna / RNA_TorsionMover.cc	pose / Pose.hh
monte_carlo / rna / RNA_TorsionMover.cc	conformation / ResidueFactory.hh
monte_carlo / rna / RNA_TorsionMover.cc	chemical / ResidueTypeSet.hh
monte_carlo / rna / RNA_TorsionMover.cc	id / TorsionID.hh
monte_carlo / rna / RNA_TorsionMover.cc	types.hh
monte_carlo / rna / RNA_TorsionMover.cc	chemical / rna / util.hh
monte_carlo / rna / RNA_TorsionMover.cc	pose / util.hh
monte_carlo / rna / RNA_TorsionMover.cc	pose / full_model_info / util.hh
monte_carlo / rna / RNA_TorsionMover.cc	chemical / VariantType.hh
monte_carlo / rna / RNA_TorsionMover.hh	pose / Pose.fwd.hh
monte_carlo / rna / RNA_TorsionMover.hh	chemical / rna / RNA_FittedTorsionInfo.hh
monte_carlo / rna / RNA_TorsionMover.hh	types.hh
sampler / screener / RNA_TorsionScreener.cc	pose / Pose.hh
sampler / screener / RNA_TorsionScreener.cc	conformation / Residue.hh
sampler / screener / RNA_TorsionScreener.cc	pose / rna / RNA_SuiteName.hh
sampler / screener / RNA_TorsionScreener.cc	chemical / rna / util.hh
sampler / screener / RNA_TorsionScreener.hh	pose / Pose.fwd.hh
sampler / screener / RNA_TorsionScreener.hh	pose / rna / RNA_SuiteName.fwd.hh
sampler / screener / RNA_TorsionScreener.hh	types.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	id / AtomID_Map.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	chemical / AtomType.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	chemical / ChemicalManager.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	pose / full_model_info / FullModelInfo.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	import_pose / import_pose.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	kinematics / MoveMap.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	pose / PDBInfo.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	pose / Pose.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	conformation / Residue.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	conformation / ResidueFactory.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	chemical / ResidueTypeSet.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	scoring / rms_util.tmpl.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	types.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	pose / rna / util.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	pose / util.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	chemical / rna / util.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	chemical / util.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	chemical / VariantType.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	pose / rna / VDW_Grid.hh
modeler / rna / checker / RNA_VDW_BinChecker.cc	pose / rna / VDW_RepScreenInfo.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	chemical / AA.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	kinematics / FoldTree.fwd.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	pose / Pose.fwd.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	pose / Pose.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	conformation / Residue.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	types.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	pose / rna / VDW_Grid.hh
modeler / rna / checker / RNA_VDW_BinChecker.hh	pose / rna / VDW_RepScreenInfo.hh
screener / SampleApplier.cc	pose / Pose.hh
screener / SampleApplier.cc	conformation / Residue.hh
screener / SampleApplier.hh	pose / Pose.hh
screener / SampleApplier.hh	conformation / Residue.fwd.hh
screener / Scorer.cc	pose / Pose.hh
screener / Scorer.cc	scoring / ScoreFunction.hh
screener / Scorer.hh	pose / Pose.fwd.hh
screener / Scorer.hh	scoring / ScoreFunction.fwd.hh
modeler / scoring_util.cc	scoring / methods / EnergyMethodOptions.hh
modeler / scoring_util.cc	scoring / etable / EtableOptions.hh
modeler / scoring_util.cc	pose / Pose.hh
modeler / scoring_util.cc	scoring / ScoreFunction.hh
modeler / scoring_util.cc	scoring / ScoreFunctionFactory.hh
modeler / scoring_util.hh	pose / Pose.fwd.hh
modeler / scoring_util.hh	scoring / ScoreFunction.fwd.hh
modeler / packer / SideChainCopier.cc	conformation / Conformation.hh
modeler / packer / SideChainCopier.cc	pose / Pose.hh
modeler / packer / SideChainCopier.cc	chemical / ResidueType.hh
modeler / packer / SideChainCopier.cc	id / TorsionID.hh
modeler / packer / SideChainCopier.cc	scoring / constraints / util.hh
modeler / packer / SideChainCopier.cc	pose / copydofs / util.hh
legacy / screener / SimplePoseSelection.cc	pose / Pose.hh
legacy / screener / SimplePoseSelection.hh	pose / Pose.hh
legacy / screener / SimpleRMSD_Screener.cc	pose / Pose.hh
legacy / screener / SimpleRMSD_Screener.cc	scoring / rms_util.hh
legacy / screener / SimpleRMSD_Screener.cc	scoring / rms_util.tmpl.hh
legacy / screener / SimpleRMSD_Screener.hh	id / AtomID.fwd.hh
legacy / screener / SimpleRMSD_Screener.hh	pose / Pose.fwd.hh
legacy / screener / SimpleRMSD_Screener.hh	types.hh
modeler / options / StepWiseBasicModelerOptions.hh	types.hh
options / StepWiseBasicOptions.hh	types.hh
modeler / working_parameters / StepWiseBasicWorkingParameters.cc	pose / Pose.hh
modeler / working_parameters / StepWiseBasicWorkingParameters.hh	pose / Pose.fwd.hh
modeler / working_parameters / StepWiseBasicWorkingParameters.hh	types.hh
modeler / align / StepWiseClusterer.cc	pose / extra_pose_info_util.hh
modeler / align / StepWiseClusterer.cc	pose / Pose.hh
modeler / align / StepWiseClusterer.cc	pose / util.hh
modeler / align / StepWiseClusterer.hh	pose / Pose.hh
modeler / align / StepWiseClusterer.hh	types.hh
modeler / StepWiseConnectionSampler.cc	id / AtomID.hh
modeler / StepWiseConnectionSampler.cc	scoring / methods / EnergyMethodOptions.hh
modeler / StepWiseConnectionSampler.cc	pose / Pose.hh
modeler / StepWiseConnectionSampler.cc	scoring / ScoreFunction.hh
modeler / StepWiseConnectionSampler.cc	scoring / ScoreType.hh
modeler / StepWiseConnectionSampler.cc	kinematics / Stub.hh
modeler / StepWiseConnectionSampler.cc	id / TorsionID.hh
modeler / StepWiseConnectionSampler.cc	types.hh
modeler / StepWiseConnectionSampler.cc	pose / full_model_info / util.hh
modeler / StepWiseConnectionSampler.cc	pose / rna / util.hh
modeler / StepWiseConnectionSampler.cc	chemical / rna / util.hh
modeler / StepWiseConnectionSampler.cc	pose / variant_util.hh
modeler / StepWiseConnectionSampler.hh	pose / Pose.fwd.hh
modeler / StepWiseConnectionSampler.hh	conformation / Residue.fwd.hh
modeler / StepWiseConnectionSampler.hh	scoring / ScoreFunction.hh
modeler / StepWiseConnectionSampler.hh	io / silent / SilentFileData.fwd.hh
modeler / StepWiseConnectionSampler.hh	kinematics / Stub.hh
modeler / align / StepWiseLegacyClusterer.cc	id / AtomID.hh
modeler / align / StepWiseLegacyClusterer.cc	chemical / ChemicalManager.hh
modeler / align / StepWiseLegacyClusterer.cc	pose / extra_pose_info_util.hh
modeler / align / StepWiseLegacyClusterer.cc	pose / Pose.hh
modeler / align / StepWiseLegacyClusterer.cc	import_pose / pose_stream / PoseInputStream.fwd.hh
modeler / align / StepWiseLegacyClusterer.cc	import_pose / pose_stream / PoseInputStream.hh
modeler / align / StepWiseLegacyClusterer.cc	chemical / ResidueTypeSet.hh
modeler / align / StepWiseLegacyClusterer.cc	scoring / rms_util.hh
modeler / align / StepWiseLegacyClusterer.cc	io / silent / SilentFileData.hh
modeler / align / StepWiseLegacyClusterer.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
modeler / align / StepWiseLegacyClusterer.cc	io / silent / SilentStruct.hh
modeler / align / StepWiseLegacyClusterer.cc	pose / subpose_manipulation_util.hh
modeler / align / StepWiseLegacyClusterer.cc	types.hh
modeler / align / StepWiseLegacyClusterer.cc	pose / util.hh
modeler / align / StepWiseLegacyClusterer.hh	pose / Pose.hh
modeler / align / StepWiseLegacyClusterer.hh	chemical / ResidueTypeSet.fwd.hh
modeler / align / StepWiseLegacyClusterer.hh	scoring / ScoreFunction.fwd.hh
modeler / align / StepWiseLegacyClusterer.hh	io / silent / SilentFileData.fwd.hh
modeler / align / StepWiseLegacyClusterer.hh	import_pose / pose_stream / SilentFilePoseInputStream.fwd.hh
modeler / align / StepWiseLegacyClusterer.hh	io / silent / SilentStruct.fwd.hh
