core::energy_methods Namespace Reference

Namespaces
	dfire

Classes
class	AACompositionEnergy
	AACompositionEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...
class	AACompositionEnergyCreator
class	AARepeatEnergy
	AARepeatEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...
class	AARepeatEnergyCreator
class	Abego
class	AbegoEnergyCreator
class	ArgCationPiEnergy
class	ArgCationPiEnergyCreator
class	AromaticBackboneRestraintEnergy
class	AromaticBackboneRestraintEnergyCreator
class	AspartimidePenaltyEnergy
class	AspartimidePenaltyEnergyCreator
class	BranchEnergy
	BranchEnergy class iterates across all residues in finalize() and determines a penalty between residues i and i+1 across a cutpoint by how much their virtual atoms do not align. More...
class	BranchEnergyCreator
class	Burial_v2Energy
class	Burial_v2EnergyCreator
class	BurialEnergy
class	BurialEnergyCreator
class	ResidueCartBondedParameters
class	IdealParametersDatabase
class	CartesianBondedEnergy
class	CartesianBondedEnergyCreator
class	CCS_IMMSEnergy
class	CCS_IMMSEnergyCreator
class	CenHBEnergy
class	CenHBEnergyCreator
class	CenPairEnergy
class	CenPairEnergyCreator
class	CenPairMotifDegreeEnergy
class	CenPairMotifDegreeEnergyCreator
class	CenPairMotifEnergy
class	CenPairMotifEnergyCreator
class	CenRotEnvEnergy
class	CenRotEnvEnergyCreator
class	CenRotPairEnergy
class	CenRotPairEnergyCreator
class	CentroidDisulfideEnergy
class	CentroidDisulfideEnergyCreator
class	ChainbreakEnergy
	ChainbreakEnergy class iterates across all residues in finalize() and determines a penalty between residues i and i+1 across a cutpoint by how much their virtual atoms do not align. More...
class	ChainbreakEnergyCreator
class	ChemicalShiftAnisotropyEnergy
class	ChemicalShiftAnisotropyEnergyCreator
class	ContactOrderEnergy
class	ContactOrderEnergyCreator
class	ContextDependentGeometricSolEnergy
class	ContextDependentGeometricSolEnergyCreator
class	ContextIndependentGeometricSolEnergy
class	ContextIndependentGeometricSolEnergyCreator
class	CovalentLabelingEnergy
class	CovalentLabelingEnergyCreator
class	CovalentLabelingFAEnergy
class	CovalentLabelingFAEnergyCreator
class	CustomAtomPairEnergy
class	CustomAtomPairEnergyCreator
class	D2H_SA_Energy
class	D2H_SA_EnergyCreator
class	DEEREnergy
class	DEEREnergyCreator
struct	CacheableSasaVector
class	DEPC_MS_Energy
class	DEPC_MS_EnergyCreator
class	DipolarCouplingEnergy
class	DipolarCouplingEnergyCreator
class	DirectReadoutEnergy
	Implementation of Kono and Sarai's knowledge-based protein-DNA interaction energy. More...
class	DirectReadoutEnergyCreator
class	DistanceChainbreakEnergy
	DistanceChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how far apart their N and C atom are. More...
class	DistanceChainbreakEnergyCreator
class	DisulfideMatchingEnergy
class	DisulfideMatchingEnergyCreator
class	DNA_BaseEnergy
class	DNA_BaseEnergyCreator
class	DNA_DihedralEnergy
class	DNA_DihedralEnergyCreator
class	DNA_EnvPairEnergy
	Implementation of env and pair terms for protein-DNA interactions. More...
class	DNA_EnvPairEnergyCreator
class	DNA_ReferenceEnergy
class	DNA_ReferenceEnergyCreator
class	DNAChiEnergy
class	DNAChiEnergyCreator
class	DNATorsionEnergy
class	DNATorsionEnergyCreator
class	DumpTrajectoryEnergy
	DumpTrajectoryEnergy, a util_method that allows one to dump rosetta trajectories through the use of the dump_trajectory ScoreType. More...
class	DumpTrajectoryEnergyCreator
class	ElecDensAllAtomCenEnergy
class	ElecDensAllAtomCenEnergyCreator
class	PoseSequence
class	ElecDensAtomwiseEnergy
class	ElecDensAtomwiseEnergyCreator
class	ElecDensCenEnergy
class	ElecDensCenEnergyCreator
class	ElecDensEnergy
class	ElecDensEnergyCreator
class	EnvEnergy
class	EnvEnergyCreator
class	EnvSmoothEnergy
class	EnvSmoothEnergyCreator
class	GridInfo
class	WaterWeightGridSet
class	ExactOccludedHbondSolEnergy
class	ExactOccludedHbondSolEnergyCreator
class	FA_ElecEnergyAroAll
class	FA_ElecEnergyAroAllCreator
class	FA_ElecEnergyAroAro
class	FA_ElecEnergyAroAroCreator
class	FAElecContextData
class	FA_GrpElecEnergy
class	FA_GrpElecEnergyCreator
class	Fa_MbenvEnergy
class	Fa_MbenvEnergyCreator
class	Fa_MbsolvEnergy
class	Fa_MbsolvEnergyCreator
class	FACTSEnergy
class	FACTSEnergyCreator
class	FaMPAsymEzCBEnergy
	Implementation of full-atom Membrane asymmetric EZ potential for the CB atom See Schramm et al 2012 Structure for full details on derivation Statistically derived and calculated derivatives; lookup table based on the Z-coordinate 1A bin sizes for -30:30A with a membrane center of 0. More...
class	FaMPAsymEzCBEnergyCreator
	Asym EZ potential for CB Creator Class. More...
class	FaMPAsymEzCGEnergy
	Implementation of full-atom Membrane asymmetric EZ potential for the CG atom See Schramm et al 2012 Structure for full details on derivation Statistically derived and calculated derivatives; lookup table based on the Z-coordinate 1A bin sizes for -30:30A with a membrane center of 0. More...
