energy_methods Directory Reference

Directory dependency graph for energy_methods:

Files
file	AACompositionEnergy.cc
file	AACompositionEnergy.fwd.hh
file	AACompositionEnergy.hh
file	AACompositionEnergyCreator.hh
file	AARepeatEnergy.cc
file	AARepeatEnergy.fwd.hh
file	AARepeatEnergy.hh
file	AARepeatEnergyCreator.hh
file	AbegoEnergy.cc
	ABEGO energy method class implementation.
file	AbegoEnergy.fwd.hh
	ABEGO energy method class forward declaration.
file	AbegoEnergy.hh
file	AbegoEnergyCreator.hh
file	ArgCationPiEnergy.cc
	Cation pi term that specializes in bringing Arginine and rings together.
file	ArgCationPiEnergy.fwd.hh
	Cation pi term that specializes in bringing Arginine and rings together.
file	ArgCationPiEnergy.hh
	Cation pi term that specializes in bringing Arginine and rings together.
file	ArgCationPiEnergyCreator.hh
file	AromaticBackboneRestraintEnergy.cc
	Aramid backbone restraint energy method class implementation.
file	AromaticBackboneRestraintEnergy.fwd.hh
	Noncanonical ring closure energy method class forward declaration.
file	AromaticBackboneRestraintEnergy.hh
	Aromatic backbone restraint energy method class headers.
file	AromaticBackboneRestraintEnergyCreator.hh
	Declaration for the class that connects AromaticBackboneRestraintEnergy with the ScoringManager.
file	AspartimidePenaltyEnergy.cc
file	AspartimidePenaltyEnergy.fwd.hh
	Forward declarations for the AspartimidePenaltyEnergy.
file	AspartimidePenaltyEnergy.hh
	This is a score term that penalizes sequences that are likely to result in aspartimide formation during peptide synthesis.
file	AspartimidePenaltyEnergyCreator.hh
	Declaration for the class that connects AspartimidePenaltyEnergy with the ScoringManager.
file	BranchEnergy.cc
	Method definitions for BranchEnergyCreator and BranchEnergy classes.
file	BranchEnergy.fwd.hh
file	BranchEnergy.hh
	Method declarations and typedefs for BranchEnergy.
file	BranchEnergyCreator.hh
	Declaration for the class that connects BranchEnergy with the ScoringManager.
file	Burial_v2Energy.cc
file	Burial_v2Energy.hh
	energy term use for score burial of a specific residue
file	Burial_v2EnergyCreator.hh
	Declaration for the class that connects Burial_v2Energy with the ScoringManager.
file	BurialEnergy.cc
file	BurialEnergy.hh
	energy term use for scoring predicted burial
file	BurialEnergyCreator.hh
	Declaration for the class that connects BurialEnergy with the ScoringManager.
file	CartesianBondedEnergy.cc
	Harmonic bondangle/bondlength/torsion constraints.
file	CartesianBondedEnergy.fwd.hh
file	CartesianBondedEnergy.hh
file	CartesianBondedEnergyCreator.hh
	Declaration for the class that connects CartesianBondedEnergy with the ScoringManager.
file	CenHBEnergy.cc
	Smooth, differentiable version of centroid hbond term.
file	CenHBEnergy.fwd.hh
file	CenHBEnergy.hh
	Smooth, differentiable version of centroid hbond term.
file	CenHBEnergyCreator.hh
	Declaration for the class that connects CenHBEnergy with the ScoringManager.
file	CenPairEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	CenPairEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	CenPairEnergyCreator.hh
file	CenPairMotifDegreeEnergy.cc
file	CenPairMotifDegreeEnergy.hh
file	CenPairMotifDegreeEnergyCreator.hh
file	CenPairMotifEnergy.cc
file	CenPairMotifEnergy.hh
file	CenPairMotifEnergyCreator.hh
file	CenRotEnvEnergy.cc
	CenRot version of centroid env.
file	CenRotEnvEnergy.hh
file	CenRotEnvEnergyCreator.hh
file	CenRotPairEnergy.cc
	CenRot version of cen pair.
file	CenRotPairEnergy.hh
file	CenRotPairEnergyCreator.hh
file	CentroidDisulfideEnergy.cc
	Centroid Disulfide Energy class implementation.
file	CentroidDisulfideEnergy.fwd.hh
	Centroid Disulfide Energy class forward declaration.
file	CentroidDisulfideEnergy.hh
	Centroid Disulfide Energy class declaration.
file	CentroidDisulfideEnergyCreator.hh
	Declaration for the class that connects CentroidDisulfideEnergy with the ScoringManager.
file	ChainbreakEnergy.cc
	Method definitions for ChainbreakEnergyCreator and ChainbreakEnergy classes.
file	ChainbreakEnergy.fwd.hh
file	ChainbreakEnergy.hh
	Method declarations and typedefs for ChainbreakEnergy.
file	ChainbreakEnergyCreator.hh
	Declaration for the class that connects ChainbreakEnergy with the ScoringManager.
file	ChemicalShiftAnisotropyEnergy.cc
	CSA energy - Orientation dependent chemical shift.
file	ChemicalShiftAnisotropyEnergy.fwd.hh
file	ChemicalShiftAnisotropyEnergy.hh
	CSP energy.
file	ChemicalShiftAnisotropyEnergyCreator.hh
	Declaration for the class that connects ChemicalShiftAnisotropyEnergy with the ScoringManager.
file	ContactOrderEnergy.cc
	calculates the contact order of a given conformation average sequence.
file	ContactOrderEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	ContactOrderEnergyCreator.hh
	Declaration for the class that connects ContactOrderEnergy with the ScoringManager.