modeler / align / StepWiseLegacyClusterer.hh	types.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	chemical / ChemicalManager.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	pose / extra_pose_info_util.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	pose / Pose.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	import_pose / pose_stream / PoseInputStream.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	chemical / ResidueTypeSet.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	scoring / rms_util.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	io / silent / SilentFileData.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	io / silent / SilentFileOptions.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	io / silent / SilentStruct.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	pose / subpose_manipulation_util.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	types.hh
modeler / align / StepWiseLegacyClustererSilentBased.cc	pose / util.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	id / AtomID.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	pose / Pose.fwd.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	chemical / ResidueTypeSet.fwd.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	scoring / ScoreFunction.fwd.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	io / silent / SilentFileData.fwd.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	import_pose / pose_stream / SilentFilePoseInputStream.fwd.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	io / silent / SilentStruct.fwd.hh
modeler / align / StepWiseLegacyClustererSilentBased.hh	types.hh
monte_carlo / mover / StepWiseMasterMover.cc	id / AtomID.hh
monte_carlo / mover / StepWiseMasterMover.cc	chemical / ChemicalManager.hh
monte_carlo / mover / StepWiseMasterMover.cc	pose / extra_pose_info_util.hh
monte_carlo / mover / StepWiseMasterMover.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / StepWiseMasterMover.cc	pose / PDBInfo.hh
monte_carlo / mover / StepWiseMasterMover.cc	import_pose / pose_stream / PDBPoseInputStream.hh
monte_carlo / mover / StepWiseMasterMover.cc	pose / Pose.hh
monte_carlo / mover / StepWiseMasterMover.cc	chemical / ResidueTypeSet.hh
monte_carlo / mover / StepWiseMasterMover.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
monte_carlo / mover / StepWiseMasterMover.cc	pose / full_model_info / util.hh
monte_carlo / mover / StepWiseMasterMover.cc	pose / variant_util.hh
monte_carlo / mover / StepWiseMasterMover.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / mover / StepWiseMasterMover.hh	types.hh
modeler / packer / StepWiseMasterPacker.cc	scoring / Energies.hh
modeler / packer / StepWiseMasterPacker.cc	scoring / methods / EnergyMethodOptions.hh
modeler / packer / StepWiseMasterPacker.cc	scoring / ScoreFunction.hh
modeler / packer / StepWiseMasterPacker.hh	pose / Pose.fwd.hh
modeler / packer / StepWiseMasterPacker.hh	scoring / ScoreFunction.hh
modeler / packer / StepWiseMasterPacker.hh	types.hh
modeler / StepWiseMinimizer.cc	id / AtomID.hh
modeler / StepWiseMinimizer.cc	optimization / AtomTreeMinimizer.hh
modeler / StepWiseMinimizer.cc	optimization / CartesianMinimizer.hh
modeler / StepWiseMinimizer.cc	scoring / constraints / ConstraintSet.hh
modeler / StepWiseMinimizer.cc	scoring / Energies.hh
modeler / StepWiseMinimizer.cc	scoring / EnergyGraph.hh
modeler / StepWiseMinimizer.cc	scoring / EnergyMap.hh
modeler / StepWiseMinimizer.cc	pose / extra_pose_info_util.hh
modeler / StepWiseMinimizer.cc	pose / full_model_info / FullModelInfo.hh
modeler / StepWiseMinimizer.cc	optimization / MinimizerOptions.hh
modeler / StepWiseMinimizer.cc	kinematics / MoveMap.hh
modeler / StepWiseMinimizer.cc	pose / Pose.hh
modeler / StepWiseMinimizer.cc	scoring / ScoreFunction.hh
modeler / StepWiseMinimizer.cc	pose / rna / util.hh
modeler / StepWiseMinimizer.cc	pose / util.hh
modeler / StepWiseMinimizer.hh	pose / toolbox / AtomLevelDomainMap.fwd.hh
modeler / StepWiseMinimizer.hh	optimization / AtomTreeMinimizer.fwd.hh
modeler / StepWiseMinimizer.hh	optimization / CartesianMinimizer.fwd.hh
modeler / StepWiseMinimizer.hh	optimization / MinimizerOptions.fwd.hh
modeler / StepWiseMinimizer.hh	kinematics / MoveMap.fwd.hh
modeler / StepWiseMinimizer.hh	pose / Pose.hh
modeler / StepWiseMinimizer.hh	scoring / ScoreFunction.hh
modeler / StepWiseModeler.cc	scoring / constraints / ConstraintIO.hh
modeler / StepWiseModeler.cc	scoring / constraints / ConstraintSet.hh
modeler / StepWiseModeler.cc	pose / full_model_info / FullModelInfo.hh
modeler / StepWiseModeler.cc	pose / Pose.hh
modeler / StepWiseModeler.cc	scoring / ScoreFunction.hh
modeler / StepWiseModeler.cc	pose / full_model_info / util.hh
modeler / StepWiseModeler.cc	pose / variant_util.hh
modeler / StepWiseModeler.hh	scoring / constraints / ConstraintSet.fwd.hh
modeler / StepWiseModeler.hh	kinematics / MoveMap.fwd.hh
modeler / StepWiseModeler.hh	pose / Pose.fwd.hh
modeler / StepWiseModeler.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / StepWiseMonteCarlo.cc	scoring / Energies.hh
monte_carlo / StepWiseMonteCarlo.cc	scoring / EnergyGraph.hh
monte_carlo / StepWiseMonteCarlo.cc	scoring / EnergyMap.fwd.hh
monte_carlo / StepWiseMonteCarlo.cc	scoring / EnergyMap.hh
monte_carlo / StepWiseMonteCarlo.cc	pose / extra_pose_info_util.hh
monte_carlo / StepWiseMonteCarlo.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / StepWiseMonteCarlo.cc	pose / Pose.hh
monte_carlo / StepWiseMonteCarlo.cc	chemical / ResidueType.hh
monte_carlo / StepWiseMonteCarlo.cc	scoring / ScoreFunction.hh
monte_carlo / StepWiseMonteCarlo.cc	io / silent / SilentFileData.hh
monte_carlo / StepWiseMonteCarlo.cc	io / silent / SilentFileOptions.hh
monte_carlo / StepWiseMonteCarlo.cc	io / silent / util.hh
monte_carlo / StepWiseMonteCarlo.cc	pose / full_model_info / util.hh
monte_carlo / StepWiseMonteCarlo.cc	pose / util.hh
monte_carlo / StepWiseMonteCarlo.cc	pose / rna / util.hh
monte_carlo / StepWiseMonteCarlo.hh	pose / Pose.fwd.hh
monte_carlo / StepWiseMonteCarlo.hh	scoring / ScoreFunction.fwd.hh
monte_carlo / StepWiseMonteCarlo.hh	types.hh
monte_carlo / options / StepWiseMonteCarloOptions.hh	types.hh
monte_carlo / mover / StepWiseMove.cc	pose / full_model_info / FullModelParameters.hh
monte_carlo / mover / StepWiseMove.hh	pose / full_model_info / FullModelParameters.fwd.hh
monte_carlo / mover / StepWiseMove.hh	types.hh
monte_carlo / mover / StepWiseMoveSelector.cc	kinematics / FoldTree.hh
monte_carlo / mover / StepWiseMoveSelector.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / StepWiseMoveSelector.cc	scoring / loop_graph / LoopGraph.hh
monte_carlo / mover / StepWiseMoveSelector.cc	pose / Pose.hh
monte_carlo / mover / StepWiseMoveSelector.cc	pose / full_model_info / SubMotifInfo.hh
monte_carlo / mover / StepWiseMoveSelector.cc	types.hh
monte_carlo / mover / StepWiseMoveSelector.cc	pose / util.hh
monte_carlo / mover / StepWiseMoveSelector.cc	pose / full_model_info / util.hh
monte_carlo / mover / StepWiseMoveSelector.cc	chemical / rna / util.hh
monte_carlo / mover / StepWiseMoveSelector.cc	chemical / VariantType.hh
monte_carlo / mover / StepWiseMoveSelector.hh	pose / Pose.fwd.hh
monte_carlo / mover / options / StepWiseMoveSelectorOptions.hh	types.hh
modeler / packer / StepWisePacker.cc	scoring / Energies.hh
modeler / packer / StepWisePacker.cc	scoring / EnergyGraph.hh
modeler / packer / StepWisePacker.cc	pack / pack_rotamers.hh
modeler / packer / StepWisePacker.cc	pack / task / PackerTask.hh
modeler / packer / StepWisePacker.cc	pose / Pose.hh
modeler / packer / StepWisePacker.cc	conformation / Residue.hh
modeler / packer / StepWisePacker.cc	pack / rotamer_trials.hh
modeler / packer / StepWisePacker.cc	scoring / ScoreFunction.hh
modeler / packer / StepWisePacker.cc	scoring / ScoreFunctionFactory.hh
modeler / packer / StepWisePacker.cc	io / silent / SilentFileData.fwd.hh
modeler / packer / StepWisePacker.cc	io / silent / SilentFileData.hh
modeler / packer / StepWisePacker.cc	pack / task / TaskFactory.hh
modeler / packer / StepWisePacker.cc	pack / task / operation / TaskOperations.hh
modeler / packer / StepWisePacker.cc	types.hh
modeler / packer / StepWisePacker.cc	pose / util.hh
modeler / packer / StepWisePacker.hh	pack / task / PackerTask.fwd.hh
modeler / packer / StepWisePacker.hh	pose / Pose.fwd.hh
modeler / packer / StepWisePacker.hh	scoring / ScoreFunction.fwd.hh
modeler / packer / StepWisePacker.hh	types.hh
modeler / align / StepWisePoseAligner.cc	kinematics / tree / Atom.hh
modeler / align / StepWisePoseAligner.cc	kinematics / AtomTree.hh
modeler / align / StepWisePoseAligner.cc	scoring / constraints / ConstraintSet.hh
modeler / align / StepWisePoseAligner.cc	scoring / constraints / CoordinateConstraint.hh
modeler / align / StepWisePoseAligner.cc	scoring / func / FlatHarmonicFunc.hh
modeler / align / StepWisePoseAligner.cc	kinematics / FoldTree.hh
modeler / align / StepWisePoseAligner.cc	pose / full_model_info / FullModelInfo.hh
modeler / align / StepWisePoseAligner.cc	pose / full_model_info / FullModelParameters.hh