class	FaMPAsymEzCGEnergyCreator
	Asym EZ potential for CG Creator Class. More...
class	FaMPEnvEnergy
	Fullatom Membrane Environment Energy. More...
class	FaMPEnvEnergyCreator
	Creator Class for Membrane CBeta Energy Method. More...
class	FaMPEnvSmoothEnergy
	Fullatom Membrane Solvation Energy - Statistically Derived, and smoothed derivatives. More...
class	FaMPEnvSmoothEnergyCreator
	Membrane Termini Penalty Creator Class. More...
class	FaMPSolvEnergy
	Energy Method: Membrane Fullaotm Solvation Energy (LK) More...
class	FaMPSolvEnergyCreator
	Creator Class for Membrane CBeta Energy Method. More...
class	FastDensEnergy
class	FastDensEnergyCreator
class	FastSAXSEnergy
class	FastSAXSEnergyCreator
class	FiberDiffractionEnergy
class	FiberDiffractionEnergyCreator
class	FiberDiffractionEnergyDens
class	FiberDiffractionEnergyDensCreator
class	FreeDOF_Energy
class	FreeDOF_EnergyCreator
class	DisulfMinData
class	FullatomDisulfideEnergy
class	FullatomDisulfideEnergyCreator
class	GaussianOverlapEnergy
class	GaussianOverlapEnergyCreator
class	GenBornEnergy
class	GenBornEnergyCreator
class	GenericBondedEnergy
class	GenericBondedEnergyCreator
class	GoapRsdType
class	GoapEnergy
class	GoapEnergyCreator
class	HackAroEnergy
class	HackAroEnergyCreator
class	HolesEnergy
class	HolesEnergyCreator
class	HRF_MSLabelingEnergy
class	HRF_MSLabelingEnergyCreator
class	HRFDynamicsEnergy
class	HRFDynamicsEnergyCreator
class	HybridVDW_Energy
class	HybridVDW_EnergyCreator
class	HydroxylTorsionEnergy
class	HydroxylTorsionEnergyCreator
class	ImplicitMembraneCoulomb
	Minimal class for computing the depth- and membrane-dependent electrostatics energy. More...
class	ImplicitMembraneElecEnergy
	Energy method for computing the depth- and membrane-dependent electrostatics energy The Two Body Energy Method specifies an interface for all two body methods: both long and short range, both context dependent and independent. Any two body method must implement this interface as well as the EnergyMethod interface. More...
class	ImplicitMembraneElecEnergyCreator
class	IntermolEnergy
class	IntermolEnergyCreator
class	LinearBranchEnergy
	LinearBranchEnergy class iterates across all residues in finalize() and determines the penalty between branch-connected residues by how much their psueduo atoms do not align (if they have them). More...
class	LinearBranchEnergyCreator
class	LinearChainbreakEnergy
	LinearChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align. More...
class	LinearChainbreakEnergyCreator
class	LK_SigmoidalFunc
class	LK_hack
class	LK_hackCreator
class	LK_PolarNonPolarEnergy
class	LK_PolarNonPolarEnergyCreator
class	LoopCloseEnergy
class	LoopCloseEnergyCreator
class	MembraneCbetaEnergy
class	MembraneCbetaEnergyCreator
class	MembraneCenPairEnergy
class	MembraneCenPairEnergyCreator
class	MembraneEnvEnergy
class	MembraneEnvEnergyCreator
class	MembraneEnvPenalties
class	MembraneEnvPenaltiesCreator
class	MembraneEnvSmoothEnergy
class	MembraneEnvSmoothEnergyCreator
class	MembraneLipo
class	MembraneLipoCreator
class	MgEnergy
class	MgEnergyCreator
class	ScoreCache
	A cache of epitope scores (considered and commited) at each position, to enable efficient updating of only those scores affected by a substitution during annealing. More...
class	MHCEpitopeEnergy
class	MHCEpitopeEnergyCreator
class	MissingEnergy
class	MissingEnergyCreator
class	MotifDockEnergy
class	MotifDockEnergyCreator
class	MPCbetaEnergy
	Membrane Environemnt CBeta Energy Term. More...
class	MPCbetaEnergyCreator
	Creator Class for Membrane CBeta Energy Method. More...
class	MPEnvEnergy
	Mmebrane Environemnt Energy Term. More...
class	MPEnvEnergyCreator
	Creator Class for Membrane CBeta Energy Method. More...
class	MPHelicalityEnergy
	Fullatom Membrane Solvation Energy - Statistically Derived, and smoothed derivatives. More...
class	MPHelicalityEnergyCreator
	Membrane Termini Penalty Creator Class. More...
class	MPPairEnergy
	Membrane Environemtn Residue Pair Energy Term. More...
class	MPPairEnergyCreator
	Creator Class for Membrane Residue Pair Energy Method. More...
class	MPResidueLipophilicityEnergy
	Fullatom Membrane Solvation Energy - Statistically Derived, and smoothed derivatives. More...
class	MPResidueLipophilicityEnergyCreator
	Membrane Termini Penalty Creator Class. More...
class	MPSpanAngleEnergy
class	MPSpanAngleEnergyCreator
class	MPSpanInsertionEnergy
class	MPSpanInsertionEnergyCreator
class	MultipoleElecResPairMinData
class	MultipoleElecEnergy
class	MultipoleElecEnergyCreator
class	NetChargeEnergy
	NetChargeEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...
class	NetChargeEnergyCreator
class	NPDHBondEnergy
	First pass implementation; somewhat ineffecient. The NPDHbondEnergy will cache a map of all hbonds by donor and acceptor in the Pose during setup_for_scoring, and will then retrieve these values during calls to residue_pair_energy. Doesn't work properly for packing. More...