file	ContextDependentGeometricSolEnergy.cc
file	ContextDependentGeometricSolEnergy.fwd.hh
file	ContextDependentGeometricSolEnergy.hh
file	ContextDependentGeometricSolEnergyCreator.hh
file	ContextIndependentGeometricSolEnergy.cc
file	ContextIndependentGeometricSolEnergy.fwd.hh
file	ContextIndependentGeometricSolEnergy.hh
file	ContextIndependentGeometricSolEnergyCreator.hh
file	CovalentLabelingEnergy.cc
file	CovalentLabelingEnergy.fwd.hh
file	CovalentLabelingEnergy.hh
	energy term use for scoring predicted CovalentLabeling
file	CovalentLabelingEnergyCreator.hh
	Declaration for the class that connects CovalentLabelingEnergy with the ScoringManager.
file	CovalentLabelingFAEnergy.cc
file	CovalentLabelingFAEnergy.fwd.hh
file	CovalentLabelingFAEnergy.hh
	energy term use for scoring predicted CovalentLabelingFA
file	CovalentLabelingFAEnergyCreator.hh
	Declaration for the class that connects CovalentLabelingFAEnergy with the ScoringManager.
file	CustomAtomPairEnergy.cc
	Simple EnergyMethod for calculating residue-residue constraints under some interaction cutoff.
file	CustomAtomPairEnergy.fwd.hh
	Statistically derived rotamer pair potential class forward declaration.
file	CustomAtomPairEnergy.hh
file	CustomAtomPairEnergyCreator.hh
	Declaration for the class that connects CustomAtomPairEnergy with the ScoringManager.
file	D2H_SA_Energy.cc
	sa energy function definition.
file	D2H_SA_Energy.hh
	Statistically derived rotamer pair potential class declaration.
file	D2H_SA_EnergyCreator.hh
	Declaration for the class that connects D2H_SA_Energy with the ScoringManager.
file	DFIRE_Energy.cc
file	DFIRE_Energy.fwd.hh
file	DFIRE_Energy.hh
file	DFIRE_EnergyCreator.hh
file	DipolarCouplingEnergy.cc
	DC energy - Orientation dependent chemical shift.
file	DipolarCouplingEnergy.fwd.hh
file	DipolarCouplingEnergy.hh
	CSP energy.
file	DipolarCouplingEnergyCreator.hh
	Declaration for the class that connects DipolarCouplingEnergy with the ScoringManager.
file	DirectReadoutEnergy.cc
	Statistically derived DNA contact potential class implementation.
file	DirectReadoutEnergy.fwd.hh
file	DirectReadoutEnergy.hh
	Statistically derived DNA contact potential class declaration.
file	DirectReadoutEnergyCreator.hh
	Declaration for the class that connects DirectReadoutEnergy with the ScoringManager.
file	DistanceChainbreakEnergy.cc
file	DistanceChainbreakEnergy.fwd.hh
file	DistanceChainbreakEnergy.hh
file	DistanceChainbreakEnergyCreator.hh
	Declaration for the class that connects DistanceChainbreakEnergy with the ScoringManager.
file	DisulfideMatchingEnergy.cc
	Centroid Disulfide Energy class implementation.
file	DisulfideMatchingEnergy.fwd.hh
	Centroid Disulfide Energy class forward declaration.
file	DisulfideMatchingEnergy.hh
	Centroid Disulfide Energy class declaration.
file	DisulfideMatchingEnergyCreator.hh
	Declaration for the class that connects DisulfideMatchingEnergy with the ScoringManager.
file	DNA_BaseEnergy.cc
file	DNA_BaseEnergy.fwd.hh
file	DNA_BaseEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	DNA_BaseEnergyCreator.hh
	Declaration for the class that connects DNA_BaseEnergy with the ScoringManager.
file	DNA_DihedralEnergy.cc
	dna scoring
file	DNA_DihedralEnergy.fwd.hh
	dna scoring
file	DNA_DihedralEnergy.hh
	dna scoring
file	DNA_DihedralEnergyCreator.hh
	dna scoring
file	DNA_EnvPairEnergy.cc
	dna scoring
file	DNA_EnvPairEnergy.fwd.hh
	dna scoring
file	DNA_EnvPairEnergy.hh
	dna scoring
file	DNA_EnvPairEnergyCreator.hh
	dna scoring
file	DNA_ReferenceEnergy.cc
	dna scoring
file	DNA_ReferenceEnergy.fwd.hh
	dna scoring
file	DNA_ReferenceEnergy.hh
	dna scoring
file	DNA_ReferenceEnergyCreator.hh
	dna scoring
file	DNAChiEnergy.cc
file	DNAChiEnergy.fwd.hh
file	DNAChiEnergy.hh
file	DNAChiEnergyCreator.hh
	Declaration for the class that connects DNAChiEnergy with the ScoringManager.
file	DNATorsionEnergy.cc
	DNATorsion energy method class implementation.
file	DNATorsionEnergy.fwd.hh
file	DNATorsionEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	DNATorsionEnergyCreator.hh
	Declaration for the class that connects DNATorsionEnergy with the ScoringManager.
file	DumpTrajectoryEnergy.cc
	An EnergyMethod that dumps trajectories to file.
file	DumpTrajectoryEnergy.fwd.hh
	Forward declarations for an EnergyMethod that dumps trajectories to file.
file	DumpTrajectoryEnergy.hh
	Headers for an EnergyMethod that dumps trajectories to file.
file	DumpTrajectoryEnergyCreator.hh
	Creator for an EnergyMethod that dump trajectories to file.
file	ElecDensAllAtomCenEnergy.cc
file	ElecDensAllAtomCenEnergy.hh
file	ElecDensAllAtomCenEnergyCreator.hh
file	ElecDensAtomwiseEnergy.cc
file	ElecDensAtomwiseEnergy.fwd.hh
file	ElecDensAtomwiseEnergy.hh
file	ElecDensAtomwiseEnergyCreator.hh
file	ElecDensCenEnergy.cc
file	ElecDensCenEnergy.hh
file	ElecDensCenEnergyCreator.hh
file	ElecDensEnergy.cc
file	ElecDensEnergy.hh
file	ElecDensEnergyCreator.hh
file	EnvEnergy.cc
file	EnvEnergy.hh
	EnergyMethod that evaluates env and cbeta energies.