modeler / align / StepWisePoseAligner.cc	pose / Pose.hh
modeler / align / StepWisePoseAligner.cc	conformation / Residue.hh
modeler / align / StepWisePoseAligner.cc	chemical / ResidueType.hh
modeler / align / StepWisePoseAligner.cc	scoring / rms_util.hh
modeler / align / StepWisePoseAligner.cc	pose / rna / util.hh
modeler / align / StepWisePoseAligner.cc	pose / full_model_info / util.hh
modeler / align / StepWisePoseAligner.cc	conformation / util.hh
modeler / align / StepWisePoseAligner.cc	chemical / rna / util.hh
modeler / align / StepWisePoseAligner.cc	chemical / VariantType.hh
modeler / align / StepWisePoseAligner.hh	id / AtomID.hh
modeler / align / StepWisePoseAligner.hh	pose / Pose.fwd.hh
modeler / align / StepWisePoseAligner.hh	types.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	pose / annotated_sequence.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	id / AtomID.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	chemical / ChemicalManager.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / dssp / Dssp.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / Energies.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	kinematics / Jump.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	pose / Pose.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	io / silent / ProteinSilentStruct.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / Ramachandran.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / RamaPrePro.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / rms_util.tmpl.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / ScoreFunction.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / ScoreFunctionFactory.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / ScoreType.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	scoring / ScoringManager.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	io / silent / SilentFileData.fwd.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	io / silent / SilentFileData.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	util / SwitchResidueTypeSet.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	id / TorsionID.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	types.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	pose / rna / util.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	pose / full_model_info / util.hh
modeler / protein / StepWiseProteinBackboneSampler.cc	pose / variant_util.hh
modeler / protein / StepWiseProteinBackboneSampler.hh	kinematics / FoldTree.fwd.hh
modeler / protein / StepWiseProteinBackboneSampler.hh	pose / Pose.fwd.hh
modeler / protein / StepWiseProteinBackboneSampler.hh	scoring / Ramachandran.fwd.hh
modeler / protein / StepWiseProteinBackboneSampler.hh	scoring / RamaPrePro.fwd.hh
modeler / protein / StepWiseProteinBackboneSampler.hh	scoring / ScoreFunction.fwd.hh
modeler / protein / StepWiseProteinBackboneSampler.hh	id / TorsionID.fwd.hh
modeler / protein / StepWiseProteinBackboneSampler.hh	types.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	id / AtomID.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	kinematics / Jump.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	pose / Pose.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	conformation / Residue.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	chemical / ResidueType.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	id / TorsionID.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	types.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.cc	chemical / VariantType.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.hh	kinematics / MoveMap.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.hh	pose / Pose.fwd.hh
modeler / protein / loop_close / StepWiseProteinCCD_Closer.hh	id / TorsionID.hh
modeler / protein / loop_close / StepWiseProteinCCD_MultiPoseCloser.cc	pose / Pose.hh
modeler / protein / loop_close / StepWiseProteinCCD_MultiPoseCloser.hh	pose / Pose.fwd.hh
modeler / protein / loop_close / StepWiseProteinCCD_MultiPoseCloser.hh	id / TorsionID.fwd.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	kinematics / FoldTree.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	kinematics / Jump.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	pose / Pose.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	scoring / Ramachandran.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	conformation / Residue.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	chemical / ResidueConnection.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	io / silent / SilentFileData.fwd.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	id / TorsionID.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	types.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	pose / rna / util.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.cc	chemical / VariantType.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.hh	pose / Pose.fwd.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.hh	scoring / Ramachandran.hh
modeler / protein / loop_close / StepWiseProteinKIC_LoopBridger.hh	id / TorsionID.fwd.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	optimization / AtomTreeMinimizer.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	optimization / CartesianMinimizer.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	conformation / Conformation.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	scoring / constraints / ConstraintSet.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	scoring / Energies.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	scoring / EnergyGraph.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	optimization / MinimizerOptions.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	kinematics / MoveMap.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	pose / Pose.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	scoring / ScoreFunction.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	scoring / ScoreFunctionFactory.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	id / TorsionID.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	scoring / constraints / util.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	pose / util.hh
legacy / modeler / protein / StepWiseProteinMinimizer.cc	conformation / util.hh
legacy / modeler / protein / StepWiseProteinMinimizer.hh	kinematics / MoveMap.fwd.hh
legacy / modeler / protein / StepWiseProteinMinimizer.hh	pose / Pose.hh
legacy / modeler / protein / StepWiseProteinMinimizer.hh	scoring / ScoreFunction.fwd.hh
legacy / modeler / protein / StepWiseProteinMinimizer.hh	types.hh
modeler / options / StepWiseProteinModelerOptions.hh	types.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	pose / annotated_sequence.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / constraints / AtomPairConstraint.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	chemical / ChemicalManager.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	conformation / Conformation.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / constraints / ConstraintIO.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / constraints / ConstraintSet.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	io / raw_data / DisulfideFile.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / func / FadeFunc.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	kinematics / FoldTree.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	pose / full_model_info / FullModelInfo.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	pose / full_model_info / FullModelParameters.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / func / Func.fwd.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	import_pose / import_pose.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	pose / Pose.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	conformation / Residue.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	conformation / ResidueFactory.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	chemical / ResidueType.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / rms_util.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / ScoreFunction.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	scoring / ScoreType.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	pose / subpose_manipulation_util.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	id / TorsionID.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	types.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	chemical / rna / util.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	pose / rna / util.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	pose / variant_util.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.cc	chemical / VariantType.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	id / AtomID.fwd.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	id / AtomID_Map.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	scoring / constraints / ConstraintSet.fwd.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	pose / Pose.fwd.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	conformation / Residue.fwd.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	chemical / ResidueType.fwd.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	chemical / ResidueTypeSet.fwd.hh
