hybridization → core Relation

File in src/protocols/hybridization	Includes file in src/core
AllResiduesChanged.hh	fragment / FragSet.fwd.hh
AllResiduesChanged.hh	pose / Pose.hh
AllResiduesChanged.hh	conformation / Residue.hh
CartesianHybridize.cc	scoring / constraints / AtomPairConstraint.hh
CartesianHybridize.cc	optimization / AtomTreeMinimizer.hh
CartesianHybridize.cc	pose / datacache / CacheableDataType.hh
CartesianHybridize.cc	optimization / CartesianMinimizer.hh
CartesianHybridize.cc	chemical / ChemicalManager.hh
CartesianHybridize.cc	fragment / ConstantLengthFragSet.hh
CartesianHybridize.cc	scoring / dssp / Dssp.hh
CartesianHybridize.cc	scoring / Energies.hh
CartesianHybridize.cc	scoring / methods / EnergyMethodOptions.hh
CartesianHybridize.cc	kinematics / FoldTree.hh
CartesianHybridize.cc	fragment / FragData.hh
CartesianHybridize.cc	fragment / FragmentIO.hh
CartesianHybridize.cc	fragment / FragSet.hh
CartesianHybridize.cc	fragment / Frame.hh
CartesianHybridize.cc	fragment / FrameIterator.hh
CartesianHybridize.cc	import_pose / import_pose.hh
CartesianHybridize.cc	optimization / MinimizerOptions.hh
CartesianHybridize.cc	kinematics / MoveMap.hh
CartesianHybridize.cc	pack / pack_rotamers.hh
CartesianHybridize.cc	pack / task / PackerTask.hh
CartesianHybridize.cc	pose / PDBInfo.hh
CartesianHybridize.cc	pose / Pose.hh
CartesianHybridize.cc	pose / Remarks.hh
CartesianHybridize.cc	scoring / rms_util.hh
CartesianHybridize.cc	scoring / constraints / ScalarWeightedFunc.hh
CartesianHybridize.cc	scoring / ScoreFunction.hh
CartesianHybridize.cc	scoring / ScoreFunctionFactory.hh
CartesianHybridize.cc	sequence / Sequence.hh
CartesianHybridize.cc	sequence / SequenceAlignment.hh
CartesianHybridize.cc	id / SequenceMapping.hh
CartesianHybridize.cc	scoring / constraints / SOGFunc.hh
CartesianHybridize.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
CartesianHybridize.cc	conformation / symmetry / SymmetricConformation.hh
CartesianHybridize.cc	scoring / symmetry / SymmetricScoreFunction.hh
CartesianHybridize.cc	conformation / symmetry / SymmetryInfo.hh
CartesianHybridize.cc	pack / task / TaskFactory.hh
CartesianHybridize.cc	pack / task / operation / TaskOperations.hh
CartesianHybridize.cc	pose / symmetry / util.hh
CartesianHybridize.cc	conformation / util.hh
CartesianHybridize.cc	pose / util.hh
CartesianHybridize.cc	sequence / util.hh
CartesianHybridize.hh	id / AtomID.hh
CartesianHybridize.hh	id / AtomID_Map.hh
CartesianHybridize.hh	fragment / FragData.hh
CartesianHybridize.hh	fragment / FragSet.hh
CartesianHybridize.hh	util / kinematics_util.hh
CartesianHybridize.hh	scoring / ScoreFunction.hh
CartesianSampler.cc	scoring / constraints / AtomPairConstraint.hh
CartesianSampler.cc	optimization / AtomTreeMinimizer.hh
CartesianSampler.cc	pose / datacache / CacheableDataType.hh
CartesianSampler.cc	optimization / CartesianMinimizer.hh
CartesianSampler.cc	chemical / ChemicalManager.hh
CartesianSampler.cc	fragment / ConstantLengthFragSet.hh
CartesianSampler.cc	scoring / electron_density / ElectronDensity.hh
CartesianSampler.cc	scoring / Energies.hh
CartesianSampler.cc	scoring / methods / EnergyMethodOptions.hh
CartesianSampler.cc	kinematics / FoldTree.hh
CartesianSampler.cc	fragment / FragData.hh
CartesianSampler.cc	fragment / FragmentIO.hh
CartesianSampler.cc	fragment / FragSet.hh