file	EnvEnergyCreator.hh
	Declaration for the class that connects EnvEnergy with the ScoringManager.
file	EnvSmoothEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	EnvSmoothEnergy.fwd.hh
file	EnvSmoothEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	EnvSmoothEnergyCreator.hh
	Declaration for the class that connects EnvSmoothEnergy with the ScoringManager.
file	ExactOccludedHbondSolEnergy.cc
file	ExactOccludedHbondSolEnergy.fwd.hh
file	ExactOccludedHbondSolEnergy.hh
file	ExactOccludedHbondSolEnergyCreator.hh
file	FA_ElecEnergyAroAll.cc
	Electrostatics energy method for aromatic side chain (stand-in for pi/pi interactions).
file	FA_ElecEnergyAroAll.fwd.hh
	Electrostatics for RNA class forward declaration.
file	FA_ElecEnergyAroAll.hh
file	FA_ElecEnergyAroAllCreator.hh
	Declaration for the class that connects FA_ElecEnergyAroAll with the ScoringManager.
file	FA_ElecEnergyAroAro.cc
	Electrostatics energy method for aromatic side chain (stand-in for pi/pi interactions).
file	FA_ElecEnergyAroAro.fwd.hh
	Electrostatics for RNA class forward declaration.
file	FA_ElecEnergyAroAro.hh
file	FA_ElecEnergyAroAroCreator.hh
	Declaration for the class that connects FA_ElecEnergyAroAro with the ScoringManager.
file	FA_GrpElecEnergy.cc
file	FA_GrpElecEnergy.fwd.hh
file	FA_GrpElecEnergy.hh
file	FA_GrpElecEnergyCreator.hh
	Declaration for the class that connects FA_ElecEnergy with the ScoringManager.
file	Fa_MbenvEnergy.cc
file	Fa_MbenvEnergy.fwd.hh
	Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
file	Fa_MbenvEnergy.hh
file	Fa_MbenvEnergyCreator.hh
	Declaration for the class that connects Fa_MbenvEnergy with the ScoringManager.
file	Fa_MbsolvEnergy.cc
file	Fa_MbsolvEnergy.fwd.hh
file	Fa_MbsolvEnergy.hh
	LK Solvation using hemisphere culling class forward declaration.
file	Fa_MbsolvEnergyCreator.hh
	Declaration for the class that connects Fa_MbsolvEnergy with the ScoringManager.
file	FACTSEnergy.cc
file	FACTSEnergy.fwd.hh
file	FACTSEnergy.hh
file	FACTSEnergyCreator.hh
file	FaMPEnvEnergy.cc
file	FaMPEnvEnergy.fwd.hh
file	FaMPEnvEnergy.hh
	LK-Type Membrane Environment Energy.
file	FaMPEnvEnergyCreator.hh
file	FaMPEnvSmoothEnergy.cc
file	FaMPEnvSmoothEnergy.fwd.hh
file	FaMPEnvSmoothEnergy.hh
	Fullatom Smoothed Membrane Environment Energy.
file	FaMPEnvSmoothEnergyCreator.hh
file	FaMPSolvEnergy.cc
	LK-Type Membrane Solvation Energy.
file	FaMPSolvEnergy.fwd.hh
file	FaMPSolvEnergy.hh
	LK-Type Membrane Solvation Energy.
file	FaMPSolvEnergyCreator.hh
file	FastDensEnergy.cc
file	FastDensEnergy.hh
file	FastDensEnergyCreator.hh
file	FastSAXSEnergy.cc
file	FastSAXSEnergy.hh
file	FastSAXSEnergyCreator.hh
file	FiberDiffractionEnergy.cc
file	FiberDiffractionEnergy.hh
file	FiberDiffractionEnergyCreator.hh
file	FiberDiffractionEnergyDens.cc
file	FiberDiffractionEnergyDens.hh
file	FiberDiffractionEnergyDensCreator.hh
file	FiberDiffractionEnergyGpu.cc
file	FiberDiffractionEnergyGpu.hh
file	FiberDiffractionEnergyGpuCreator.hh
file	FreeDOF_Energy.cc
	FreeMoiety energy method implementation.
file	FreeDOF_Energy.fwd.hh
	FreeMoiety energy method forward declaration.
file	FreeDOF_Energy.hh
	Score function class.
file	FreeDOF_EnergyCreator.hh
	Declaration for the class that connects FreeDOF_Energy with the ScoringManager.
file	FullatomDisulfideEnergy.cc
file	FullatomDisulfideEnergy.fwd.hh
file	FullatomDisulfideEnergy.hh
file	FullatomDisulfideEnergyCreator.hh
	Declaration for the class that connects FullatomDisulfideEnergy with the ScoringManager.
file	GaussianOverlapEnergy.cc
	Gaussian Overlap Energy.
file	GaussianOverlapEnergy.fwd.hh
	golap
file	GaussianOverlapEnergy.hh
	energy of overlaps
file	GaussianOverlapEnergyCreator.hh
	Declaration for the class that connects GaussianOverlapEnergy with the ScoringManager.
file	GenBornEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	GenBornEnergy.fwd.hh
file	GenBornEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	GenBornEnergyCreator.hh
	Declaration for the class that connects GenBornEnergy with the ScoringManager.
file	GenericBondedEnergy.cc
	A "generic" (atom-type-only-based) torsional potential.
file	GenericBondedEnergy.fwd.hh
file	GenericBondedEnergy.hh
	A "generic" (atom-type-only-based) torsional potential.
file	GenericBondedEnergyCreator.hh
	Declaration for the class that connects GenericBondedEnergy with the ScoringManager.