class	NPDHBondEnergyCreator
class	OccludedHbondSolEnergy
class	OccludedHbondSolEnergy_onebody
class	OccludedHbondSolEnergy_onebodyCreator
class	OccludedHbondSolEnergyCreator
class	OmegaTetherEnergy
class	OmegaTetherEnergyCreator
class	OtherPoseEnergy
class	OtherPoseEnergyCreator
class	P_AA_Energy
class	P_AA_EnergyCreator
class	P_AA_pp_Energy
class	P_AA_pp_EnergyCreator
class	P_AA_ss_Energy
class	P_AA_ss_EnergyCreator
class	PackStatEnergy
class	PackStatEnergyCreator
class	PairEnergy
class	PairEnergyCreator
class	PeptideBondEnergy
	PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment. More...
class	PeptideBondEnergyCreator
class	pHEnergy
class	pHEnergyCreator
class	PointWaterEnergy
class	PointWaterEnergyCreator
class	PBLifetimeCache
class	PoissonBoltzmannEnergy
class	PoissonBoltzmannEnergyCreator
class	ProClosureEnergy
class	ProClosureEnergyCreator
class	ProQ_Energy
class	ProQ_EnergyCreator
class	RamachandranEnergy
class	RamachandranEnergy2B
class	RamachandranEnergy2BCreator
class	RamachandranEnergyCreator
class	RamaPreProEnergy
class	RamaPreProEnergyCreator
class	ReferenceEnergy
class	ReferenceEnergyCreator
class	ReferenceEnergyNoncanonical
class	ReferenceEnergyNoncanonicalCreator
class	ResidualDipolarCouplingEnergy
class	ResidualDipolarCouplingEnergy_Rohl
class	ResidualDipolarCouplingEnergy_RohlCreator
class	ResidualDipolarCouplingEnergyCreator
class	RG_MinData
class	RG_Energy_Fast
class	RG_Energy_FastCreator
class	RG_Energy_RNA
class	RG_Energy_RNACreator
class	RG_Local_MinData
class	RG_LocalEnergy
class	RG_LocalEnergyCreator
class	RingClosureEnergy
class	RingClosureEnergyCreator
class	RMS_Energy
class	RMS_EnergyCreator
class	RNA_BulgeEnergy
class	RNA_BulgeEnergyCreator
class	RNA_ChemicalMappingEnergy
class	RNA_ChemicalMappingEnergyCreator
class	RNA_ChemicalShiftEnergy
class	RNA_ChemicalShiftEnergyCreator
class	RNA_CoarseDistEnergy
	Score two-body energies in coarse RNA poses between P, S, and CEN using a statistical potential. The Two Body Energy Method specifies an interface for all two body methods: both long and short range, both context dependent and independent. Any two body method must implement this interface as well as the EnergyMethod interface. More...
class	RNA_CoarseDistEnergyCreator
class	RNA_DataBackboneEnergy
class	RNA_DataBackboneEnergyCreator
class	RNA_FA_ElecEnergy
class	RNA_FA_ElecEnergyCreator
class	RNA_FullAtomStackingEnergy
class	RNA_FullAtomStackingEnergyCreator
class	RNA_FullAtomVDW_BasePhosphate
class	RNA_FullAtomVDW_BasePhosphateCreator
class	RNA_JR_SuiteEnergy
class	RNA_JR_SuiteEnergyCreator
class	RNA_LJ_BaseEnergy
class	RNA_LJ_BaseEnergyCreator
class	RNA_MgPointEnergy
class	RNA_MgPointEnergyCreator
class	RNA_PairwiseLowResolutionEnergy
class	RNA_PairwiseLowResolutionEnergyCreator
class	RNA_PartitionEnergy
class	RNA_PartitionEnergyCreator
class	RNA_StubCoordinateEnergy
class	RNA_StubCoordinateEnergyCreator
class	RNA_SugarCloseEnergy
class	RNA_SugarCloseEnergyCreator
class	RNA_SuiteEnergy
class	RNA_SuiteEnergyCreator
class	RNA_TorsionEnergy
class	RNA_TorsionEnergyCreator
class	RNA_VDW_Energy
class	RNA_VDW_EnergyCreator
class	RNP_LowResEnergy
class	RNP_LowResEnergyCreator
class	RNP_LowResPairDistEnergy
class	RNP_LowResPairDistEnergyCreator
class	RNP_LowResStackEnergy
class	RNP_LowResStackEnergyCreator
class	SA_Energy
class	SA_EnergyCreator
class	SASAEnergy
class	SASAEnergyCreator
class	SAXSEnergy
class	SAXSEnergyCEN
class	SAXSEnergyCreator
class	SAXSEnergyCreatorCEN
class	SAXSEnergyCreatorFA
class	SAXSEnergyFA
class	SecondaryStructureEnergy
class	SecondaryStructureEnergyCreator
class	SequenceDependentRefEnergy
class	SequenceDependentRefEnergyCreator
class	SmoothCenPairEnergy
class	SmoothCenPairEnergyCreator
class	SmoothEnvEnergy
class	SmoothEnvEnergyCreator
class	SplitUnfoldedTwoBodyEnergy
class	SplitUnfoldedTwoBodyEnergyCreator
class	SSElementMotifContactEnergy
class	SSElementMotifContactEnergyCreator
class	StackElecEnergy
class	StackElecEnergyCreator
class	SuckerEnergy
class	SuckerEnergyCreator
class	SugarBackboneEnergy
class	SugarBackboneEnergyCreator
	EnergyMethodCreator allowing the core::scoring::ScoringManager to create a SugarBackboneEnergy method class. More...