CartesianSampler.cc	fragment / Frame.hh
CartesianSampler.cc	fragment / FrameIterator.hh
CartesianSampler.cc	optimization / MinimizerOptions.hh
CartesianSampler.cc	kinematics / MoveMap.hh
CartesianSampler.cc	pack / pack_rotamers.hh
CartesianSampler.cc	pack / task / PackerTask.hh
CartesianSampler.cc	pose / PDBInfo.hh
CartesianSampler.cc	pose / Pose.hh
CartesianSampler.cc	pose / Remarks.hh
CartesianSampler.cc	scoring / rms_util.hh
CartesianSampler.cc	scoring / constraints / ScalarWeightedFunc.hh
CartesianSampler.cc	scoring / ScoreFunction.hh
CartesianSampler.cc	scoring / ScoreFunctionFactory.hh
CartesianSampler.cc	pose / selection.hh
CartesianSampler.cc	sequence / Sequence.hh
CartesianSampler.cc	sequence / SequenceAlignment.hh
CartesianSampler.cc	id / SequenceMapping.hh
CartesianSampler.cc	scoring / constraints / SOGFunc.hh
CartesianSampler.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
CartesianSampler.cc	conformation / symmetry / SymmetricConformation.hh
CartesianSampler.cc	scoring / symmetry / SymmetricScoreFunction.hh
CartesianSampler.cc	conformation / symmetry / SymmetryInfo.hh
CartesianSampler.cc	pack / task / TaskFactory.hh
CartesianSampler.cc	pack / task / operation / TaskOperations.hh
CartesianSampler.cc	pose / symmetry / util.hh
CartesianSampler.cc	conformation / util.hh
CartesianSampler.cc	pose / util.hh
CartesianSampler.cc	sequence / util.hh
CartesianSampler.hh	id / AtomID.hh
CartesianSampler.hh	id / AtomID_Map.hh
CartesianSampler.hh	fragment / FragData.hh
CartesianSampler.hh	fragment / FragSet.hh
CartesianSampler.hh	util / kinematics_util.hh
CartesianSampler.hh	scoring / ScoreFunction.hh
ChunkTrialMover.cc	id / AtomID.hh
ChunkTrialMover.cc	id / AtomID_Map.hh
ChunkTrialMover.cc	kinematics / FoldTree.hh
ChunkTrialMover.cc	fragment / Frame.hh
ChunkTrialMover.cc	fragment / FrameIterator.hh
ChunkTrialMover.cc	util / kinematics_util.hh
ChunkTrialMover.cc	pose / PDBInfo.hh
ChunkTrialMover.cc	conformation / Residue.hh
ChunkTrialMover.hh	id / AtomID.hh
ChunkTrialMover.hh	id / AtomID_Map.hh
ChunkTrialMover.hh	fragment / Frame.hh
ChunkTrialMover.hh	fragment / FrameIterator.hh
ChunkTrialMover.hh	util / kinematics_util.hh
DDomainParse.cc	scoring / constraints / AtomPairConstraint.hh
DDomainParse.cc	scoring / constraints / Constraint.hh
DDomainParse.cc	scoring / constraints / ConstraintIO.hh
DDomainParse.cc	scoring / constraints / ConstraintSet.hh
DDomainParse.cc	kinematics / Edge.hh
DDomainParse.cc	kinematics / FoldTree.hh
DDomainParse.cc	kinematics / Jump.hh
DDomainParse.cc	pack / task / PackerTask.hh
DDomainParse.cc	pose / PDBInfo.hh
DDomainParse.cc	pose / Pose.hh
DDomainParse.cc	conformation / Residue.hh
DDomainParse.cc	chemical / ResidueType.hh
DDomainParse.cc	scoring / constraints / ScalarWeightedFunc.hh
DDomainParse.cc	scoring / constraints / SOGFunc.hh
DDomainParse.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
DDomainParse.cc	conformation / symmetry / SymmetricConformation.hh
DDomainParse.cc	conformation / symmetry / SymmetryInfo.hh
DDomainParse.cc	types.hh
DDomainParse.cc	pose / symmetry / util.hh
DDomainParse.cc	scoring / constraints / util.hh
DDomainParse.hh	kinematics / Edge.hh
DDomainParse.hh	kinematics / FoldTree.hh
DDomainParse.hh	kinematics / Jump.hh
DDomainParse.hh	pose / Pose.hh
DDomainParse.hh	conformation / Residue.hh
DDomainParse.hh	chemical / ResidueType.hh
