cyclic_peptide → core Relation

File in src/protocols/cyclic_peptide	Includes file in src/core
crosslinker / 1_4_BBMB_Helper.cc	chemical / AA.hh
crosslinker / 1_4_BBMB_Helper.cc	id / AtomID.hh
crosslinker / 1_4_BBMB_Helper.cc	chemical / ChemicalManager.hh
crosslinker / 1_4_BBMB_Helper.cc	pose / Pose.hh
crosslinker / 1_4_BBMB_Helper.cc	conformation / Residue.hh
crosslinker / 1_4_BBMB_Helper.cc	conformation / ResidueFactory.hh
crosslinker / 1_4_BBMB_Helper.cc	select / residue_selector / ResidueIndexSelector.hh
crosslinker / 1_4_BBMB_Helper.cc	chemical / ResidueType.hh
crosslinker / 1_4_BBMB_Helper.cc	chemical / ResidueTypeSet.hh
crosslinker / 1_4_BBMB_Helper.cc	scoring / rms_util.hh
crosslinker / 1_4_BBMB_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / 1_4_BBMB_Helper.cc	conformation / symmetry / SymmetryInfo.hh
crosslinker / 1_4_BBMB_Helper.hh	pose / Pose.fwd.hh
crosslinker / 1_4_BBMB_Helper.hh	types.hh
CrankshaftFlipMover.cc	chemical / AA.hh
CrankshaftFlipMover.cc	pose / Pose.hh
CrankshaftFlipMover.cc	conformation / Residue.hh
CrankshaftFlipMover.cc	select / residue_selector / ResidueSelector.hh
CrankshaftFlipMover.cc	chemical / ResidueType.hh
CrankshaftFlipMover.hh	pose / Pose.fwd.hh
CrankshaftFlipMover.hh	select / residue_selector / ResidueSelector.fwd.hh
CreateAngleConstraint.cc	scoring / constraints / AngleConstraint.hh
CreateAngleConstraint.cc	scoring / constraints / Constraint.fwd.hh
CreateAngleConstraint.cc	scoring / func / Func.hh
CreateAngleConstraint.cc	scoring / func / FuncFactory.hh
CreateAngleConstraint.cc	pose / Pose.hh
CreateAngleConstraint.cc	chemical / ResidueType.hh
CreateDistanceConstraint.cc	id / AtomID.hh
CreateDistanceConstraint.cc	scoring / constraints / AtomPairConstraint.hh
CreateDistanceConstraint.cc	scoring / func / Func.hh
CreateDistanceConstraint.cc	scoring / func / FuncFactory.hh
CreateDistanceConstraint.cc	pose / Pose.hh
CreateDistanceConstraint.cc	chemical / ResidueType.hh
CreateTorsionConstraint.cc	scoring / constraints / AmbiguousConstraint.hh
CreateTorsionConstraint.cc	scoring / constraints / Constraint.fwd.hh
CreateTorsionConstraint.cc	scoring / constraints / DihedralConstraint.hh
CreateTorsionConstraint.cc	scoring / func / Func.hh
CreateTorsionConstraint.cc	scoring / func / FuncFactory.hh
CreateTorsionConstraint.cc	pose / Pose.hh
CreateTorsionConstraint.cc	chemical / ResidueType.hh
CrosslinkerMover.cc	scoring / Energies.hh
CrosslinkerMover.cc	kinematics / FoldTree.hh
CrosslinkerMover.cc	kinematics / MoveMap.hh
CrosslinkerMover.cc	pose / Pose.hh
CrosslinkerMover.cc	select / residue_selector / ResidueSelector.hh
CrosslinkerMover.cc	scoring / ScoreFunction.hh
CrosslinkerMover.cc	conformation / symmetry / util.hh
CrosslinkerMover.cc	select / residue_selector / util.hh
CrosslinkerMover.hh	pose / Pose.fwd.hh
CrosslinkerMover.hh	select / residue_selector / ResidueSelector.fwd.hh
CrosslinkerMover.hh	scoring / ScoreFunction.fwd.hh
crosslinker / CrosslinkerMoverHelper.cc	scoring / Energies.hh
crosslinker / CrosslinkerMoverHelper.cc	pose / Pose.hh
crosslinker / CrosslinkerMoverHelper.cc	scoring / ScoreFunction.hh