class	SurfEnergy
class	SurfEnergyCreator
class	SurfVolEnergy
class	SurfVolEnergyCreator
class	SymmetricLigandEnergy
class	SymmetricLigandEnergyCreator
class	TNA_SuiteEnergy
class	TNA_SuiteEnergyCreator
class	UnfoldedStateEnergy
class	UnfoldedStateEnergyCreator
class	VdWTinkerResPairMinData
class	VdWTinkerEnergy
class	VdWTinkerEnergyCreator
class	WaterAdductHBondEnergy
class	WaterAdductHBondEnergyCreator
class	WaterAdductIntraEnergy
class	WaterAdductIntraEnergyCreator
class	WaterSpecificEnergy
class	WaterSpecificEnergyCreator
class	XtalMLEnergy
class	XtalMLEnergyCreator
class	YHHPlanarityEnergy
class	YHHPlanarityEnergyCreator

Typedefs
typedef utility::pointer::shared_ptr< AACompositionEnergy >	AACompositionEnergyOP
typedef utility::pointer::shared_ptr< AARepeatEnergy >	AARepeatEnergyOP
typedef utility::pointer::shared_ptr< Abego >	AbegoOP
typedef utility::pointer::shared_ptr< Abego const >	AbegoCOP
typedef utility::pointer::shared_ptr< ArgCationPiEnergy >	ArgCationPiEnergyOP
typedef utility::pointer::shared_ptr< ArgCationPiEnergy const >	ArgCationPiEnergyCOP
typedef utility::pointer::shared_ptr< AromaticBackboneRestraintEnergy >	AromaticBackboneRestraintEnergyOP
typedef utility::pointer::shared_ptr< AromaticBackboneRestraintEnergy const >	AromaticBackboneRestraintEnergyCOP
typedef utility::pointer::weak_ptr< AspartimidePenaltyEnergy >	AspartimidePenaltyEnergyAP
typedef utility::pointer::weak_ptr< AspartimidePenaltyEnergy const >	AspartimidePenaltyEnergyCAP
typedef utility::pointer::shared_ptr< AspartimidePenaltyEnergy >	AspartimidePenaltyEnergyOP
typedef utility::pointer::shared_ptr< AspartimidePenaltyEnergy const >	AspartimidePenaltyEnergyCOP
typedef utility::pointer::weak_ptr< ResidueCartBondedParameters >	ResidueCartBondedParametersAP
typedef utility::pointer::weak_ptr< ResidueCartBondedParameters const >	ResidueCartBondedParametersCAP
typedef utility::pointer::shared_ptr< ResidueCartBondedParameters >	ResidueCartBondedParametersOP
typedef utility::pointer::shared_ptr< ResidueCartBondedParameters const >	ResidueCartBondedParametersCOP
typedef utility::pointer::weak_ptr< IdealParametersDatabase >	IdealParametersDatabaseAP
typedef utility::pointer::weak_ptr< IdealParametersDatabase const >	IdealParametersDatabaseCAP
typedef utility::pointer::shared_ptr< IdealParametersDatabase >	IdealParametersDatabaseOP
typedef utility::pointer::shared_ptr< IdealParametersDatabase const >	IdealParametersDatabaseCOP
typedef utility::pointer::weak_ptr< CartesianBondedEnergy >	CartesianBondedEnergyAP
typedef utility::pointer::weak_ptr< CartesianBondedEnergy const >	CartesianBondedEnergyCAP
typedef utility::pointer::shared_ptr< CartesianBondedEnergy >	CartesianBondedEnergyOP
typedef utility::pointer::shared_ptr< CartesianBondedEnergy const >	CartesianBondedEnergyCOP
typedef utility::vector1< std::pair< atm_name_quad, core::scoring::methods::CartBondedParametersCOP > >	torsionparam_vector
typedef utility::pointer::shared_ptr< CentroidDisulfideEnergy >	CentroidDisulfideEnergyOP
typedef utility::pointer::shared_ptr< CentroidDisulfideEnergy const >	CentroidDisulfideEnergyCOP
typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropyEnergy >	ChemicalShiftAnisotropyEnergyOP
typedef utility::pointer::shared_ptr< DEEREnergy >	DEEREnergyOP
typedef utility::pointer::shared_ptr< DEEREnergy const >	DEEREnergyCOP
typedef utility::pointer::shared_ptr< CacheableSasaVector const >	CacheableSasaVectorCOP
typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy >	PoissonBoltzmannEnergyOP
typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy const >	PoissonBoltzmannEnergyCOP
typedef utility::pointer::shared_ptr< DipolarCouplingEnergy >	DipolarCouplingEnergyOP
typedef utility::pointer::shared_ptr< DisulfideMatchingEnergy >	DisulfideMatchingEnergyOP
typedef utility::pointer::shared_ptr< DisulfideMatchingEnergy const >	DisulfideMatchingEnergyCOP
typedef utility::pointer::shared_ptr< DNATorsionEnergy >	DNATorsionEnergyOP
typedef utility::pointer::shared_ptr< DNATorsionEnergy const >	DNATorsionEnergyCOP
typedef utility::pointer::shared_ptr< DumpTrajectoryEnergy >	DumpTrajectoryEnergyOP
typedef utility::pointer::shared_ptr< ElecDensAtomwiseEnergy >	ElecDensAtomwiseEnergyOP
typedef utility::pointer::shared_ptr< ElecDensAtomwiseEnergy const >	ElecDensAtomwiseEnergyCOP
typedef std::shared_ptr< PoseSequence >	PoseSequenceOP
typedef std::shared_ptr< PoseSequence const >	PoseSequenceCOP
typedef utility::pointer::shared_ptr< ExactOccludedHbondSolEnergy >	ExactOccludedHbondSolEnergyOP
typedef utility::pointer::shared_ptr< ExactOccludedHbondSolEnergy const >	ExactOccludedHbondSolEnergyCOP
typedef std::map< core::scoring::hbonds::HBEvalType, WaterWeightGridSet::Grid >::const_iterator	all_water_weights_iterator
typedef std::map< core::scoring::hbonds::HBEvalType, core::Real >::const_iterator	sum_water_weights_iterator
typedef utility::pointer::shared_ptr< FA_GrpElecEnergy >	FA_GrpElecEnergyOP