file	GoapEnergy.cc
	C++ implementaion of GOAP(Generalized Orientation-dependent, All-atom statistical Potential) by Zhou H & Skolnick J, Biophys J 2011, 101(8):2043-52.
file	GoapEnergy.fwd.hh
file	GoapEnergy.hh
file	GoapEnergyCreator.hh
file	HackAroEnergy.cc
file	HackAroEnergy.fwd.hh
file	HackAroEnergy.hh
file	HackAroEnergyCreator.hh
file	HolesEnergy.cc
file	HolesEnergy.hh
file	HolesEnergyCreator.hh
file	HRF_MSLabelingEnergy.cc
file	HRF_MSLabelingEnergy.fwd.hh
file	HRF_MSLabelingEnergy.hh
	energy term use for scoring predicted HRF_MSLabeling
file	HRF_MSLabelingEnergyCreator.hh
	Declaration for the class that connects HRF_MSLabelingEnergy with the ScoringManager.
file	HybridVDW_Energy.cc
	Statistically derived rotamer pair potential class implementation.
file	HybridVDW_Energy.fwd.hh
file	HybridVDW_Energy.hh
	Statistically derived rotamer pair potential class declaration.
file	HybridVDW_EnergyCreator.hh
	Declaration for the class that connects HybridVDW_Energy with the ScoringManager.
file	HydroxylTorsionEnergy.cc
file	HydroxylTorsionEnergy.fwd.hh
file	HydroxylTorsionEnergy.hh
	Term for proton_chi on Ser/Thr/Tyr residues.
file	HydroxylTorsionEnergyCreator.hh
file	IntermolEnergy.cc
	Cost of bringing two chains together.
file	IntermolEnergy.hh
	Radius of gyration score for METHODS, to match Rosetta++.
file	IntermolEnergyCreator.hh
	Declaration for the class that connects IntermolEnergy with the ScoringManager.
file	LinearBranchEnergy.cc
	Atom pair energy functions.
file	LinearBranchEnergy.fwd.hh
file	LinearBranchEnergy.hh
file	LinearBranchEnergyCreator.cc
	LinearBranchEnergyCreator implementation.
file	LinearBranchEnergyCreator.hh
	Declaration for the class that connects LinearBranchEnergy with the ScoringManager.
file	LinearChainbreakEnergy.cc
	Atom pair energy functions.
file	LinearChainbreakEnergy.fwd.hh
file	LinearChainbreakEnergy.hh
file	LinearChainbreakEnergyCreator.cc
	LinearChainbreakEnergyCreator implementation.
file	LinearChainbreakEnergyCreator.hh
	Declaration for the class that connects LinearChainbreakEnergy with the ScoringManager.
file	LK_hack.cc
file	LK_hack.fwd.hh
file	LK_hack.hh
	LK Solvation using hemisphere culling class declaration.
file	LK_hackCreator.hh
	Declaration for the class that connects LK_hack with the ScoringManager.
file	LK_PolarNonPolarEnergy.cc
file	LK_PolarNonPolarEnergy.fwd.hh
file	LK_PolarNonPolarEnergy.hh
	LK Solvation using hemisphere culling class forward declaration.
file	LK_PolarNonPolarEnergyCreator.hh
	Declaration for the class that connects LK_PolarNonPolarEnergy with the ScoringManager.
file	LoopCloseEnergy.cc
	Cost of bringing two chains together.
file	LoopCloseEnergy.hh
file	LoopCloseEnergyCreator.hh
	Declaration for the class that connects LoopCloseEnergy with the ScoringManager.
file	MembraneCbetaEnergy.cc
file	MembraneCbetaEnergy.fwd.hh
file	MembraneCbetaEnergy.hh
	Membrane Environment Cbeta Energy.
file	MembraneCbetaEnergyCreator.hh
	Declaration for the class that connects MembraneCbetaEnergy with the ScoringManager.
file	MembraneCenPairEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	MembraneCenPairEnergy.fwd.hh
file	MembraneCenPairEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	MembraneCenPairEnergyCreator.hh
	Declaration for the class that connects MembraneCenPairEnergy with the ScoringManager.
file	MembraneEnvEnergy.cc
file	MembraneEnvEnergy.fwd.hh
file	MembraneEnvEnergy.hh
	Membrane Environment Cbeta Energy.
file	MembraneEnvEnergyCreator.hh
	Declaration for the class that connects MembraneEnvEnergy with the ScoringManager.
file	MembraneEnvPenalties.cc
file	MembraneEnvPenalties.fwd.hh
file	MembraneEnvPenalties.hh
	RMS Energy function. Used to optimize the RMSD between two structures.
file	MembraneEnvPenaltiesCreator.hh
	Declaration for the class that connects MembraneEnvPenalties with the ScoringManager.
file	MembraneEnvSmoothEnergy.cc
	Statistically derived smooth membrane environment potential class implementation.
file	MembraneEnvSmoothEnergy.fwd.hh
file	MembraneEnvSmoothEnergy.hh
	Statistically derived smooth membrane environment potential class declaration.
file	MembraneEnvSmoothEnergyCreator.hh
	Declaration for the class that connects MembraneEnvSmoothEnergy with the ScoringManager.
file	MembraneLipo.cc
file	MembraneLipo.fwd.hh
file	MembraneLipo.hh
	RMS Energy function. Used to optimize the RMSD between two structures.
file	MembraneLipoCreator.hh
	Declaration for the class that connects MembraneLipo with the ScoringManager.
file	MgEnergy.cc
file	MgEnergy.fwd.hh
file	MgEnergy.hh
file	MgEnergyCreator.hh
	Declaration for the class that connects MgEnergy with the ScoringManager.
file	MHCEpitopeEnergy.cc
file	MHCEpitopeEnergy.fwd.hh
file	MHCEpitopeEnergy.hh
file	MHCEpitopeEnergyCreator.hh
file	MissingEnergy.cc
	Cost of failing to close loops.