crosslinker / CrosslinkerMoverHelper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / CrosslinkerMoverHelper.cc	conformation / symmetry / SymmetryInfo.hh
crosslinker / CrosslinkerMoverHelper.hh	pose / Pose.fwd.hh
crosslinker / CrosslinkerMoverHelper.hh	select / residue_selector / ResidueSelector.fwd.hh
crosslinker / CrosslinkerMoverHelper.hh	types.hh
CycpepRigidBodyPermutationMover.cc	id / AtomID.hh
CycpepRigidBodyPermutationMover.cc	conformation / Conformation.hh
CycpepRigidBodyPermutationMover.cc	pose / Pose.hh
CycpepRigidBodyPermutationMover.cc	conformation / Residue.hh
CycpepRigidBodyPermutationMover.cc	chemical / ResidueConnection.hh
CycpepRigidBodyPermutationMover.cc	select / residue_selector / ResidueSelector.hh
CycpepRigidBodyPermutationMover.cc	chemical / ResidueType.hh
CycpepRigidBodyPermutationMover.cc	scoring / rms_util.hh
CycpepRigidBodyPermutationMover.cc	select / residue_selector / util.hh
CycpepRigidBodyPermutationMover.hh	pose / Pose.fwd.hh
CycpepRigidBodyPermutationMover.hh	select / residue_selector / ResidueSelector.fwd.hh
CycpepRigidBodyPermutationMover.hh	types.hh
CycpepSymmetryFilter.cc	pose / Pose.hh
CycpepSymmetryFilter.cc	conformation / Residue.hh
CycpepSymmetryFilter.cc	select / residue_selector / ResidueSelector.hh
CycpepSymmetryFilter.cc	chemical / ResidueType.hh
CycpepSymmetryFilter.cc	select / residue_selector / util.hh
CycpepSymmetryFilter.hh	pose / Pose.fwd.hh
CycpepSymmetryFilter.hh	select / residue_selector / ResidueSelector.fwd.hh
FlipChiralityMover.cc	id / AtomID.hh
FlipChiralityMover.cc	pose / Pose.hh
FlipChiralityMover.cc	conformation / Residue.hh
FlipChiralityMover.cc	select / residue_selector / ResidueSelector.hh
FlipChiralityMover.cc	chemical / ResidueTypeSet.fwd.hh
FlipChiralityMover.cc	select / residue_selector / util.hh
FlipChiralityMover.hh	pose / Pose.fwd.hh
FlipChiralityMover.hh	select / residue_selector / ResidueSelector.fwd.hh
FlipChiralityMover.hh	types.hh
crosslinker / Lanthionine_Helper.cc	pose / Pose.hh
crosslinker / Lanthionine_Helper.cc	conformation / Residue.hh
crosslinker / Lanthionine_Helper.cc	chemical / ResidueType.hh
crosslinker / Lanthionine_Helper.cc	chemical / ResidueTypeSet.hh
crosslinker / Lanthionine_Helper.cc	select / util.hh
crosslinker / Lanthionine_Helper.hh	pose / Pose.fwd.hh
crosslinker / Lanthionine_Helper.hh	types.hh
crosslinker / lanthionine_util.cc	scoring / func / AmberPeriodicFunc.hh
crosslinker / lanthionine_util.cc	scoring / constraints / AngleConstraint.hh
crosslinker / lanthionine_util.cc	scoring / constraints / AtomPairConstraint.hh
crosslinker / lanthionine_util.cc	scoring / func / CircularHarmonicFunc.hh
crosslinker / lanthionine_util.cc	conformation / Conformation.hh
crosslinker / lanthionine_util.cc	scoring / constraints / DihedralConstraint.hh
crosslinker / lanthionine_util.cc	id / DOF_ID.hh
crosslinker / lanthionine_util.cc	scoring / func / HarmonicFunc.hh
crosslinker / lanthionine_util.cc	pose / Pose.hh
crosslinker / lanthionine_util.cc	chemical / ResidueType.hh
crosslinker / lanthionine_util.cc	pose / variant_util.hh
crosslinker / lanthionine_util.cc	chemical / VariantType.hh