typedef utility::pointer::shared_ptr< FA_GrpElecEnergy const >	FA_GrpElecEnergyCOP
typedef utility::pointer::shared_ptr< FAElecContextData >	FAElecContextDataOP
typedef utility::pointer::shared_ptr< FAElecContextData const >	FAElecContextDataCOP
typedef utility::pointer::shared_ptr< Fa_MbenvEnergy >	Fa_MbenvEnergyOP
typedef utility::pointer::shared_ptr< FaMPAsymEzCBEnergy >	FaMPAsymEzCBEnergyOP
typedef utility::pointer::shared_ptr< FaMPAsymEzCBEnergy const >	FaMPAsymEzCBEnergyCOP
typedef utility::pointer::shared_ptr< FaMPAsymEzCGEnergy >	FaMPAsymEzCGEnergyOP
typedef utility::pointer::shared_ptr< FaMPAsymEzCGEnergy const >	FaMPAsymEzCGEnergyCOP
typedef utility::pointer::shared_ptr< FaMPEnvEnergy >	FaMPEnvEnergyOP
typedef utility::pointer::shared_ptr< FaMPEnvEnergy const >	FaMPEnvEnergyCOP
typedef utility::pointer::shared_ptr< FaMPEnvSmoothEnergy >	FaMPEnvSmoothEnergyOP
typedef utility::pointer::shared_ptr< FaMPEnvSmoothEnergy const >	FaMPEnvSmoothEnergyCOP
typedef utility::pointer::shared_ptr< FaMPSolvEnergy >	FaMPSolvEnergyOP
typedef utility::pointer::shared_ptr< FaMPSolvEnergy const >	FaMPSolvEnergyCOP
using	DisulfMinDataOP = utility::pointer::shared_ptr< DisulfMinData >
using	DisulfMinDataCOP = utility::pointer::shared_ptr< const DisulfMinData >
typedef utility::pointer::shared_ptr< FullatomDisulfideEnergy >	FullatomDisulfideEnergyOP
typedef utility::pointer::shared_ptr< FullatomDisulfideEnergy const >	FullatomDisulfideEnergyCOP
typedef utility::pointer::shared_ptr< GenericBondedEnergy >	GenericBondedEnergyOP
typedef utility::pointer::shared_ptr< GoapRsdType >	GoapRsdTypeOP
typedef utility::pointer::shared_ptr< GoapRsdType const >	GoapRsdTypeCOP
typedef utility::pointer::shared_ptr< GoapEnergy >	GoapEnergyOP
typedef std::map< std::string, GoapRsdTypeOP >	GoapRsdTypeMap
typedef utility::pointer::shared_ptr< HydroxylTorsionEnergy >	HydroxylTorsionEnergyOP
using	ImplicitMembraneCoulombOP = utility::pointer::shared_ptr< ImplicitMembraneCoulomb >
using	ImplicitMembraneCoulombCOP = utility::pointer::shared_ptr< ImplicitMembraneCoulomb const >
using	ImplicitMembraneElecEnergyOP = utility::pointer::shared_ptr< ImplicitMembraneElecEnergy >
using	ImplicitMembraneElecEnergyCOP = utility::pointer::shared_ptr< ImplicitMembraneElecEnergy const >
typedef utility::pointer::shared_ptr< MgEnergy >	MgEnergyOP
typedef utility::pointer::shared_ptr< MgEnergy const >	MgEnergyCOP
typedef utility::pointer::shared_ptr< ScoreCache >	ScoreCacheOP
typedef utility::pointer::shared_ptr< ScoreCache const >	ScoreCacheCOP
typedef utility::pointer::shared_ptr< MHCEpitopeEnergy >	MHCEpitopeEnergyOP
typedef utility::pointer::shared_ptr< MHCEpitopeEnergy const >	MHCEpitopeEnergyCOP
typedef utility::pointer::shared_ptr< MotifDockEnergy >	MotifDockEnergyOP
typedef utility::pointer::shared_ptr< MotifDockEnergy const >	MotifDockEnergyCOP
typedef utility::pointer::shared_ptr< MPCbetaEnergy >	MPCbetaEnergyOP
typedef utility::pointer::shared_ptr< MPCbetaEnergy const >	MPCbetaEnergyCOP
typedef utility::pointer::shared_ptr< MPEnvEnergy >	MPEnvEnergyOP
typedef utility::pointer::shared_ptr< MPEnvEnergy const >	MPEnvEnergyCOP
typedef utility::pointer::shared_ptr< MPHelicalityEnergy >	MPHelicalityEnergyOP
typedef utility::pointer::shared_ptr< MPHelicalityEnergy const >	MPHelicalityEnergyCOP
typedef utility::pointer::shared_ptr< MPPairEnergy >	MPPairEnergyOP
typedef utility::pointer::shared_ptr< MPPairEnergy const >	MPPairEnergyCOP
typedef utility::pointer::shared_ptr< MPResidueLipophilicityEnergy >	MPResidueLipophilicityEnergyOP
typedef utility::pointer::shared_ptr< MPResidueLipophilicityEnergy const >	MPResidueLipophilicityEnergyCOP
using	MultipoleElecResPairMinDataOP = utility::pointer::shared_ptr< MultipoleElecResPairMinData >
using	MultipoleElecResPairMinDataCOP = utility::pointer::shared_ptr< const MultipoleElecResPairMinData >
typedef utility::pointer::shared_ptr< NetChargeEnergy >	NetChargeEnergyOP
typedef utility::pointer::shared_ptr< HBondEnergy >	HBondEnergyOP
typedef utility::pointer::shared_ptr< HBondEnergy const >	HBondEnergyCOP
typedef utility::pointer::weak_ptr< HBondEnergy const >	HBondEnergyCAP
typedef utility::pointer::shared_ptr< OmegaTetherEnergy >	OmegaTetherEnergyOP
typedef utility::pointer::shared_ptr< OmegaTetherEnergy const >	OmegaTetherEnergyCOP
typedef utility::pointer::shared_ptr< OtherPoseEnergy >	OtherPoseEnergyOP
typedef utility::pointer::shared_ptr< OtherPoseEnergy const >	OtherPoseEnergyCOP
typedef utility::pointer::shared_ptr< P_AA_Energy >	P_AA_EnergyOP
typedef utility::pointer::shared_ptr< P_AA_pp_Energy >	P_AA_pp_EnergyOP
typedef utility::pointer::shared_ptr< P_AA_ss_Energy >	P_AA_ss_EnergyOP
typedef utility::pointer::shared_ptr< pHEnergy >	pHEnergyOP
typedef utility::pointer::shared_ptr< PointWaterEnergy >	PointWaterEnergyOP
typedef utility::pointer::shared_ptr< PointWaterEnergy const >	PointWaterEnergyCOP
typedef utility::pointer::weak_ptr< PoissonBoltzmannEnergy >	PoissonBoltzmannEnergyAP