legacy / modeler / protein / StepWiseProteinPoseSetup.hh	types.hh
modeler / rna / StepWiseRNA_Classes.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_Classes.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / StepWiseRNA_Classes.hh	io / silent / SilentFileData.fwd.hh
modeler / rna / StepWiseRNA_Classes.hh	id / TorsionID.hh
modeler / rna / StepWiseRNA_Classes.hh	types.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / BinarySilentStruct.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	chemical / ChemicalManager.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	scoring / Energies.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	pose / extra_pose_info_util.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	pose / Pose.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	import_pose / pose_stream / PoseInputStream.fwd.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	import_pose / pose_stream / PoseInputStream.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	chemical / ResidueTypeSet.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	scoring / rms_util.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	scoring / rms_util.tmpl.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	scoring / ScoreFunction.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	scoring / ScoreFunctionFactory.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentFileData.fwd.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentFileData.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentFileOptions.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentStruct.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	types.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	chemical / rna / util.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	pose / rna / util.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.cc	pose / util.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	pose / Pose.fwd.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	pose / Pose.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	chemical / ResidueTypeSet.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	scoring / ScoreFunction.fwd.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	io / silent / SilentFileData.fwd.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	import_pose / pose_stream / SilentFilePoseInputStream.fwd.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	io / silent / SilentStruct.fwd.hh
legacy / modeler / rna / StepWiseRNA_Clusterer.hh	types.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	scoring / constraints / AtomPairConstraint.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	chemical / AtomType.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	chemical / ChemicalManager.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	scoring / constraints / ConstraintSet.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	pose / extra_pose_info_util.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	kinematics / FoldTree.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	import_pose / import_pose.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	import_pose / pose_stream / PoseInputStream.fwd.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	import_pose / pose_stream / PoseInputStream.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	conformation / Residue.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	chemical / ResidueTypeSet.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	scoring / rms_util.tmpl.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	import_pose / pose_stream / SilentFilePoseInputStream.fwd.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	id / TorsionID.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	types.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	pose / util.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	chemical / util.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	pose / util.tmpl.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.cc	chemical / VariantType.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.hh	chemical / ResidueTypeSet.fwd.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.hh	import_pose / pose_stream / SilentFilePoseInputStream.fwd.hh
modeler / rna / StepWiseRNA_CombineLongLoopFilterer.hh	types.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	id / AtomID.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	optimization / AtomTreeMinimizer.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	chemical / AtomType.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	io / silent / BinarySilentStruct.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	optimization / CartesianMinimizer.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	conformation / Conformation.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / Energies.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / EnergyGraph.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / EnergyMap.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	optimization / MinimizerOptions.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	pose / Pose.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / rms_util.tmpl.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / rna / RNA_TorsionPotential.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / ScoreFunction.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / ScoreFunctionFactory.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	scoring / ScoreType.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	io / silent / SilentFileData.fwd.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	io / silent / SilentFileData.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	id / TorsionID.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	types.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	chemical / util.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	chemical / rna / util.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	pose / util.hh
legacy / modeler / rna / StepWiseRNA_Minimizer.cc	chemical / VariantType.hh
modeler / options / StepWiseRNA_ModelerOptions.hh	types.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / constraints / AngleConstraint.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / constraints / AtomPairConstraint.hh
modeler / rna / StepWiseRNA_OutputData.cc	optimization / AtomTreeMinimizer.hh
modeler / rna / StepWiseRNA_OutputData.cc	chemical / AtomType.hh
modeler / rna / StepWiseRNA_OutputData.cc	io / silent / BinarySilentStruct.hh
modeler / rna / StepWiseRNA_OutputData.cc	chemical / ChemicalManager.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / constraints / ConstraintSet.fwd.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / constraints / ConstraintSet.hh
modeler / rna / StepWiseRNA_OutputData.cc	kinematics / MoveMap.hh
modeler / rna / StepWiseRNA_OutputData.cc	pack / pack_rotamers.hh
modeler / rna / StepWiseRNA_OutputData.cc	pack / task / PackerTask.hh
modeler / rna / StepWiseRNA_OutputData.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_OutputData.cc	conformation / Residue.hh
modeler / rna / StepWiseRNA_OutputData.cc	chemical / ResidueTypeSet.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / rms_util.tmpl.hh
modeler / rna / StepWiseRNA_OutputData.cc	pose / rna / RNA_BaseDoubletClasses.hh
modeler / rna / StepWiseRNA_OutputData.cc	pose / rna / RNA_BasePairClassifier.hh
modeler / rna / StepWiseRNA_OutputData.cc	chemical / rna / RNA_FittedTorsionInfo.hh
modeler / rna / StepWiseRNA_OutputData.cc	pack / rotamer_trials.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / ScoreFunction.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / ScoreType.hh
modeler / rna / StepWiseRNA_OutputData.cc	io / silent / SilentFileData.hh