crosslinker / lanthionine_util.hh	pose / Pose.fwd.hh
crosslinker / lanthionine_util.hh	types.hh
crosslinker / Metal_HelperBase.cc	pose / Pose.hh
crosslinker / Metal_HelperBase.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / Metal_HelperBase.cc	conformation / symmetry / SymmetryInfo.hh
crosslinker / Metal_HelperBase.cc	pose / symmetry / util.hh
crosslinker / Metal_HelperBase.cc	pose / variant_util.hh
crosslinker / Metal_HelperBase.cc	chemical / VariantType.hh
crosslinker / Metal_HelperBase.hh	pose / Pose.fwd.hh
crosslinker / Metal_HelperBase.hh	select / residue_selector / ResidueSelector.fwd.hh
crosslinker / Metal_HelperBase.hh	chemical / ResidueType.fwd.hh
crosslinker / Metal_HelperBase.hh	types.hh
crosslinker / OctahedralMetal_Helper.cc	scoring / constraints / ConstraintIO.hh
crosslinker / OctahedralMetal_Helper.cc	scoring / constraints / ConstraintSet.hh
crosslinker / OctahedralMetal_Helper.cc	pose / Pose.hh
crosslinker / OctahedralMetal_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / OctahedralMetal_Helper.hh	pose / Pose.fwd.hh
crosslinker / OctahedralMetal_Helper.hh	chemical / ResidueType.fwd.hh
crosslinker / OctahedralMetal_Helper.hh	types.hh
OversaturatedHbondAcceptorFilter.cc	scoring / EnergyMap.hh
OversaturatedHbondAcceptorFilter.cc	scoring / methods / EnergyMethodOptions.hh
OversaturatedHbondAcceptorFilter.cc	scoring / hbonds / HBondDatabase.hh
OversaturatedHbondAcceptorFilter.cc	scoring / hbonds / HBondOptions.hh
OversaturatedHbondAcceptorFilter.cc	scoring / hbonds / hbonds.hh
OversaturatedHbondAcceptorFilter.cc	scoring / hbonds / HBondSet.hh
OversaturatedHbondAcceptorFilter.cc	pose / Pose.hh
OversaturatedHbondAcceptorFilter.cc	conformation / Residue.hh
OversaturatedHbondAcceptorFilter.cc	select / residue_selector / ResidueSelector.hh
OversaturatedHbondAcceptorFilter.cc	scoring / ScoreFunction.hh
OversaturatedHbondAcceptorFilter.cc	scoring / ScoreFunctionFactory.hh
OversaturatedHbondAcceptorFilter.cc	select / residue_selector / util.hh
OversaturatedHbondAcceptorFilter.hh	pose / Pose.fwd.hh
OversaturatedHbondAcceptorFilter.hh	select / residue_selector / ResidueSelector.fwd.hh
OversaturatedHbondAcceptorFilter.hh	scoring / ScoreFunction.fwd.hh
PeptideCyclizeMover.cc	chemical / ChemicalManager.hh
PeptideCyclizeMover.cc	pose / Pose.hh
PeptideCyclizeMover.cc	chemical / ResidueConnection.hh
PeptideCyclizeMover.cc	select / residue_selector / ResidueSelector.hh
PeptideCyclizeMover.cc	chemical / ResidueType.hh
PeptideCyclizeMover.cc	chemical / ResidueTypeSet.hh
PeptideCyclizeMover.cc	types.hh
PeptideCyclizeMover.cc	select / residue_selector / util.hh
PeptideCyclizeMover.cc	select / util.hh
PeptideCyclizeMover.hh	pose / Pose.fwd.hh
PeptideCyclizeMover.hh	select / residue_selector / ResidueSelector.fwd.hh
PeptideCyclizeMover.hh	types.hh
PeptideInternalHbondsFilter.cc	select / residue_selector / ResidueSelector.hh
PeptideInternalHbondsFilter.cc	scoring / ScoreFunction.hh
PeptideInternalHbondsFilter.hh	pose / Pose.fwd.hh
PeptideInternalHbondsFilter.hh	select / residue_selector / ResidueSelector.fwd.hh
PeptideInternalHbondsFilter.hh	scoring / ScoreFunction.fwd.hh