file	MissingEnergy.hh
	Cost of failing to close loops.
file	MissingEnergyCreator.hh
	Declaration for the class that connects MissingEnergy with the ScoringManager.
file	MotifDockEnergy.cc
	Adaptation of Motif score for Docking.
file	MotifDockEnergy.fwd.hh
file	MotifDockEnergy.hh
	Adaptation of Motif score for Docking.
file	MotifDockEnergyCreator.hh
	Adaptation of Motif score for Docking.
file	MPCBetaEnergy.cc
file	MPCBetaEnergy.fwd.hh
file	MPCBetaEnergy.hh
file	MPCBetaEnergyCreator.hh
file	MPEnvEnergy.cc
	Membrane Environemnt Energy.
file	MPEnvEnergy.fwd.hh
	Membrane Environemnt Energy.
file	MPEnvEnergy.hh
	Membrane Environemnt Energy.
file	MPEnvEnergyCreator.hh
file	MPHelicalityEnergy.cc
	Fullatom and centroid level smooth membrane non-helicality penalty.
file	MPHelicalityEnergy.fwd.hh
file	MPHelicalityEnergy.hh
	Fullatom and centroid level smooth membrane non-helicality penalty.
file	MPHelicalityEnergyCreator.hh
file	MPPairEnergy.cc
	Membrane Residue Pair Energy Term.
file	MPPairEnergy.fwd.hh
file	MPPairEnergy.hh
	Membrane Residue Pair Energy Term.
file	MPPairEnergyCreator.hh
file	MPResidueLipophilicityEnergy.cc
	Fullatom Smoothed Membrane Environment Energy.
file	MPResidueLipophilicityEnergy.fwd.hh
file	MPResidueLipophilicityEnergy.hh
	Fullatom Smoothed Membrane Environment Energy.
file	MPResidueLipophilicityEnergyCreator.hh
file	MPSpanAngleEnergy.cc
	penalize spans with unnatural dG of insertion
file	MPSpanAngleEnergy.hh
file	MPSpanAngleEnergyCreator.hh
file	MPSpanInsertionEnergy.cc
	penalize spans with unnatural dG of insertion
file	MPSpanInsertionEnergy.hh
file	MPSpanInsertionEnergyCreator.hh
file	MultipoleElecEnergy.cc
	Fixed multipole electrostatics using Jay Ponder's approach in Tinker/Amoeba.
file	MultipoleElecEnergy.fwd.hh
file	MultipoleElecEnergy.hh
	Fixed multipole electrostatics using Jay Ponder's approach in Tinker/Amoeba.
file	MultipoleElecEnergyCreator.hh
	Declaration for the class that connects MultipoleElecEnergy with the ScoringManager.
file	NetChargeEnergy.cc
file	NetChargeEnergy.fwd.hh
file	NetChargeEnergy.hh
file	NetChargeEnergyCreator.hh
file	non_scorefxn_exact_model.cc
file	non_scorefxn_exact_model.hh
file	NPDHBondEnergy.cc
file	NPDHBondEnergy.fwd.hh
file	NPDHBondEnergy.hh
file	NPDHBondEnergyCreator.hh
	Declaration for the class that connects NPDHBondEnergy with the ScoringManager.
file	OccludedHbondSolEnergy.cc
file	OccludedHbondSolEnergy.fwd.hh
file	OccludedHbondSolEnergy.hh
file	OccludedHbondSolEnergy_onebody.cc
file	OccludedHbondSolEnergy_onebody.fwd.hh
file	OccludedHbondSolEnergy_onebody.hh
file	OccludedHbondSolEnergy_onebodyCreator.hh
file	OccludedHbondSolEnergyCreator.hh
file	OmegaTetherEnergy.cc
	OmegaTether energy method class implementation.
file	OmegaTetherEnergy.fwd.hh
	OmegaTether energy method class forward declaration.
file	OmegaTetherEnergy.hh
	OmegaTether energy method class declaration.
file	OmegaTetherEnergyCreator.hh
	Declaration for the class that connects OmegaTetherEnergy with the ScoringManager.
file	OtherPoseEnergy.cc
	Way to handle scoring of a collection of poses, allowing shift of focus between poses.
file	OtherPoseEnergy.fwd.hh
file	OtherPoseEnergy.hh
file	OtherPoseEnergyCreator.hh
	Declaration for the class that connects OtherPoseEnergy with the ScoringManager.
file	P_AA_Energy.cc
	Probability of observing an amino acid (NOT conditional on phi/psi), energy method implementation.
file	P_AA_Energy.fwd.hh
	Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
file	P_AA_Energy.hh
	Probability of observing an amino acid (NOT conditional on phi/psi), energy method declaration.
file	P_AA_EnergyCreator.hh
	Declaration for the class that connects P_AA_Energy with the ScoringManager.
file	P_AA_pp_Energy.cc
	Probability of observing an amino acid, given its phi/psi energy method declaration.
file	P_AA_pp_Energy.fwd.hh
file	P_AA_pp_Energy.hh
	Probability of observing an amino acid, given its phi/psi energy method forward declaration.
file	P_AA_pp_EnergyCreator.hh
	Declaration for the class that connects P_AA_pp_Energy with the ScoringManager.
file	P_AA_ss_Energy.cc
	Probability of observing an amino acid (NOT conditional on phi/psi), energy method implementation.
file	P_AA_ss_Energy.fwd.hh
	Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
file	P_AA_ss_Energy.hh
	Probability of observing an amino acid (NOT conditional on phi/psi), energy method declaration.
file	P_AA_ss_EnergyCreator.hh
	Declaration for the class that connects P_AA_ss_Energy with the ScoringManager.
file	PackStatEnergy.cc
	Radius of gyration energy function definition. Returns -1 * RG for a given Pose.
file	PackStatEnergy.hh
file	PackStatEnergyCreator.hh
	Declaration for the class that connects PackStatEnergy with the ScoringManager.