typedef utility::pointer::weak_ptr< PoissonBoltzmannEnergy const >	PoissonBoltzmannEnergyCAP
typedef utility::pointer::shared_ptr< PBLifetimeCache >	PBLifetimeCacheOP
typedef utility::pointer::shared_ptr< PBLifetimeCache const >	PBLifetimeCacheCOP
typedef utility::pointer::weak_ptr< PBLifetimeCache >	PBLifetimeCacheAP
typedef utility::pointer::weak_ptr< PBLifetimeCache const >	PBLifetimeCacheCAP
typedef utility::pointer::shared_ptr< ProClosureEnergy >	ProClosureEnergyOP
typedef utility::pointer::shared_ptr< ProClosureEnergy const >	ProClosureEnergyCOP
typedef utility::pointer::shared_ptr< RamachandranEnergy >	RamachandranEnergyOP
typedef utility::pointer::shared_ptr< RamachandranEnergy const >	RamachandranEnergyCOP
typedef utility::pointer::shared_ptr< RamachandranEnergy2B >	RamachandranEnergy2BOP
typedef utility::pointer::shared_ptr< RamachandranEnergy2B const >	RamachandranEnergy2BCOP
typedef utility::pointer::weak_ptr< RamaPreProEnergy >	RamaPreProEnergyAP
typedef utility::pointer::weak_ptr< RamaPreProEnergy const >	RamaPreProEnergyCAP
typedef utility::pointer::shared_ptr< RamaPreProEnergy >	RamaPreProEnergyOP
typedef utility::pointer::shared_ptr< RamaPreProEnergy const >	RamaPreProEnergyCOP
typedef utility::pointer::shared_ptr< ReferenceEnergy >	ReferenceEnergyOP
typedef utility::pointer::shared_ptr< ReferenceEnergy const >	ReferenceEnergyCOP
typedef utility::pointer::shared_ptr< ReferenceEnergyNoncanonical >	ReferenceEnergyNoncanonicalOP
typedef utility::pointer::shared_ptr< ReferenceEnergyNoncanonical const >	ReferenceEnergyNoncanonicalCOP
typedef utility::pointer::shared_ptr< ResidualDipolarCouplingEnergy >	ResidualDipolarCouplingEnergyOP
typedef utility::pointer::shared_ptr< RG_MinData >	RG_MinDataOP
typedef utility::pointer::shared_ptr< RG_Local_MinData >	RG_Local_MinDataOP
typedef utility::pointer::shared_ptr< RingClosureEnergy >	RingClosureEnergyOP
typedef utility::pointer::shared_ptr< RingClosureEnergy const >	RingClosureEnergyCOP
typedef utility::pointer::shared_ptr< RNA_ChemicalMappingEnergy >	RNA_ChemicalMappingEnergyOP
typedef utility::pointer::shared_ptr< RNA_ChemicalMappingEnergy const >	RNA_ChemicalMappingEnergyCOP
using	RNA_CoarseDistEnergyOP = utility::pointer::shared_ptr< RNA_CoarseDistEnergy >
using	RNA_CoarseDistEnergyCOP = utility::pointer::shared_ptr< RNA_CoarseDistEnergy const >
using	Vector = numeric::xyzVector< core::Real >
using	Matrix = numeric::xyzMatrix< Real >
typedef utility::pointer::shared_ptr< RNA_FullAtomVDW_BasePhosphate >	RNA_FullAtomVDW_BasePhosphateOP
typedef utility::pointer::shared_ptr< RNA_FullAtomVDW_BasePhosphate const >	RNA_FullAtomVDW_BasePhosphateCOP
typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy >	RNA_SugarCloseEnergyOP
typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy const >	RNA_SugarCloseEnergyCOP
typedef utility::pointer::shared_ptr< RNA_TorsionEnergy >	RNA_TorsionEnergyOP
typedef utility::pointer::shared_ptr< RNA_TorsionEnergy const >	RNA_TorsionEnergyCOP
typedef utility::pointer::shared_ptr< SequenceDependentRefEnergy >	SequenceDependentRefEnergyOP
typedef utility::pointer::shared_ptr< SequenceDependentRefEnergy const >	SequenceDependentRefEnergyCOP
typedef utility::pointer::shared_ptr< SplitUnfoldedTwoBodyEnergy >	SplitUnfoldedTwoBodyEnergyOP
typedef utility::pointer::shared_ptr< SugarBackboneEnergy >	SugarBackboneEnergyOP
typedef utility::pointer::shared_ptr< SugarBackboneEnergy const >	SugarBackboneEnergyCOP
typedef utility::pointer::shared_ptr< UnfoldedStateEnergy >	UnfoldedStateEnergyOP
using	VdWTinkerResPairMinDataOP = utility::pointer::shared_ptr< VdWTinkerResPairMinData >
using	VdWTinkerResPairMinDataCOP = utility::pointer::shared_ptr< const VdWTinkerResPairMinData >
typedef utility::pointer::shared_ptr< WaterAdductIntraEnergy >	WaterAdductIntraEnergyOP
typedef utility::pointer::shared_ptr< WaterSpecificEnergy >	WaterSpecificEnergyOP
typedef utility::pointer::shared_ptr< YHHPlanarityEnergy >	YHHPlanarityEnergyOP

Functions
static basic::Tracer	TR ("core.energy_methods.AACompositionEnergy")
static basic::Tracer	TR ("core.energy_methods.AARepeatEnergy")
Real	point_line_distance (numeric::xyzVector< Real > const &point, numeric::xyzVector< Real > const &line_base, numeric::xyzVector< Real > const &line_ray)
static basic::Tracer	TR ("core.energy_methods.AromaticBackboneRestraintEnergy")
void	eval (Real const phi0, Real const weight, Size const rt1, Size const rt2, Size const rt3, Size const rt4, conformation::Residue const &rsd, utility::vector1< core::scoring::DerivVectorPair > &atom_derivs)
static basic::Tracer	TR ("core.energy_methods.AspartimidePenaltyEnergy")
static basic::Tracer	tr ("core.energy_methods.BranchEnergy")
static basic::Tracer	TR ("core.energy_methods.CartesianBondedEnergy")
static basic::Tracer	GEOMETRIES ("core.energy_methods.CartesianBondedEnergy.GEOMETRIES")
std::string	get_restag (core::chemical::ResidueType const &restype)
	helper function More...