PeptideInternalHbondsMetric.cc	id / AtomID.hh
PeptideInternalHbondsMetric.cc	scoring / methods / EnergyMethodOptions.hh
PeptideInternalHbondsMetric.cc	scoring / hbonds / HBondOptions.hh
PeptideInternalHbondsMetric.cc	scoring / hbonds / hbonds.hh
PeptideInternalHbondsMetric.cc	scoring / hbonds / HBondSet.hh
PeptideInternalHbondsMetric.cc	pose / Pose.hh
PeptideInternalHbondsMetric.cc	conformation / Residue.hh
PeptideInternalHbondsMetric.cc	select / residue_selector / ResidueSelector.hh
PeptideInternalHbondsMetric.cc	chemical / ResidueType.hh
PeptideInternalHbondsMetric.cc	scoring / ScoreFunction.hh
PeptideInternalHbondsMetric.cc	scoring / ScoreFunctionFactory.hh
PeptideInternalHbondsMetric.cc	scoring / ScoreType.hh
PeptideInternalHbondsMetric.cc	select / residue_selector / util.hh
PeptideInternalHbondsMetric.cc	simple_metrics / util.hh
PeptideInternalHbondsMetric.cc	scoring / xml_util.hh
PeptideInternalHbondsMetric.hh	simple_metrics / RealMetric.hh
PeptideInternalHbondsMetric.hh	select / residue_selector / ResidueSelector.fwd.hh
PeptideInternalHbondsMetric.hh	scoring / ScoreFunction.fwd.hh
PeptideInternalHbondsMetric.hh	types.hh
PeptideInternalHbondsMetricCreator.hh	simple_metrics / SimpleMetric.fwd.hh
PeptideInternalHbondsMetricCreator.hh	simple_metrics / SimpleMetricCreator.hh
PeptideStubMover.cc	chemical / AtomICoor.hh
PeptideStubMover.cc	id / AtomID.hh
PeptideStubMover.cc	chemical / ChemicalManager.fwd.hh
PeptideStubMover.cc	conformation / Conformation.hh
PeptideStubMover.cc	kinematics / FoldTree.hh
PeptideStubMover.cc	select / iterators.hh
PeptideStubMover.cc	pose / PDBInfo.hh
PeptideStubMover.cc	pose / Pose.hh
PeptideStubMover.cc	conformation / Residue.hh
PeptideStubMover.cc	chemical / ResidueConnection.hh
PeptideStubMover.cc	conformation / ResidueFactory.hh
PeptideStubMover.cc	select / residue_selector / ResidueSelector.fwd.hh
PeptideStubMover.cc	chemical / ResidueType.hh
PeptideStubMover.cc	chemical / ResidueTypeSet.hh
PeptideStubMover.cc	chemical / types.hh
PeptideStubMover.cc	select / residue_selector / util.hh
PeptideStubMover.cc	pose / variant_util.hh
PeptideStubMover.cc	chemical / VariantType.hh
PeptideStubMover.hh	conformation / Residue.fwd.hh
PeptideStubMover.hh	select / residue_selector / ResidueSelector.fwd.hh
PeptideStubMover.hh	chemical / ResidueTypeSet.fwd.hh
RamaMutationSelector.cc	pose / Pose.hh
RamaMutationSelector.cc	scoring / RamaPrePro.hh
RamaMutationSelector.cc	conformation / Residue.hh
RamaMutationSelector.cc	chemical / ResidueType.hh
RamaMutationSelector.cc	chemical / ResidueTypeFinder.hh
RamaMutationSelector.cc	chemical / ResidueTypeSet.fwd.hh
RamaMutationSelector.cc	scoring / ScoringManager.hh
RamaMutationSelector.cc	select / residue_selector / util.hh
RamaMutationSelector.hh	pose / Pose.fwd.hh
RamaMutationSelector.hh	conformation / Residue.fwd.hh
RamaMutationSelector.hh	select / residue_selector / ResidueSelector.hh
RamaMutationSelector.hh	types.hh
RamaMutationSelectorCreator.hh	select / residue_selector / ResidueSelectorCreator.hh
crosslinker / SquarePlanarMetal_Helper.cc	scoring / constraints / ConstraintIO.hh