DDomainParse.hh	types.hh
DomainAssembly.cc	id / AtomID.hh
DomainAssembly.cc	id / AtomID_Map.hh
DomainAssembly.cc	conformation / Conformation.hh
DomainAssembly.cc	scoring / Energies.hh
DomainAssembly.cc	scoring / methods / EnergyMethodOptions.hh
DomainAssembly.cc	pose / PDBInfo.hh
DomainAssembly.cc	scoring / ScoreFunction.hh
DomainAssembly.cc	scoring / ScoreFunctionFactory.hh
DomainAssembly.cc	types.hh
DomainAssembly.cc	pose / util.hh
DomainAssembly.cc	chemical / VariantType.hh
DomainAssembly.hh	scoring / constraints / AtomPairConstraint.hh
DomainAssembly.hh	scoring / constraints / BoundConstraint.hh
DomainAssembly.hh	chemical / ChemicalManager.hh
DomainAssembly.hh	kinematics / FoldTree.hh
DomainAssembly.hh	fragment / FragSet.fwd.hh
DomainAssembly.hh	fragment / FragSet.hh
DomainAssembly.hh	kinematics / Jump.hh
DomainAssembly.hh	pose / Pose.hh
DomainAssembly.hh	conformation / Residue.hh
DomainAssembly.hh	scoring / ScoreFunction.hh
DomainAssembly.hh	scoring / ScoreFunctionFactory.hh
DomainAssembly.hh	types.hh
FoldTreeHybridize.cc	id / AtomID.hh
FoldTreeHybridize.cc	id / AtomID_Map.hh
FoldTreeHybridize.cc	scoring / constraints / AtomPairConstraint.hh
FoldTreeHybridize.cc	scoring / constraints / BoundConstraint.hh
FoldTreeHybridize.cc	conformation / Conformation.hh
FoldTreeHybridize.cc	fragment / ConstantLengthFragSet.hh
FoldTreeHybridize.cc	scoring / constraints / ConstraintIO.hh
FoldTreeHybridize.cc	scoring / constraints / ConstraintSet.hh
FoldTreeHybridize.cc	scoring / methods / EnergyMethodOptions.hh
FoldTreeHybridize.cc	fragment / Frame.hh
FoldTreeHybridize.cc	fragment / FrameIterator.hh
FoldTreeHybridize.cc	import_pose / import_pose.hh
FoldTreeHybridize.cc	util / kinematics_util.hh
FoldTreeHybridize.cc	kinematics / MoveMap.hh
FoldTreeHybridize.cc	pack / task / PackerTask.hh
FoldTreeHybridize.cc	pose / PDBInfo.hh
FoldTreeHybridize.cc	pose / Pose.fwd.hh
FoldTreeHybridize.cc	pose / Pose.hh
FoldTreeHybridize.cc	conformation / Residue.hh
FoldTreeHybridize.cc	conformation / ResidueFactory.hh
FoldTreeHybridize.cc	chemical / ResidueTypeSet.hh
FoldTreeHybridize.cc	scoring / rms_util.hh
FoldTreeHybridize.cc	scoring / ScoreFunction.hh
FoldTreeHybridize.cc	scoring / ScoreFunctionFactory.hh
FoldTreeHybridize.cc	fragment / SecondaryStructure.hh
FoldTreeHybridize.cc	sequence / Sequence.hh
FoldTreeHybridize.cc	scoring / dssp / StrandPairing.hh
FoldTreeHybridize.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
FoldTreeHybridize.cc	conformation / symmetry / SymmetricConformation.hh
FoldTreeHybridize.cc	conformation / symmetry / SymmetryInfo.hh
FoldTreeHybridize.cc	pose / symmetry / util.hh
FoldTreeHybridize.cc	fragment / util.hh
FoldTreeHybridize.cc	conformation / util.hh
FoldTreeHybridize.cc	sequence / util.hh
FoldTreeHybridize.cc	pose / util.hh
FoldTreeHybridize.cc	chemical / VariantType.hh
FoldTreeHybridize.hh	id / AtomID.hh
FoldTreeHybridize.hh	id / AtomID_Map.hh
FoldTreeHybridize.hh	kinematics / FoldTree.hh
FoldTreeHybridize.hh	fragment / FragSet.fwd.hh
FoldTreeHybridize.hh	util / kinematics_util.hh
FoldTreeHybridize.hh	scoring / dssp / PairingsList.hh
FoldTreeHybridize.hh	scoring / ScoreFunction.hh
HybridizeFoldtreeDynamic.cc	conformation / Conformation.hh
HybridizeFoldtreeDynamic.cc	kinematics / FoldTree.hh
HybridizeFoldtreeDynamic.cc	import_pose / import_pose.hh
HybridizeFoldtreeDynamic.cc	util / kinematics_util.hh