modeler / rna / StepWiseRNA_OutputData.cc	io / silent / SilentFileOptions.hh
modeler / rna / StepWiseRNA_OutputData.cc	pack / task / TaskFactory.hh
modeler / rna / StepWiseRNA_OutputData.cc	types.hh
modeler / rna / StepWiseRNA_OutputData.cc	scoring / constraints / util.hh
modeler / rna / StepWiseRNA_OutputData.cc	chemical / util.hh
modeler / rna / StepWiseRNA_OutputData.cc	chemical / VariantType.hh
modeler / rna / StepWiseRNA_OutputData.hh	chemical / AA.hh
modeler / rna / StepWiseRNA_OutputData.hh	io / silent / BinarySilentStruct.hh
modeler / rna / StepWiseRNA_OutputData.hh	kinematics / FoldTree.fwd.hh
modeler / rna / StepWiseRNA_OutputData.hh	optimization / MinimizerOptions.hh
modeler / rna / StepWiseRNA_OutputData.hh	kinematics / MoveMap.hh
modeler / rna / StepWiseRNA_OutputData.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_OutputData.hh	conformation / Residue.hh
modeler / rna / StepWiseRNA_OutputData.hh	io / silent / RNA_SilentStruct.hh
modeler / rna / StepWiseRNA_OutputData.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / StepWiseRNA_OutputData.hh	io / silent / SilentFileData.hh
modeler / rna / StepWiseRNA_OutputData.hh	types.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.cc	pose / extra_pose_info_util.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.cc	pose / Pose.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.cc	scoring / ScoreFunction.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.cc	scoring / ScoreType.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.cc	pose / rna / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.cc	pose / variant_util.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.hh	pose / Pose.fwd.hh
legacy / modeler / rna / StepWiseRNA_PoseSelection.hh	types.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / annotated_sequence.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / constraints / AtomPairConstraint.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	io / silent / BinarySilentStruct.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / ChemicalManager.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / constraints / ConstraintSet.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / func / FadeFunc.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	kinematics / FoldTree.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / full_model_info / FullModelInfo.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / full_model_info / FullModelParameters.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / func / Func.fwd.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	import_pose / import_pose.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / PDBInfo.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / Pose.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	conformation / Residue.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	conformation / ResidueFactory.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / ResidueType.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / ResidueTypeSet.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / rms_util.tmpl.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	id / TorsionID.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	types.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / rna / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / copydofs / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / full_model_info / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / rna / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	pose / variant_util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / VariantType.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.hh	pose / Pose.fwd.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.hh	chemical / ResidueTypeSet.fwd.hh
legacy / modeler / rna / StepWiseRNA_PoseSetup.hh	types.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / AA.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	kinematics / tree / Atom.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	id / AtomID.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	id / AtomID_Map.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	optimization / AtomTreeMinimizer.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / func / CharmmPeriodicFunc.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / ChemicalManager.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	conformation / Conformation.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / constraints / DihedralConstraint.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	id / DOF_ID.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / Energies.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / EnergyGraph.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / EnergyMap.fwd.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / EnergyMap.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	kinematics / FoldTree.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	import_pose / import_pose.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	init / init.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	optimization / MinimizerOptions.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	pose / MiniPose.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	kinematics / MoveMap.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	pose / PDBInfo.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	pose / Pose.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	conformation / Residue.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	conformation / ResidueFactory.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	conformation / ResidueMatcher.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / ResidueTypeSet.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / rms_util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / rna / RNA_FittedTorsionInfo.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / ScoreFunction.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / ScoreFunctionFactory.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / ScoringManager.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	sequence / Sequence.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	io / silent / SilentFileData.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	io / silent / SilentStruct.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	types.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	io / silent / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	pose / rna / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	pose / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	sequence / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / rna / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / util.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / VariantType.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.hh	pose / Pose.fwd.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.hh	scoring / ScoreFunction.fwd.hh
legacy / modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.hh	types.hh
modeler / rna / StepWiseRNA_ResidueInfo.cc	chemical / AtomType.hh
modeler / rna / StepWiseRNA_ResidueInfo.cc	conformation / Conformation.hh
modeler / rna / StepWiseRNA_ResidueInfo.cc	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_ResidueInfo.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_ResidueInfo.cc	conformation / Residue.hh
modeler / rna / StepWiseRNA_ResidueInfo.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_ResidueInfo.hh	types.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	scoring / constraints / AtomPairConstraint.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / ChemicalManager.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	scoring / constraints / ConstraintSet.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	scoring / func / FadeFunc.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	kinematics / FoldTree.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	pose / Pose.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	conformation / Residue.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / ResidueTypeFinder.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / ResidueTypeSet.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	scoring / rms_util.tmpl.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	id / TorsionID.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	types.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	pose / rna / util.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	pose / util.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / rna / util.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / util.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / VariantType.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.hh	pose / Pose.fwd.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.hh	chemical / ResidueTypeSet.fwd.hh