crosslinker / SquarePlanarMetal_Helper.cc	scoring / constraints / ConstraintSet.hh
crosslinker / SquarePlanarMetal_Helper.cc	pose / Pose.hh
crosslinker / SquarePlanarMetal_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / SquarePlanarMetal_Helper.hh	pose / Pose.fwd.hh
crosslinker / SquarePlanarMetal_Helper.hh	chemical / ResidueType.fwd.hh
crosslinker / SquarePlanarMetal_Helper.hh	types.hh
crosslinker / SquarePyramidalMetal_Helper.cc	scoring / constraints / ConstraintIO.hh
crosslinker / SquarePyramidalMetal_Helper.cc	scoring / constraints / ConstraintSet.hh
crosslinker / SquarePyramidalMetal_Helper.cc	pose / Pose.hh
crosslinker / SquarePyramidalMetal_Helper.hh	pose / Pose.fwd.hh
crosslinker / SquarePyramidalMetal_Helper.hh	types.hh
SymmetricCycpepAlign.cc	kinematics / FoldTree.hh
SymmetricCycpepAlign.cc	pose / Pose.hh
SymmetricCycpepAlign.cc	conformation / Residue.hh
SymmetricCycpepAlign.cc	chemical / ResidueType.hh
SymmetricCycpepAlign.cc	select / residue_selector / ReturnResidueSubsetSelector.hh
SymmetricCycpepAlign.hh	pose / Pose.fwd.hh
SymmetricCycpepAlign.hh	select / residue_selector / ResidueSelector.fwd.hh
crosslinker / TBMB_Helper.cc	chemical / AA.hh
crosslinker / TBMB_Helper.cc	id / AtomID.hh
crosslinker / TBMB_Helper.cc	chemical / ChemicalManager.hh
crosslinker / TBMB_Helper.cc	pose / Pose.hh
crosslinker / TBMB_Helper.cc	conformation / Residue.hh
crosslinker / TBMB_Helper.cc	conformation / ResidueFactory.hh
crosslinker / TBMB_Helper.cc	select / residue_selector / ResidueIndexSelector.hh
crosslinker / TBMB_Helper.cc	chemical / ResidueType.hh
crosslinker / TBMB_Helper.cc	chemical / ResidueTypeSet.hh
crosslinker / TBMB_Helper.cc	scoring / rms_util.hh
crosslinker / TBMB_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / TBMB_Helper.cc	conformation / symmetry / SymmetryInfo.hh
crosslinker / TBMB_Helper.hh	pose / Pose.fwd.hh
crosslinker / TBMB_Helper.hh	types.hh
crosslinker / TetrahedralMetal_Helper.cc	scoring / constraints / ConstraintIO.hh
crosslinker / TetrahedralMetal_Helper.cc	scoring / constraints / ConstraintSet.hh
crosslinker / TetrahedralMetal_Helper.cc	pose / Pose.hh
crosslinker / TetrahedralMetal_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / TetrahedralMetal_Helper.hh	pose / Pose.fwd.hh
crosslinker / TetrahedralMetal_Helper.hh	chemical / ResidueType.fwd.hh
crosslinker / TetrahedralMetal_Helper.hh	types.hh
crosslinker / Thioether_Helper.cc	pose / Pose.hh
crosslinker / Thioether_Helper.cc	conformation / Residue.hh
crosslinker / Thioether_Helper.cc	chemical / ResidueType.hh
crosslinker / Thioether_Helper.hh	pose / Pose.fwd.hh
crosslinker / Thioether_Helper.hh	types.hh
crosslinker / thioether_util.cc	scoring / constraints / AngleConstraint.hh
crosslinker / thioether_util.cc	scoring / constraints / AtomPairConstraint.hh
crosslinker / thioether_util.cc	scoring / func / CharmmPeriodicFunc.hh
crosslinker / thioether_util.cc	scoring / func / CircularHarmonicFunc.hh
crosslinker / thioether_util.cc	conformation / Conformation.hh
crosslinker / thioether_util.cc	scoring / constraints / DihedralConstraint.hh