HybridizeFoldtreeDynamic.cc	pack / task / PackerTask.hh
HybridizeFoldtreeDynamic.cc	pose / Pose.hh
HybridizeFoldtreeDynamic.cc	scoring / rms_util.hh
HybridizeFoldtreeDynamic.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
HybridizeFoldtreeDynamic.cc	conformation / symmetry / SymmetricConformation.hh
HybridizeFoldtreeDynamic.cc	conformation / symmetry / SymmetryInfo.hh
HybridizeFoldtreeDynamic.cc	types.hh
HybridizeFoldtreeDynamic.cc	conformation / symmetry / util.hh
HybridizeFoldtreeDynamic.cc	pose / symmetry / util.hh
HybridizeFoldtreeDynamic.cc	pose / util.hh
HybridizeFoldtreeDynamic.hh	kinematics / FoldTree.hh
HybridizeFoldtreeDynamic.hh	pose / Pose.fwd.hh
HybridizeFoldtreeDynamic.hh	types.hh
HybridizeProtocol.cc	pose / datacache / CacheableDataType.hh
HybridizeProtocol.cc	optimization / CartesianMinimizer.hh
HybridizeProtocol.cc	chemical / ChemicalManager.hh
HybridizeProtocol.cc	fragment / ConstantLengthFragSet.hh
HybridizeProtocol.cc	scoring / constraints / Constraint.hh
HybridizeProtocol.cc	scoring / constraints / ConstraintIO.hh
HybridizeProtocol.cc	scoring / constraints / ConstraintSet.hh
HybridizeProtocol.cc	scoring / constraints / CoordinateConstraint.hh
HybridizeProtocol.cc	scoring / dssp / Dssp.hh
HybridizeProtocol.cc	kinematics / FoldTree.hh
HybridizeProtocol.cc	fragment / FragData.hh
HybridizeProtocol.cc	fragment / FragmentIO.hh
HybridizeProtocol.cc	fragment / FragSet.hh
HybridizeProtocol.cc	fragment / Frame.hh
HybridizeProtocol.cc	fragment / FrameIterator.hh
HybridizeProtocol.cc	scoring / constraints / HarmonicFunc.hh
HybridizeProtocol.cc	import_pose / import_pose.hh
HybridizeProtocol.cc	fragment / IndependentBBTorsionSRFD.hh
HybridizeProtocol.cc	optimization / MinimizerOptions.hh
HybridizeProtocol.cc	kinematics / MoveMap.hh
HybridizeProtocol.cc	pack / task / operation / NoRepackDisulfides.hh
HybridizeProtocol.cc	pack / task / operation / OperateOnCertainResidues.hh
HybridizeProtocol.cc	pack / task / PackerTask.hh
HybridizeProtocol.cc	pose / PDBInfo.hh
HybridizeProtocol.cc	pose / Pose.hh
HybridizeProtocol.cc	pack / task / operation / ResFilters.hh
HybridizeProtocol.cc	conformation / Residue.hh
HybridizeProtocol.cc	conformation / ResidueFactory.hh
HybridizeProtocol.cc	chemical / ResidueType.hh
HybridizeProtocol.cc	chemical / ResidueTypeSet.hh
HybridizeProtocol.cc	pack / task / operation / ResLvlTaskOperations.hh
HybridizeProtocol.cc	scoring / rms_util.hh
HybridizeProtocol.cc	scoring / ScoreFunctionFactory.hh
HybridizeProtocol.cc	pose / selection.hh
HybridizeProtocol.cc	io / silent / SilentStruct.hh
HybridizeProtocol.cc	io / silent / SilentStructFactory.hh
HybridizeProtocol.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
HybridizeProtocol.cc	conformation / symmetry / SymmetricConformation.hh
HybridizeProtocol.cc	conformation / symmetry / SymmetryInfo.hh
HybridizeProtocol.cc	pack / task / TaskFactory.hh
HybridizeProtocol.cc	pack / task / operation / TaskOperation.hh
HybridizeProtocol.cc	pack / task / operation / TaskOperations.hh
HybridizeProtocol.cc	pose / symmetry / util.hh
HybridizeProtocol.cc	scoring / constraints / util.hh
HybridizeProtocol.cc	sequence / util.hh
HybridizeProtocol.cc	fragment / util.hh
HybridizeProtocol.cc	pose / util.hh
HybridizeProtocol.cc	fragment / picking_old / vall / util.hh
HybridizeProtocol.hh	scoring / constraints / ConstraintSet.fwd.hh