file	PairEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	PairEnergy.fwd.hh
	Statistically derived rotamer pair potential class forward declaration.
file	PairEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	PairEnergyCreator.hh
	Declaration for the class that connects PairEnergy with the ScoringManager.
file	PeptideBondEnergy.cc
file	PeptideBondEnergy.fwd.hh
file	PeptideBondEnergy.hh
	scoring method that defines ideal bond lengths between carbonyl carbon of residue N and nitrogen of residue N+1.
file	PeptideBondEnergyCreator.hh
	Declaration for the class that connects PeptideBondEnergy with the ScoringManager.
file	pHEnergy.cc
	Energy due to ionization state of the residue at a particular pH (see pHEnergy.hh for a detailed description)
file	pHEnergy.fwd.hh
	pH energy forward declaration
file	pHEnergy.hh
file	pHEnergyCreator.hh
file	PointWaterEnergy.cc
file	PointWaterEnergy.fwd.hh
file	PointWaterEnergy.hh
	Statistical point water energy function.
file	PointWaterEnergyCreator.hh
file	PoissonBoltzmannEnergy.cc
	Ramachandran energy method class implementation.
file	PoissonBoltzmannEnergy.fwd.hh
	Ramachandran energy method class forward declaration.
file	PoissonBoltzmannEnergy.hh
	Membrane Environment Cbeta Energy.
file	PoissonBoltzmannEnergyCreator.hh
file	ProClosureEnergy.cc
	Proline ring closure energy method class implementation.
file	ProClosureEnergy.fwd.hh
	Proline ring closure energy method class forward declaration.
file	ProClosureEnergy.hh
	Proline ring closure energy method class declaration.
file	ProClosureEnergyCreator.hh
	Declaration for the class that connects ProClosureEnergy with the ScoringManager.
file	ProQ_Energy.cc
	ProQ energy function definition.
file	ProQ_Energy.hh
	Statistically derived rotamer pair potential class declaration.
file	ProQ_EnergyCreator.hh
	Declaration for the class that connects ProQ_Energy with the ScoringManager.
file	PyEnergy.hh
	Various Energy classes for subclassing in PyRosetta.
file	RamachandranEnergy.cc
	Ramachandran energy method class implementation.
file	RamachandranEnergy.fwd.hh
	Ramachandran energy method class forward declaration.
file	RamachandranEnergy.hh
	Ramachandran energy method class declaration.
file	RamachandranEnergy2B.cc
file	RamachandranEnergy2B.fwd.hh
file	RamachandranEnergy2B.hh
	Ramachandran energy method class declaration.
file	RamachandranEnergy2BCreator.hh
	Declaration for the class that connects RamachandranEnergy2B with the ScoringManager.
file	RamachandranEnergyCreator.hh
	Declaration for the class that connects RamachandranEnergy with the ScoringManager.
file	RamaPreProEnergy.cc
	A variation on the Ramachandran scorefunction that has separate probability tables for residues that precede prolines.
file	RamaPreProEnergy.fwd.hh
file	RamaPreProEnergy.hh
	A variation on the Ramachandran scorefunction that has separate probability tables for residues that precede prolines.
file	RamaPreProEnergyCreator.hh
	Declaration for the class that connects RamaPreProEnergy with the ScoringManager.
file	ReferenceEnergy.cc
file	ReferenceEnergy.fwd.hh
	Reference energy method forward declaration.
file	ReferenceEnergy.hh
	Reference energy method implementation.
file	ReferenceEnergyCreator.hh
	Declaration for the class that connects ReferenceEnergy with the ScoringManager.
file	ReferenceEnergyNoncanonical.cc
	Reference energy method implementation.
file	ReferenceEnergyNoncanonical.fwd.hh
	Reference energy method forward declaration.
file	ReferenceEnergyNoncanonical.hh
	Reference energy method declaration.
file	ReferenceEnergyNoncanonicalCreator.hh
	Declaration for the class that connects ReferenceEnergyNoncanonical with the ScoringManager.
file	ResidualDipolarCouplingEnergy.cc
	RDC energy - comparing experimental RDC values to calculated values.
file	ResidualDipolarCouplingEnergy.fwd.hh
file	ResidualDipolarCouplingEnergy.hh
	RDC energy - comparing experimental RDC values to calculated values.
file	ResidualDipolarCouplingEnergy_Rohl.cc
	RDC energy - comparing experimental RDC values to calculated values.
file	ResidualDipolarCouplingEnergy_Rohl.hh
file	ResidualDipolarCouplingEnergy_RohlCreator.hh
	Declaration for the class that connects ResidualDipolarCouplingEnergy_Rohl with the ScoringManager.
file	ResidualDipolarCouplingEnergyCreator.hh
	Declaration for the class that connects ResidualDipolarCouplingEnergy with the ScoringManager.
file	RG_Energy_Fast.cc
	Radius of gyration energy function definition.
file	RG_Energy_Fast.hh
	Statistically derived rotamer pair potential class declaration.
file	RG_Energy_FastCreator.hh
	Declaration for the class that connects RG_Energy_Fast with the ScoringManager.
file	RG_Energy_RNA.cc
file	RG_Energy_RNA.hh
file	RG_Energy_RNACreator.hh
file	RG_LocalEnergy.cc
	Radius of gyration for local region.
file	RG_LocalEnergy.hh
	only calculates RG the length of the repeat. Uses code from RG_Energy_fast
file	RG_LocalEnergyCreator.hh
file	RingClosureEnergy.cc
	Noncanonical ring closure energy method class implementation.
file	RingClosureEnergy.fwd.hh
	Noncanonical ring closure energy method class forward declaration.
file	RingClosureEnergy.hh
	Noncanonical ring closure energy method class headers.
file	RingClosureEnergyCreator.hh
	Declaration for the class that connects RingClosureEnergy with the ScoringManager.