crosslinker / thioether_util.cc	id / DOF_ID.hh
crosslinker / thioether_util.cc	scoring / func / HarmonicFunc.hh
crosslinker / thioether_util.cc	pose / Pose.hh
crosslinker / thioether_util.cc	chemical / ResidueType.hh
crosslinker / thioether_util.cc	pose / variant_util.hh
crosslinker / thioether_util.cc	chemical / VariantType.hh
crosslinker / thioether_util.hh	pose / Pose.fwd.hh
crosslinker / thioether_util.hh	types.hh
crosslinker / TMA_Helper.cc	chemical / AA.hh
crosslinker / TMA_Helper.cc	id / AtomID.hh
crosslinker / TMA_Helper.cc	chemical / ChemicalManager.hh
crosslinker / TMA_Helper.cc	conformation / Conformation.hh
crosslinker / TMA_Helper.cc	pose / Pose.hh
crosslinker / TMA_Helper.cc	conformation / Residue.hh
crosslinker / TMA_Helper.cc	conformation / ResidueFactory.hh
crosslinker / TMA_Helper.cc	select / residue_selector / ResidueIndexSelector.hh
crosslinker / TMA_Helper.cc	chemical / ResidueType.hh
crosslinker / TMA_Helper.cc	chemical / ResidueTypeSet.hh
crosslinker / TMA_Helper.cc	scoring / rms_util.hh
crosslinker / TMA_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / TMA_Helper.cc	conformation / symmetry / SymmetryInfo.hh
crosslinker / TMA_Helper.cc	pose / symmetry / util.hh
crosslinker / TMA_Helper.hh	pose / Pose.fwd.hh
crosslinker / TMA_Helper.hh	conformation / Residue.fwd.hh
crosslinker / TMA_Helper.hh	chemical / ResidueType.fwd.hh
crosslinker / TMA_Helper.hh	types.hh
crosslinker / TrigonalPlanarMetal_Helper.cc	scoring / constraints / ConstraintIO.hh
crosslinker / TrigonalPlanarMetal_Helper.cc	scoring / constraints / ConstraintSet.hh
crosslinker / TrigonalPlanarMetal_Helper.cc	pose / Pose.hh
crosslinker / TrigonalPlanarMetal_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / TrigonalPlanarMetal_Helper.hh	pose / Pose.fwd.hh
crosslinker / TrigonalPlanarMetal_Helper.hh	chemical / ResidueType.fwd.hh
crosslinker / TrigonalPlanarMetal_Helper.hh	types.hh
crosslinker / TrigonalPyramidalMetal_Helper.cc	scoring / constraints / ConstraintIO.hh
crosslinker / TrigonalPyramidalMetal_Helper.cc	scoring / constraints / ConstraintSet.hh
crosslinker / TrigonalPyramidalMetal_Helper.cc	pose / Pose.hh
crosslinker / TrigonalPyramidalMetal_Helper.cc	conformation / symmetry / SymmetricConformation.hh
crosslinker / TrigonalPyramidalMetal_Helper.hh	pose / Pose.fwd.hh
crosslinker / TrigonalPyramidalMetal_Helper.hh	chemical / ResidueType.fwd.hh
crosslinker / TrigonalPyramidalMetal_Helper.hh	types.hh
TryDisulfPermutations.cc	scoring / Energies.hh
TryDisulfPermutations.cc	kinematics / MoveMap.hh
TryDisulfPermutations.cc	pose / Pose.hh
TryDisulfPermutations.cc	conformation / Residue.hh
TryDisulfPermutations.cc	select / residue_selector / ResidueSelector.hh
TryDisulfPermutations.cc	scoring / ScoreFunction.hh
TryDisulfPermutations.cc	pack / task / TaskFactory.hh
TryDisulfPermutations.cc	pack / task / operation / TaskOperations.hh
TryDisulfPermutations.cc	types.hh
TryDisulfPermutations.cc	select / residue_selector / util.hh
TryDisulfPermutations.cc	conformation / util.hh
TryDisulfPermutations.hh	pose / Pose.fwd.hh
TryDisulfPermutations.hh	select / residue_selector / ResidueSelector.fwd.hh