HybridizeProtocol.hh	fragment / FragSet.fwd.hh
HybridizeProtocol.hh	pose / Pose.fwd.hh
HybridizeProtocol.hh	sequence / SequenceAlignment.fwd.hh
HybridizeProtocol.hh	sequence / SequenceAlignment.hh
HybridizeProtocol.hh	pack / task / TaskFactory.fwd.hh
InsertChunkMover.cc	id / AtomID.hh
InsertChunkMover.cc	id / AtomID_Map.hh
InsertChunkMover.cc	kinematics / AtomTree.hh
InsertChunkMover.cc	pose / datacache / CacheableDataType.hh
InsertChunkMover.cc	fragment / Frame.hh
InsertChunkMover.cc	fragment / FrameIterator.hh
InsertChunkMover.cc	util / kinematics_util.hh
InsertChunkMover.cc	pose / Pose.hh
InsertChunkMover.cc	conformation / Residue.hh
InsertChunkMover.cc	conformation / util.hh
InsertChunkMover.cc	pose / util.hh
InsertChunkMover.cc	pose / util.tmpl.hh
InsertChunkMover.hh	id / AtomID.hh
InsertChunkMover.hh	id / AtomID_Map.hh
InsertChunkMover.hh	fragment / Frame.hh
InsertChunkMover.hh	fragment / FrameIterator.hh
InsertChunkMover.hh	util / kinematics_util.hh
InsertChunkMover.hh	pose / Pose.fwd.hh
InsertChunkMover.hh	pose / Pose.hh
TemplateHistory.cc	pose / datacache / CacheableDataType.hh
TemplateHistory.cc	pose / Pose.hh
TemplateHistory.hh	pose / Pose.fwd.hh
TemplateHistory.hh	types.hh
TMalign.hh	id / AtomID.hh
TMalign.hh	id / AtomID_Map.hh
TMalign.hh	pose / PDBInfo.hh
TMalign.hh	pose / Pose.hh
TMalign.hh	conformation / Residue.hh
util.cc	scoring / constraints / AtomPairConstraint.hh
util.cc	fragment / ConstantLengthFragSet.hh
util.cc	scoring / constraints / Constraint.hh
util.cc	scoring / constraints / ConstraintIO.hh
util.cc	scoring / constraints / ConstraintSet.hh
util.cc	scoring / dssp / Dssp.hh
util.cc	kinematics / Edge.hh
util.cc	kinematics / FoldTree.hh
util.cc	fragment / FragSet.hh
util.cc	fragment / Frame.hh
util.cc	fragment / IndependentBBTorsionSRFD.hh
util.cc	kinematics / Jump.hh
util.cc	pack / task / PackerTask.hh
util.cc	pose / PDBInfo.hh
util.cc	pose / Pose.hh
util.cc	conformation / Residue.hh
util.cc	chemical / ResidueType.hh
util.cc	scoring / rms_util.hh
util.cc	scoring / constraints / ScalarWeightedFunc.hh
util.cc	sequence / Sequence.hh
util.cc	scoring / constraints / SOGFunc.hh
util.cc	optimization / symmetry / SymAtomTreeMinimizer.hh
util.cc	conformation / symmetry / SymmetricConformation.hh
util.cc	conformation / symmetry / SymmetryInfo.hh
util.cc	types.hh
util.cc	sequence / util.hh
util.cc	pose / symmetry / util.hh
util.cc	fragment / picking_old / vall / util.hh
util.cc	scoring / constraints / util.hh
util.cc	pose / util.hh
util.hh	id / AtomID.hh
util.hh	id / AtomID_Map.hh
util.hh	kinematics / Edge.hh
util.hh	kinematics / FoldTree.hh
util.hh	fragment / FragSet.fwd.hh
util.hh	kinematics / Jump.hh
util.hh	pose / Pose.hh
util.hh	conformation / Residue.hh
util.hh	chemical / ResidueType.hh
util.hh	sequence / SequenceAlignment.hh
util.hh	types.hh
WeightedFragmentSmoothTrialMover.cc	fragment / Frame.hh
WeightedFragmentSmoothTrialMover.cc	fragment / FrameIterator.hh
WeightedFragmentSmoothTrialMover.hh	fragment / FragSet.hh
WeightedFragmentSmoothTrialMover.hh	fragment / Frame.hh
WeightedFragmentSmoothTrialMover.hh	fragment / FrameList.hh
WeightedFragmentSmoothTrialMover.hh	types.hh
WeightedFragmentTrialMover.cc	fragment / Frame.hh
WeightedFragmentTrialMover.cc	fragment / FrameIterator.hh
WeightedFragmentTrialMover.hh	fragment / FragSet.hh