static basic::Tracer	tr ("core.energy_methods.CCS_IMMSEnergy")
core::Real	parcs_ccs (core::pose::Pose &mypose, core::Size const nrot, core::Real const prad)
static basic::Tracer	TR ("core.energy_methods.CenHBEnergy")
static basic::Tracer	TR ("core.energy_methods.CenPairMotifDegreeEnergy")
static basic::Tracer	TR ("core.energy_methods.CenPairMotifEnergy")
static basic::Tracer	TR ("core.energy_methods.CentroidDisulfideEnergy")
static basic::Tracer	tr ("core.energy_methods.ChainbreakEnergy")
static basic::Tracer	tr ("core.energy_methods.CustomAtomPairEnergy")
void	swap_seqpos (core::Size &seqpos1, core::Size &seqpos2)
static basic::Tracer	TR ("core.energy_methods.D2H_SA_Energy")
static basic::Tracer	TR ("core.energy_methods.DEEREnergy")
	Tracer used for error messages. More...
static basic::Tracer	TR ("core.energy_methods.DisulfideMatchingEnergy")
std::string const	dna_deriv_atom (" C5 ")
	the atom through which the knowledge based potential applies a force More...
bool	count_pair_bs (Size const pos1, Size const pos2, BasePartner const &partner)
	ordered!!!! requires pos1<pos2 More...
BasePartner const &	retrieve_base_partner_from_pose_inline (pose::Pose const &pose)
	same as core::scoring::dna::retrieve_base_partner_from_pose More...
static basic::Tracer	TR ("core.energy_methods.DNA_DihedralEnergy")
static basic::Tracer	TR ("core.energy_methods.DNA_ReferenceEnergy")
static basic::Tracer	TR ("core.energy_methods.DumpTrajectoryEnergy")
static basic::Tracer	TR ("core.energy_methods.ElecDensAllAtomCenEnergy")
core::Real	SQ (core::Real N)
static basic::Tracer	TR ("core.energy_methods.ElecDensAtomwiseEnergy")
static basic::Tracer	TR ("core.energy_methods.ElecDensCenEnergy")
static basic::Tracer	TR ("core.energy_methods.ElecDensEnergy")
Real	sqr (Real x)
ExactOccludedHbondSolEnergyOP	create_ExactSHOEnergy_from_cmdline (core::scoring::methods::EnergyMethodOptions const &options)
	creates an ExactOccludedHbondSolEnergy object according to command-line options More...
bool	atom_is_aro2 (conformation::Residue const &rsd, Size const i)
bool	atom_is_aro (conformation::Residue const &rsd, Size const i)
static basic::Tracer	TR ("core.energy_methods.FastDensEnergy")
static basic::Tracer	TR ("core.energy_methods.FastSAXSEnergy")
core::Size	aa2idx (core::chemical::AA aa)
void	load_fastsax_spectrum (core::Size &nq, utility::vector1< core::Real >::iterator &q, utility::vector1< core::Real >::iterator &i_obs, utility::vector1< core::Real >::iterator &i_sig)
void	load_form_factors (core::Size nq, utility::vector1< core::Real >::iterator &q_in, utility::vector1< utility::vector1< core::Real > >::iterator &spectrum)
static basic::Tracer	TR ("core.energy_methods.FiberDiffractionEnergy")
static basic::Tracer	TR ("core.energy_methods.FiberDiffractionEnergyDens")
void	gnl_R_qfht (ObjexxFCL::FArray3D< float > &fourier_in, utility::vector0< utility::vector0< int > >::iterator &nvals, core::Size &lmax, core::Real &max_r_value, double &qfht_K1, double &qfht_K2, ObjexxFCL::FArray3D< std::complex< float > > &Gnl)
utility::pointer::shared_ptr< numeric::interpolation::spline::Interpolator >	fit_layer_lines_with_splines (ObjexxFCL::FArray1D< float > xvals, ObjexxFCL::FArray1D< float > yvals)
bool	count_atom (int const &atype)
static basic::Tracer	TR ("core.energy_methods.GenericBondedEnergy")
static basic::Tracer	TR ("core.energy_methods.GoapEnergy")
Size	chi2_torsion_atom_index (conformation::Residue const &rsd)
Real const	vdw_scale_factor (0.8)
static basic::Tracer	TR ("core.energy_methods.HydroxylTorsionEnergy")
static basic::Tracer	tr ("core.energy_methods.LinearBranchEnergy")
static basic::Tracer	tr ("core.energy_methods.LinearChainbreakEnergy")
static basic::Tracer	TR ("core.energy_methods.MHCEpitopeEnergy")
std::string	get_seq (utility::vector1< core::conformation::ResidueCOP > const &reslist, utility::vector1< core::Size > &symm_multipliers)
	Helper for testing – returns the AA sequence, with X for noncanonical and space between chains. More...