legacy / modeler / rna / StepWiseRNA_WorkingParametersSetup.hh	types.hh
StepWiseSampleAndScreen.hh	types.hh
sampler / StepWiseSamplerComb.cc	pose / Pose.hh
sampler / StepWiseSamplerOneDOF.cc	pose / Pose.hh
sampler / StepWiseSamplerOneDOF.hh	id / AtomID.hh
sampler / StepWiseSamplerOneDOF.hh	id / DOF_ID.hh
sampler / StepWiseSamplerOneTorsion.cc	pose / Pose.hh
sampler / StepWiseSamplerOneTorsion.hh	id / TorsionID.hh
sampler / StepWiseSamplerOneValue.cc	pose / Pose.hh
sampler / StepWiseSamplerRingConformer.cc	pose / Pose.hh
sampler / StepWiseSamplerRingConformer.cc	chemical / rings / RingConformer.hh
sampler / StepWiseSamplerRingConformer.cc	chemical / rings / RingConformerSet.hh
sampler / StepWiseSamplerRingConformer.hh	chemical / rings / RingConformer.hh
sampler / StepWiseSamplerRingConformer.hh	chemical / rings / RingConformerSet.fwd.hh
sampler / StepWiseSamplerRingConformer.hh	id / TorsionID.hh
sampler / StepWiseSamplerSized.cc	pose / Pose.hh
sampler / StepWiseSamplerSizedAny.cc	pose / Pose.hh
sampler / StepWiseSamplerSizedComb.cc	pose / Pose.hh
screener / StepWiseScreener.hh	types.hh
modeler / working_parameters / StepWiseWorkingParameters.cc	kinematics / FoldTree.hh
modeler / working_parameters / StepWiseWorkingParameters.cc	pose / rna / util.hh
modeler / working_parameters / StepWiseWorkingParameters.hh	kinematics / FoldTree.hh
modeler / working_parameters / StepWiseWorkingParameters.hh	pose / Pose.fwd.hh
screener / StubApplier.hh	kinematics / Stub.hh
screener / StubDistanceScreener.hh	kinematics / Stub.hh
monte_carlo / submotif / SubMotifLibrary.cc	chemical / AA.hh
monte_carlo / submotif / SubMotifLibrary.cc	pose / annotated_sequence.hh
monte_carlo / submotif / SubMotifLibrary.cc	chemical / ChemicalManager.hh
monte_carlo / submotif / SubMotifLibrary.cc	pose / extra_pose_info_util.hh
monte_carlo / submotif / SubMotifLibrary.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / submotif / SubMotifLibrary.cc	import_pose / import_pose.hh
monte_carlo / submotif / SubMotifLibrary.cc	kinematics / Jump.hh
monte_carlo / submotif / SubMotifLibrary.cc	pose / Pose.hh
monte_carlo / submotif / SubMotifLibrary.cc	chemical / ResidueTypeFinder.hh
monte_carlo / submotif / SubMotifLibrary.cc	chemical / ResidueTypeSet.hh
monte_carlo / submotif / SubMotifLibrary.cc	import_pose / libraries / RNA_JumpLibrary.hh
monte_carlo / submotif / SubMotifLibrary.cc	import_pose / libraries / RNA_LibraryManager.hh
monte_carlo / submotif / SubMotifLibrary.cc	pose / full_model_info / util.hh
monte_carlo / submotif / SubMotifLibrary.cc	pose / rna / util.hh
monte_carlo / submotif / SubMotifLibrary.cc	pose / variant_util.hh
monte_carlo / submotif / SubMotifLibrary.hh	pose / Pose.fwd.hh
monte_carlo / submotif / SubMotifLibrary.hh	chemical / ResidueTypeSet.fwd.hh
modeler / rna / sugar / SugarInstantiateMover.cc	pose / Pose.hh
modeler / rna / sugar / SugarInstantiateMover.cc	conformation / Residue.hh
modeler / rna / sugar / SugarInstantiateMover.cc	chemical / types.hh
modeler / rna / sugar / SugarInstantiateMover.cc	pose / variant_util.hh
screener / SugarInstantiator.cc	conformation / Residue.hh
screener / SugarInstantiator.cc	pose / rna / util.hh
modeler / rna / sugar / SugarModeling.cc	pose / Pose.hh
modeler / rna / sugar / SugarModeling.cc	types.hh
modeler / rna / sugar / SugarModeling.cc	chemical / rna / util.hh
modeler / rna / sugar / SugarModeling.cc	pose / util.hh
modeler / rna / sugar / SugarModeling.hh	pose / Pose.fwd.hh
modeler / rna / sugar / SugarModeling.hh	types.hh
modeler / rna / sugar / SugarModeling.hh	chemical / rna / util.hh
modeler / rna / sugar / SugarVirtualizeMover.cc	pose / Pose.hh
modeler / rna / sugar / SugarVirtualizeMover.cc	conformation / Residue.hh
modeler / rna / sugar / SugarVirtualizeMover.cc	chemical / types.hh
modeler / rna / sugar / SugarVirtualizeMover.cc	pose / variant_util.hh
screener / TagDefinition.cc	pose / extra_pose_info_util.hh
screener / TagDefinition.cc	pose / Pose.hh
screener / TagDefinition.cc	conformation / Residue.hh
screener / TagDefinition.hh	pose / Pose.fwd.hh
screener / TagDefinition.hh	types.hh
monte_carlo / mover / TransientCutpointHandler.cc	pose / Pose.hh
monte_carlo / mover / TransientCutpointHandler.cc	scoring / ScoreFunction.hh
monte_carlo / mover / TransientCutpointHandler.cc	id / TorsionID.hh
monte_carlo / mover / TransientCutpointHandler.cc	types.hh
monte_carlo / mover / TransientCutpointHandler.cc	pose / rna / util.hh
monte_carlo / mover / TransientCutpointHandler.cc	chemical / rna / util.hh
monte_carlo / mover / TransientCutpointHandler.cc	pose / variant_util.hh
monte_carlo / mover / TransientCutpointHandler.cc	chemical / VariantType.hh
monte_carlo / mover / TransientCutpointHandler.hh	kinematics / FoldTree.hh
monte_carlo / mover / TransientCutpointHandler.hh	pose / Pose.fwd.hh
monte_carlo / mover / TransientCutpointHandler.hh	types.hh
modeler / rna / util.cc	scoring / constraints / AngleConstraint.hh
modeler / rna / rigid_body / util.cc	scoring / constraints / AngleConstraint.hh
sampler / protein / util.cc	pose / annotated_sequence.hh
modeler / rna / util.cc	id / AtomID.hh
legacy / modeler / protein / util.cc	id / AtomID.hh
modeler / protein / util.cc	id / AtomID.hh
modeler / util.cc	id / AtomID.hh
modeler / rna / util.cc	id / AtomID_Map.hh
legacy / modeler / protein / util.cc	id / AtomID_Map.hh
modeler / protein / util.cc	id / AtomID_Map.hh
modeler / util.cc	id / AtomID_Map.hh
modeler / working_parameters / util.cc	pose / toolbox / AtomLevelDomainMap.hh
modeler / rna / util.cc	pose / toolbox / AtomLevelDomainMap.hh
modeler / rna / util.cc	scoring / constraints / AtomPairConstraint.hh
modeler / rna / rigid_body / util.cc	scoring / constraints / AtomPairConstraint.hh
modeler / rna / sugar / util.cc	optimization / AtomTreeMinimizer.hh
modeler / rna / util.cc	optimization / AtomTreeMinimizer.hh
modeler / rna / util.cc	chemical / AtomType.hh
modeler / rna / rigid_body / util.cc	chemical / AtomType.hh
legacy / modeler / protein / util.cc	io / silent / BinarySilentStruct.hh
sampler / protein / util.cc	io / silent / BinarySilentStruct.hh
monte_carlo / util.cc	io / silent / BinarySilentStruct.hh
modeler / util.cc	pose / datacache / CacheableDataType.hh
modeler / util.cc	scoring / methods / chainbreak_util.hh
legacy / modeler / rna / util.cc	chemical / ChemicalManager.hh
modeler / rna / util.cc	chemical / ChemicalManager.hh
modeler / rna / rigid_body / util.cc	chemical / ChemicalManager.hh
sampler / protein / util.cc	chemical / ChemicalManager.hh
modeler / rna / util.cc	scoring / func / CircularSplineFunc.hh
modeler / movemap / util.cc	conformation / Conformation.hh
modeler / util.cc	conformation / Conformation.hh
modeler / protein / util.cc	fragment / ConstantLengthFragSet.hh
modeler / rna / rigid_body / util.cc	scoring / constraints / ConstraintSet.fwd.hh
modeler / rna / util.cc	scoring / constraints / ConstraintSet.hh
modeler / rna / rigid_body / util.cc	scoring / constraints / ConstraintSet.hh
modeler / util.cc	scoring / constraints / ConstraintSet.hh
modeler / rna / util.cc	scoring / constraints / DihedralConstraint.hh
modeler / util.cc	kinematics / Edge.hh
modeler / packer / util.cc	scoring / Energies.hh
modeler / util.cc	scoring / Energies.hh
modeler / packer / util.cc	scoring / EnergyGraph.hh
modeler / rna / phosphate / util.cc	scoring / methods / EnergyMethodOptions.hh
modeler / rna / sugar / util.cc	pose / extra_pose_info_util.hh
monte_carlo / util.cc	pose / extra_pose_info_util.hh
modeler / util.cc	pose / extra_pose_info_util.hh
modeler / rna / util.cc	scoring / func / FadeFunc.hh
modeler / working_parameters / util.cc	kinematics / FoldTree.hh
modeler / protein / util.cc	fragment / FragData.hh
modeler / protein / util.cc	fragment / FragSet.hh
legacy / modeler / protein / util.cc	fragment / Frame.hh
modeler / protein / util.cc	fragment / Frame.hh
modeler / protein / util.cc	fragment / FrameList.hh
modeler / working_parameters / util.cc	pose / full_model_info / FullModelInfo.hh
modeler / rna / util.cc	pose / full_model_info / FullModelInfo.hh
sampler / rna / util.cc	pose / full_model_info / FullModelInfo.hh
modeler / protein / util.cc	pose / full_model_info / FullModelInfo.hh