file	RMS_Energy.cc
	RMS Energy function. Used to optimize the RMSD between two structures.
file	RMS_Energy.hh
	RMS Energy function. Used to optimize the RMSD between two structures.
file	RMS_EnergyCreator.hh
	Declaration for the class that connects RMS_Energy with the ScoringManager.
file	RNA_BulgeEnergy.cc
file	RNA_BulgeEnergy.fwd.hh
file	RNA_BulgeEnergy.hh
file	RNA_BulgeEnergyCreator.hh
file	RNA_ChemicalMappingEnergy.cc
file	RNA_ChemicalMappingEnergy.fwd.hh
file	RNA_ChemicalMappingEnergy.hh
file	RNA_ChemicalMappingEnergyCreator.hh
file	RNA_ChemicalShiftEnergy.cc
	Energy score based on the agreement between experimentally determined and theoretically calculated NMR chemical_shift.
file	RNA_ChemicalShiftEnergy.hh
	Energy score based on the agreement between experimentally determined and theoretically calculated NMR chemical_shift.
file	RNA_ChemicalShiftEnergyCreator.hh
file	RNA_DataBackboneEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	RNA_DataBackboneEnergy.fwd.hh
file	RNA_DataBackboneEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	RNA_DataBackboneEnergyCreator.hh
file	RNA_FA_ElecEnergy.cc
	Electrostatics energy method for RNA class implementation.
file	RNA_FA_ElecEnergy.fwd.hh
	Electrostatics for RNA class forward declaration.
file	RNA_FA_ElecEnergy.hh
file	RNA_FA_ElecEnergyCreator.hh
	Declaration for the class that connects RNA_FA_ElecEnergy with the ScoringManager.
file	RNA_FullAtomStackingEnergy.cc
file	RNA_FullAtomStackingEnergy.fwd.hh
file	RNA_FullAtomStackingEnergy.hh
file	RNA_FullAtomStackingEnergyCreator.hh
file	RNA_FullAtomVDW_BasePhosphate.cc
file	RNA_FullAtomVDW_BasePhosphate.fwd.hh
file	RNA_FullAtomVDW_BasePhosphate.hh
	FullAtom VDW energy between the base and phosphate group in the same (intra) nucleotide.
file	RNA_FullAtomVDW_BasePhosphateCreator.fwd.hh
file	RNA_FullAtomVDW_BasePhosphateCreator.hh
file	RNA_JR_SuiteEnergy.cc
file	RNA_JR_SuiteEnergy.fwd.hh
file	RNA_JR_SuiteEnergy.hh
file	RNA_JR_SuiteEnergyCreator.hh
file	RNA_LJ_BaseEnergy.cc
file	RNA_LJ_BaseEnergy.fwd.hh
file	RNA_LJ_BaseEnergy.hh
file	RNA_LJ_BaseEnergyCreator.hh
file	RNA_MgPointEnergy.cc
	Statistically derived Mg(2+) binding potential for RNA.
file	RNA_MgPointEnergy.hh
	Statistically derived Mg(2+) binding potential for RNA.
file	RNA_MgPointEnergyCreator.hh
	Declaration for the class that connects RNA_MgPointEnergy with the ScoringManager.
file	RNA_PairwiseLowResolutionEnergy.cc
file	RNA_PairwiseLowResolutionEnergy.fwd.hh
file	RNA_PairwiseLowResolutionEnergy.hh
file	RNA_PairwiseLowResolutionEnergyCreator.hh
file	RNA_PartitionEnergy.cc
file	RNA_PartitionEnergy.hh
file	RNA_PartitionEnergyCreator.hh
file	RNA_StubCoordinateEnergy.cc
file	RNA_StubCoordinateEnergy.fwd.hh
file	RNA_StubCoordinateEnergy.hh
file	RNA_StubCoordinateEnergyCreator.hh
file	RNA_SugarCloseEnergy.cc
file	RNA_SugarCloseEnergy.fwd.hh
file	RNA_SugarCloseEnergy.hh
file	RNA_SugarCloseEnergyCreator.hh
file	RNA_SuiteEnergy.cc
file	RNA_SuiteEnergy.fwd.hh
file	RNA_SuiteEnergy.hh
file	RNA_SuiteEnergyCreator.hh
file	RNA_TorsionEnergy.cc
file	RNA_TorsionEnergy.fwd.hh
file	RNA_TorsionEnergy.hh
file	RNA_TorsionEnergyCreator.hh
file	RNA_VDW_Energy.cc
file	RNA_VDW_Energy.fwd.hh
file	RNA_VDW_Energy.hh
file	RNA_VDW_EnergyCreator.hh
file	RNP_LowResEnergy.cc
file	RNP_LowResEnergy.fwd.hh
file	RNP_LowResEnergy.hh
file	RNP_LowResEnergyCreator.hh
file	RNP_LowResPairDistEnergy.cc
file	RNP_LowResPairDistEnergy.fwd.hh
file	RNP_LowResPairDistEnergy.hh
file	RNP_LowResPairDistEnergyCreator.hh
file	RNP_LowResStackEnergy.cc
file	RNP_LowResStackEnergy.fwd.hh
file	RNP_LowResStackEnergy.hh
file	RNP_LowResStackEnergyCreator.hh
file	SA_Energy.cc
	sa energy function definition.
file	SA_Energy.hh
	Statistically derived rotamer pair potential class declaration.
file	SA_EnergyCreator.hh
file	SASAEnergy.cc
	Power Diagram-derived solvent-accessible surface area energy.
file	SASAEnergy.fwd.hh
	Power Diagram-derived solvent-accessible surface area energy.
file	SASAEnergy.hh
	Power Diagram-derived solvent-accessible surface area energy.
file	SASAEnergyCreator.hh
	Declaration for the class that connects SASAEnergy with the ScoringManager.
file	SAXSEnergy.cc
	FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010)
file	SAXSEnergy.hh
file	SAXSEnergyCEN.hh
file	SAXSEnergyCreator.hh
file	SAXSEnergyCreatorCEN.cc
file	SAXSEnergyCreatorCEN.hh
	Declaration for the class that connects SAXSEnergyCreatorCEN with the ScoringManager.
file	SAXSEnergyCreatorFA.cc
file	SAXSEnergyCreatorFA.hh
	Declaration for the class that connects SAXSEnergyCreatorFA with the ScoringManager.
file	SAXSEnergyFA.hh
file	SecondaryStructureEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	SecondaryStructureEnergy.fwd.hh
file	SecondaryStructureEnergy.hh
	Statistically derived rotamer pair potential class declaration.
file	SecondaryStructureEnergyCreator.hh
	Declaration for the class that connects SecondaryStructureEnergy with the ScoringManager.
file	SequenceDependentRefEnergy.cc
file	SequenceDependentRefEnergy.fwd.hh
	Reference energy method forward declaration.
file	SequenceDependentRefEnergy.hh
	Reference energy method implementation.
file	SequenceDependentRefEnergyCreator.hh
	Declaration for the class that connects SequenceDependentRefEnergy with the ScoringManager.
file	SmoothCenPairEnergy.cc
	Smooth, differentiable, version of cenpair.
file	SmoothCenPairEnergy.hh
file	SmoothCenPairEnergyCreator.hh
file	SmoothEnvEnergy.cc
	Smooth, differentiable, version of centroid env.
file	SmoothEnvEnergy.hh
file	SmoothEnvEnergyCreator.hh
file	SplitUnfoldedTwoBodyEnergy.cc
	Split unfolded energy two body energy method.
file	SplitUnfoldedTwoBodyEnergy.fwd.hh
	Forward header for energy method for the two body portion of the split unfolded energy.
file	SplitUnfoldedTwoBodyEnergy.hh
	Header for the split unfolded energy two body component energy method.
file	SplitUnfoldedTwoBodyEnergyCreator.cc
file	SplitUnfoldedTwoBodyEnergyCreator.hh
	Energy creator for the split unfolded two body energy method.
file	SSElementMotifContactEnergy.cc
file	SSElementMotifContactEnergy.h
file	SSElementMotifContactEnergy.hh
	Will's motif score to determine how well packed the protein core is.
file	SSElementMotifContactEnergyCreator.hh
file	StackElecEnergy.cc
file	StackElecEnergy.fwd.hh
file	StackElecEnergy.hh
file	StackElecEnergyCreator.hh
file	SuckerEnergy.cc
	Statistically derived rotamer pair potential class implementation.
file	SuckerEnergy.fwd.hh
	Statistically derived rotamer pair potential class forward declaration.
file	SuckerEnergy.hh
	energy attracting atoms to sucker atoms
file	SuckerEnergyCreator.hh
	Declaration for the class that connects SuckerEnergy with the ScoringManager.
file	SugarBackboneEnergy.cc
file	SugarBackboneEnergy.fwd.hh
	Forward declarations for SugarBackboneEnergy.
file	SugarBackboneEnergy.hh
	Method definitions for SugarBackboneEnergy and SugarBackboneEnergyCreator.
file	SugarBackboneEnergyCreator.hh
file	SurfEnergy.cc
	Packing Score.
file	SurfEnergy.hh
	Packing Score.
file	SurfEnergyCreator.hh
file	SurfVolEnergy.cc
	Packing Score.
file	SurfVolEnergy.hh
file	SurfVolEnergyCreator.hh
file	SymmetricLigandEnergy.cc
	Dunbrack energy method implementation.
file	SymmetricLigandEnergy.fwd.hh
	Dunbrack energy method forward declaration.
file	SymmetricLigandEnergy.hh
	score for implicit ligand interactions from symmetric geometry
file	SymmetricLigandEnergyCreator.hh
file	TNA_SuiteEnergy.cc
file	TNA_SuiteEnergy.fwd.hh
file	TNA_SuiteEnergy.hh
file	TNA_SuiteEnergyCreator.hh
file	UnfoldedStateEnergy.cc
	Unfolded state energy method implementation; energies based on eneriges of residues in fragments.
file	UnfoldedStateEnergy.fwd.hh
	Unfolded state energy method, forward declaration.
file	UnfoldedStateEnergy.hh
	Unfolded state energy declaration header file.
file	UnfoldedStateEnergyCreator.hh
	Declaration for the class that connects UnfoldedStateEnergy with the ScoringManager.
file	VdWTinkerEnergy.cc
	VdW treatment using buffered 14-7 approach in Tinker/Amoeba.
file	VdWTinkerEnergy.fwd.hh
file	VdWTinkerEnergy.hh
file	VdWTinkerEnergyCreator.hh
file	WaterAdductHBondEnergy.cc
file	WaterAdductHBondEnergy.fwd.hh
file	WaterAdductHBondEnergy.hh
file	WaterAdductHBondEnergyCreator.hh
file	WaterAdductIntraEnergy.cc
file	WaterAdductIntraEnergy.fwd.hh
file	WaterAdductIntraEnergy.hh
	Energetic offset/cost for placing a water adduct on an amino or nucleic acid.
file	WaterAdductIntraEnergyCreator.hh
file	WaterSpecificEnergy.cc
file	WaterSpecificEnergy.fwd.hh
file	WaterSpecificEnergy.hh
	Energetic considerations for explicit water molecules,.
file	WaterSpecificEnergyCreator.hh
file	XtalMLEnergy.cc
file	XtalMLEnergy.hh
file	XtalMLEnergyCreator.hh
file	YHHPlanarityEnergy.cc
file	YHHPlanarityEnergy.fwd.hh
file	YHHPlanarityEnergy.hh
	Term for chi3 on tyrosine residues to prefer the hydrogen lie in the plane of the ring.
file	YHHPlanarityEnergyCreator.hh