modeler / movemap / util.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / util.cc	pose / full_model_info / FullModelInfo.hh
modeler / util.cc	pose / full_model_info / FullModelInfo.hh
modeler / align / util.cc	pose / full_model_info / FullModelInfo.hh
modeler / working_parameters / util.cc	pose / full_model_info / FullModelParameters.hh
modeler / rna / util.cc	scoring / func / HarmonicFunc.hh
modeler / util.cc	scoring / func / HarmonicFunc.hh
sampler / protein / util.cc	scoring / hbonds / HBondOptions.hh
sampler / protein / util.cc	scoring / hbonds / hbonds.hh
sampler / protein / util.cc	scoring / hbonds / HBondSet.hh
modeler / rna / util.cc	import_pose / import_pose.hh
sampler / protein / util.cc	import_pose / import_pose.hh
modeler / util.cc	import_pose / import_pose.hh
modeler / util.cc	scoring / loop_graph / LoopGraph.hh
modeler / rna / sugar / util.cc	optimization / MinimizerOptions.hh
modeler / rna / rigid_body / util.cc	optimization / MinimizerOptions.hh
modeler / working_parameters / util.cc	kinematics / MoveMap.hh
modeler / rna / sugar / util.cc	kinematics / MoveMap.hh
modeler / rna / util.cc	kinematics / MoveMap.hh
modeler / movemap / util.cc	kinematics / MoveMap.hh
modeler / util.cc	kinematics / MoveMap.hh
legacy / modeler / protein / util.cc	id / NamedAtomID.hh
modeler / protein / util.cc	id / NamedAtomID.hh
sampler / protein / util.cc	id / NamedAtomID.hh
modeler / rna / phosphate / util.cc	id / NamedAtomID.hh
modeler / movemap / util.cc	id / NamedAtomID.hh
modeler / rna / util.cc	pack / pack_rotamers.hh
modeler / rna / util.cc	pack / task / PackerTask.hh
modeler / rna / sugar / util.cc	pose / PDBInfo.hh
modeler / util.cc	pose / PDBInfo.hh
modeler / working_parameters / util.cc	pose / Pose.hh
modeler / rna / sugar / util.cc	pose / Pose.hh
legacy / modeler / rna / util.cc	pose / Pose.hh
modeler / rna / util.cc	pose / Pose.hh
sampler / rna / util.cc	pose / Pose.hh
modeler / rna / rigid_body / util.cc	pose / Pose.hh
legacy / modeler / protein / util.cc	pose / Pose.hh
modeler / protein / util.cc	pose / Pose.hh
sampler / protein / util.cc	pose / Pose.hh
modeler / polar_hydrogens / util.cc	pose / Pose.hh
modeler / rna / phosphate / util.cc	pose / Pose.hh
modeler / packer / util.cc	pose / Pose.hh
modeler / movemap / util.cc	pose / Pose.hh
monte_carlo / util.cc	pose / Pose.hh
modeler / util.cc	pose / Pose.hh
modeler / protein / loop_close / util.cc	pose / Pose.hh
modeler / align / util.cc	pose / Pose.hh
legacy / modeler / rna / util.cc	conformation / Residue.hh
modeler / rna / util.cc	conformation / Residue.hh
modeler / rna / rigid_body / util.cc	conformation / Residue.hh
modeler / packer / util.cc	conformation / Residue.hh
modeler / movemap / util.cc	conformation / Residue.hh
modeler / util.cc	conformation / Residue.hh
modeler / rna / util.cc	conformation / ResidueFactory.hh
modeler / rna / rigid_body / util.cc	conformation / ResidueFactory.hh
modeler / rna / phosphate / util.cc	conformation / ResidueFactory.hh
modeler / rna / util.cc	chemical / ResidueProperties.hh
modeler / rna / util.cc	chemical / ResidueType.hh
sampler / rna / util.cc	chemical / ResidueType.hh
modeler / polar_hydrogens / util.cc	chemical / ResidueType.hh
modeler / packer / util.cc	chemical / ResidueType.hh
modeler / movemap / util.cc	chemical / ResidueType.hh
modeler / rna / util.cc	chemical / ResidueTypeSet.hh
modeler / rna / rigid_body / util.cc	chemical / ResidueTypeSet.hh
modeler / rna / phosphate / util.cc	chemical / ResidueTypeSet.hh
modeler / util.cc	chemical / ResidueTypeSet.hh
legacy / modeler / protein / util.cc	scoring / rms_util.hh
modeler / protein / util.cc	scoring / rms_util.hh
monte_carlo / util.cc	scoring / rms_util.hh
modeler / align / util.cc	scoring / rms_util.hh
modeler / rna / util.cc	scoring / rms_util.tmpl.hh
modeler / rna / rigid_body / util.cc	scoring / rms_util.tmpl.hh
modeler / rna / util.cc	pose / rna / RNA_BaseDoubletClasses.hh
modeler / rna / util.cc	pose / rna / RNA_BasePairClassifier.hh
modeler / util.cc	scoring / rna / RNA_CentroidInfo.hh
legacy / modeler / rna / util.cc	chemical / rna / RNA_FittedTorsionInfo.hh
modeler / rna / rigid_body / util.cc	chemical / rna / RNA_FittedTorsionInfo.hh
modeler / packer / util.cc	chemical / rna / RNA_Info.hh
modeler / util.cc	scoring / rna / RNA_ScoringInfo.hh
modeler / util.cc	pose / rna / secstruct_legacy / RNA_SecStructLegacyInfo.hh
modeler / rna / rigid_body / util.cc	scoring / rna / RNA_TorsionPotential.hh
modeler / rna / util.cc	pack / rotamer_trials.hh
modeler / rna / sugar / util.cc	scoring / ScoreFunction.hh
modeler / rna / util.cc	scoring / ScoreFunction.hh
modeler / rna / rigid_body / util.cc	scoring / ScoreFunction.hh
sampler / protein / util.cc	scoring / ScoreFunction.hh
modeler / rna / phosphate / util.cc	scoring / ScoreFunction.hh
modeler / packer / util.cc	scoring / ScoreFunction.hh
monte_carlo / util.cc	scoring / ScoreFunction.hh
modeler / util.cc	scoring / ScoreFunction.hh
modeler / rna / sugar / util.cc	scoring / ScoreFunctionFactory.hh
sampler / protein / util.cc	scoring / ScoreFunctionFactory.hh
modeler / util.cc	scoring / ScoreFunctionFactory.hh
modeler / rna / sugar / util.cc	scoring / ScoreType.hh
modeler / rna / util.cc	scoring / ScoreType.hh
modeler / rna / util.cc	io / silent / SilentFileData.hh
legacy / modeler / protein / util.cc	io / silent / SilentFileData.hh
sampler / protein / util.cc	io / silent / SilentFileData.hh
monte_carlo / util.cc	io / silent / SilentFileData.hh
legacy / modeler / protein / util.cc	io / silent / SilentFileOptions.hh
sampler / protein / util.cc	io / silent / SilentFileOptions.hh
monte_carlo / util.cc	io / silent / SilentFileOptions.hh
monte_carlo / util.cc	io / silent / SilentStruct.hh
modeler / working_parameters / util.cc	pose / subpose_manipulation_util.hh
modeler / rna / util.cc	pack / task / TaskFactory.hh
modeler / rna / sugar / util.cc	id / TorsionID.hh
modeler / rna / util.cc	id / TorsionID.hh
modeler / rna / rigid_body / util.cc	id / TorsionID.hh
sampler / protein / util.cc	id / TorsionID.hh
modeler / rna / phosphate / util.cc	id / TorsionID.hh
modeler / protein / loop_close / util.cc	id / TorsionID.hh
modeler / rna / util.cc	types.hh
modeler / rna / rigid_body / util.cc	types.hh
legacy / modeler / protein / util.cc	types.hh
modeler / protein / util.cc	types.hh
monte_carlo / util.cc	types.hh
modeler / util.cc	types.hh
modeler / working_parameters / util.cc	pose / util.hh
modeler / working_parameters / util.cc	pose / full_model_info / util.hh
modeler / rna / sugar / util.cc	pose / copydofs / util.hh
legacy / modeler / rna / util.cc	sequence / util.hh
legacy / modeler / rna / util.cc	pose / rna / util.hh
legacy / modeler / rna / util.cc	chemical / rna / util.hh
modeler / rna / util.cc	scoring / constraints / util.hh
modeler / rna / util.cc	chemical / rna / util.hh
modeler / rna / util.cc	pose / rna / util.hh
modeler / rna / util.cc	pose / full_model_info / util.hh
modeler / rna / util.cc	chemical / util.hh
sampler / rna / util.cc	pose / rna / util.hh
sampler / rna / util.cc	chemical / rna / util.hh
modeler / rna / rigid_body / util.cc	scoring / constraints / util.hh
modeler / rna / rigid_body / util.cc	chemical / util.hh
modeler / rna / rigid_body / util.cc	chemical / rna / util.hh
legacy / modeler / protein / util.cc	pose / util.hh
legacy / modeler / protein / util.cc	pose / full_model_info / util.hh
legacy / modeler / protein / util.cc	io / silent / util.hh
modeler / protein / util.cc	pose / util.hh
modeler / protein / util.cc	pose / full_model_info / util.hh
sampler / protein / util.cc	io / silent / util.hh
modeler / rna / phosphate / util.cc	scoring / constraints / util.hh
modeler / rna / phosphate / util.cc	chemical / rna / util.hh
modeler / packer / util.cc	pose / util.hh
modeler / movemap / util.cc	pose / full_model_info / util.hh
monte_carlo / util.cc	chemical / rna / util.hh
monte_carlo / util.cc	pose / rna / util.hh
monte_carlo / util.cc	pose / full_model_info / util.hh
monte_carlo / util.cc	io / silent / util.hh
modeler / util.cc	pose / full_model_info / util.hh
modeler / util.cc	pose / copydofs / util.hh
modeler / util.cc	chemical / rna / util.hh
modeler / align / util.cc	pose / util.hh
modeler / rna / util.cc	pose / util.tmpl.hh
modeler / util.cc	pose / util.tmpl.hh
modeler / rna / sugar / util.cc	pose / variant_util.hh
modeler / rna / util.cc	pose / variant_util.hh
sampler / protein / util.cc	pose / variant_util.hh
modeler / rna / phosphate / util.cc	pose / variant_util.hh
modeler / util.cc	pose / variant_util.hh
modeler / working_parameters / util.cc	chemical / VariantType.hh
sampler / rna / util.cc	chemical / VariantType.hh
modeler / rna / rigid_body / util.cc	chemical / VariantType.hh
sampler / protein / util.cc	chemical / VariantType.hh
modeler / rna / phosphate / util.cc	chemical / VariantType.hh
modeler / movemap / util.cc	chemical / VariantType.hh
modeler / util.cc	chemical / VariantType.hh
modeler / rna / util.hh	chemical / AA.hh
legacy / modeler / protein / util.hh	id / AtomID.fwd.hh
modeler / protein / util.hh	id / AtomID.fwd.hh
modeler / util.hh	id / AtomID.fwd.hh
modeler / align / util.hh	id / AtomID.hh
modeler / rna / util.hh	id / AtomID_Map.fwd.hh
legacy / modeler / protein / util.hh	id / AtomID_Map.fwd.hh
modeler / protein / util.hh	id / AtomID_Map.fwd.hh
modeler / util.hh	id / AtomID_Map.fwd.hh
modeler / align / util.hh	id / AtomID_Map.hh
modeler / working_parameters / util.hh	pose / toolbox / AtomLevelDomainMap.fwd.hh
modeler / movemap / util.hh	pose / toolbox / AtomLevelDomainMap.hh
modeler / rna / util.hh	io / silent / BinarySilentStruct.hh
modeler / util.hh	kinematics / Edge.fwd.hh
modeler / rna / phosphate / util.hh	scoring / methods / EnergyMethodOptions.fwd.hh
legacy / modeler / rna / util.hh	kinematics / FoldTree.fwd.hh
modeler / rna / util.hh	kinematics / FoldTree.fwd.hh
modeler / util.hh	kinematics / FoldTree.fwd.hh
modeler / util.hh	pose / full_model_info / FullModelInfo.fwd.hh
modeler / rna / util.hh	optimization / MinimizerOptions.hh
modeler / working_parameters / util.hh	kinematics / MoveMap.fwd.hh
modeler / rna / util.hh	kinematics / MoveMap.fwd.hh
modeler / movemap / util.hh	kinematics / MoveMap.fwd.hh
modeler / util.hh	kinematics / MoveMap.fwd.hh
modeler / rna / util.hh	pack / task / PackerTask.fwd.hh
modeler / working_parameters / util.hh	pose / Pose.fwd.hh
modeler / rna / sugar / util.hh	pose / Pose.fwd.hh
legacy / modeler / rna / util.hh	pose / Pose.fwd.hh
modeler / rna / util.hh	pose / Pose.fwd.hh
sampler / rna / util.hh	pose / Pose.fwd.hh
modeler / rna / rigid_body / util.hh	pose / Pose.fwd.hh
legacy / modeler / protein / util.hh	pose / Pose.fwd.hh
modeler / protein / util.hh	pose / Pose.fwd.hh
sampler / protein / util.hh	pose / Pose.fwd.hh
modeler / polar_hydrogens / util.hh	pose / Pose.fwd.hh
modeler / rna / phosphate / util.hh	pose / Pose.fwd.hh
modeler / packer / util.hh	pose / Pose.fwd.hh
modeler / movemap / util.hh	pose / Pose.fwd.hh
monte_carlo / util.hh	pose / Pose.fwd.hh
modeler / util.hh	pose / Pose.fwd.hh
modeler / protein / loop_close / util.hh	pose / Pose.fwd.hh
modeler / align / util.hh	pose / Pose.fwd.hh
modeler / rna / rigid_body / util.hh	conformation / Residue.fwd.hh
modeler / rna / util.hh	conformation / Residue.hh
modeler / polar_hydrogens / util.hh	chemical / ResidueType.fwd.hh
modeler / rna / util.hh	io / silent / RNA_SilentStruct.hh
modeler / util.hh	io / silent / RNA_SilentStruct.hh
modeler / rna / sugar / util.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / util.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / phosphate / util.hh	scoring / ScoreFunction.fwd.hh
modeler / packer / util.hh	scoring / ScoreFunction.fwd.hh
modeler / util.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / util.hh	io / silent / SilentFileData.hh
legacy / modeler / protein / util.hh	io / silent / SilentFileData.hh
modeler / protein / util.hh	io / silent / SilentFileData.hh
monte_carlo / util.hh	io / silent / SilentStruct.fwd.hh
sampler / protein / util.hh	kinematics / Stub.fwd.hh
modeler / working_parameters / util.hh	types.hh
modeler / rna / sugar / util.hh	types.hh
screener / util.hh	types.hh
legacy / modeler / rna / util.hh	types.hh
modeler / rna / util.hh	types.hh
sampler / rna / util.hh	types.hh
modeler / rna / rigid_body / util.hh	types.hh
legacy / modeler / protein / util.hh	types.hh
modeler / protein / util.hh	types.hh
sampler / protein / util.hh	types.hh
modeler / polar_hydrogens / util.hh	types.hh
modeler / rna / phosphate / util.hh	types.hh
modeler / packer / util.hh	types.hh
modeler / movemap / util.hh	types.hh
monte_carlo / util.hh	types.hh
modeler / util.hh	types.hh
modeler / align / util.hh	types.hh
modeler / util.hh	chemical / VariantType.hh
monte_carlo / mover / VaryLoopLengthMover.cc	pose / full_model_info / FullModelInfo.hh
monte_carlo / mover / VaryLoopLengthMover.cc	pose / full_model_info / FullModelParameters.hh
monte_carlo / mover / VaryLoopLengthMover.cc	pose / Pose.hh
monte_carlo / mover / VaryLoopLengthMover.cc	pose / full_model_info / util.hh
monte_carlo / mover / VaryLoopLengthMover.hh	pose / full_model_info / FullModelParameters.fwd.hh
monte_carlo / mover / VaryLoopLengthMover.hh	pose / Pose.fwd.hh
screener / VDW_BinScreener.cc	pose / Pose.hh
screener / VDW_BinScreener.cc	conformation / Residue.hh
screener / VDW_BinScreener.cc	kinematics / Stub.hh
screener / VDW_BinScreener.hh	pose / Pose.fwd.hh
screener / VDW_BinScreener.hh	conformation / Residue.fwd.hh
screener / VDW_BinScreener.hh	kinematics / Stub.fwd.hh
screener / VDW_BinScreener.hh	types.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	pose / extra_pose_info_util.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	pose / Pose.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	scoring / ScoreFunction.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	scoring / ScoreType.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	chemical / rna / util.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	pose / rna / util.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	pose / variant_util.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.cc	chemical / VariantType.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.hh	pose / Pose.fwd.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / sugar / VirtualSugarJustInTimeInstantiator.hh	types.hh
modeler / rna / sugar / VirtualSugarSampler.cc	optimization / AtomTreeMinimizer.hh
modeler / rna / sugar / VirtualSugarSampler.cc	chemical / AtomType.hh
modeler / rna / sugar / VirtualSugarSampler.cc	chemical / ChemicalManager.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / constraints / ConstraintSet.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / Energies.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / EnergyMap.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / methods / EnergyMethodOptions.hh
modeler / rna / sugar / VirtualSugarSampler.cc	pose / extra_pose_info_util.hh
modeler / rna / sugar / VirtualSugarSampler.cc	optimization / MinimizerOptions.hh
modeler / rna / sugar / VirtualSugarSampler.cc	pose / Pose.hh
modeler / rna / sugar / VirtualSugarSampler.cc	conformation / Residue.hh
modeler / rna / sugar / VirtualSugarSampler.cc	chemical / ResidueTypeSet.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / rna / RNA_TorsionPotential.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / ScoreFunction.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / ScoreFunctionFactory.hh
modeler / rna / sugar / VirtualSugarSampler.cc	types.hh
modeler / rna / sugar / VirtualSugarSampler.cc	scoring / constraints / util.hh
modeler / rna / sugar / VirtualSugarSampler.cc	pose / full_model_info / util.hh
modeler / rna / sugar / VirtualSugarSampler.cc	pose / rna / util.hh
modeler / rna / sugar / VirtualSugarSampler.cc	chemical / rna / util.hh
modeler / rna / sugar / VirtualSugarSampler.cc	chemical / util.hh
modeler / rna / sugar / VirtualSugarSampler.cc	pose / variant_util.hh
modeler / rna / sugar / VirtualSugarSampler.cc	chemical / VariantType.hh
modeler / rna / sugar / VirtualSugarSampler.hh	scoring / constraints / ConstraintSet.fwd.hh
modeler / rna / sugar / VirtualSugarSampler.hh	scoring / constraints / ConstraintSet.hh
modeler / rna / sugar / VirtualSugarSampler.hh	kinematics / FoldTree.hh
modeler / rna / sugar / VirtualSugarSampler.hh	pose / Pose.fwd.hh
modeler / rna / sugar / VirtualSugarSampler.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / sugar / VirtualSugarSampler.hh	types.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.cc	conformation / Conformation.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.cc	pose / extra_pose_info_util.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.cc	pose / full_model_info / FullModelInfo.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.cc	pose / Pose.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.cc	scoring / ScoreFunction.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.cc	pose / rna / util.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.cc	pose / variant_util.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.hh	pose / Pose.fwd.hh
modeler / rna / sugar / VirtualSugarSamplerFromStringList.hh	scoring / ScoreFunction.fwd.hh