core::scoring::MultipoleElecResidueInfo const &	retrieve_mp_residue_info (pose::Pose const &pose, Size const seqpos)
core::scoring::MultipoleElecResidueInfo &	retrieve_nonconst_mp_residue_info (pose::Pose &pose, Size const seqpos)
MultipoleElecResPairMinData &	retrieve_nonconst_mp_pairdata (core::scoring::ResPairMinimizationData &pairdata)
MultipoleElecResPairMinData const &	retrieve_mp_pairdata (core::scoring::ResPairMinimizationData const &pairdata)
core::scoring::MultipoleElecResidueInfo &	retrieve_nonconst_mp_resdata (core::scoring::ResSingleMinimizationData &resdata)
core::scoring::MultipoleElecResidueInfo const &	retrieve_mp_resdata (core::scoring::ResSingleMinimizationData const &resdata)
core::scoring::MultipoleElecResidueInfoCOP	retrieve_mp_resdata_ptr (core::scoring::ResSingleMinimizationData const &resdata)
static basic::Tracer	TR ("core.energy_methods.NetChargeEnergy")
void	add_to_individual_sol_energies (pose::Pose &input_pose, core::Size const polar_resnum, core::Size const polar_atomno, core::scoring::etable::EtableOP etable_ptr, GridInfo const &grid_info, core::Real const &grid_constant, std::vector< std::vector< std::vector< core::Real > > > const &water_weights, std::vector< std::vector< std::vector< bool > > > &occluded_sites, bool const hydrogens_can_occlude, bool const pairwise_additive, bool const pairwise_additive_output, utility::vector1< core::Real > &residue_energies)
core::Real	compute_exact_geosol (pose::Pose &input_pose, bool const hydrogens_can_occlude, bool const pairwise_additive, bool const pairwise_additive_output, utility::vector1< core::Real > &residue_energies)
static basic::Tracer	TR ("core.energy_methods.ProQ_Energy")
bool	polymeric_termini_incomplete (conformation::Residue res)
static basic::Tracer	TR ("core.energy_methods.RamaPreProEnergy")
bool	is_phosphate_2 (conformation::Residue const &rsd, Size const i)
bool	is_sugar_2 (conformation::Residue const &rsd, Size const i)
bool	is_base_2 (conformation::Residue const &rsd, Size const i)
RNAAtomType	assign_rna_atom_type (conformation::Residue const &rsd, Size const i)
Real	rna_elec_weight (core::scoring::EnergyMap const &weights, bool const b1, bool const s1, bool const p1, bool const b2, bool const s2, bool const p2)
static basic::Tracer	trSAXSEnergy ("core.energy_methods.SAXSEnergy")
static basic::Tracer	TR ("core.energy_methods.SSElementMotifContactEnergy")
core::scoring::VdWTinkerResidueInfo const &	retrieve_vdw_residue_info (pose::Pose const &pose, Size const seqpos)
core::scoring::VdWTinkerResidueInfo &	retrieve_nonconst_vdw_residue_info (pose::Pose &pose, Size const seqpos)
VdWTinkerResPairMinData &	retrieve_nonconst_vdw_pairdata (core::scoring::ResPairMinimizationData &pairdata)
VdWTinkerResPairMinData const &	retrieve_vdw_pairdata (core::scoring::ResPairMinimizationData const &pairdata)
core::scoring::VdWTinkerResidueInfo &	retrieve_nonconst_vdw_resdata (core::scoring::ResSingleMinimizationData &resdata)
core::scoring::VdWTinkerResidueInfo const &	retrieve_vdw_resdata (core::scoring::ResSingleMinimizationData const &resdata)
core::scoring::VdWTinkerResidueInfoCOP	retrieve_vdw_resdata_ptr (core::scoring::ResSingleMinimizationData const &resdata)
static basic::Tracer	TR ("core.energy_methods.XtalMLEnergy")

Variables
static const Real	K_LENGTH =300.0
static const Real	K_ANGLE =80.0
static const Real	K_TORSION =80.0
static const Real	K_TORSION_PROTON =10.0
static const Real	K_TORSION_IMPROPER =80.0
Distance const	start_sig = 9.8
Distance const	end_sig = 10.2
DistanceSquared const	start_sig2 = start_sig*start_sig
DistanceSquared const	end_sig2 = end_sig*end_sig
core::Real const	geosol_kT = { 0.593 }
core::Real const	LK_MATCHING_SLOPE = { 0.4775 }
core::Real const	LK_MATCHING_INTERCEPT = { 0 }
static const core::Real	MAX_Z_POSITION = 30.5
static const core::Real	Z_BIN_SHIFT = 31
static const core::Real	MAX_AA = 20
static const core::Real	ASYMEZ_TABLE_BINS = 61
static const core::Real	MAX_Z_POSITION = 30.5
static const core::Real	Z_BIN_SHIFT = 31
static const core::Real	MAX_AA = 20
static const core::Real	ASYMEZ_TABLE_BINS = 61
core::Real	ref_spectrum [][21]
Real const	slope_6 = 0.15
Real const	offset_6 = 20.0
Real const	slope_12 = 0.5
Real const	offset_12 = 475.0
Real const	sixA_slope = 0.15
Real const	sixA_offset = 20
Real const	twelveA_slope = 5
Real const	twelveA_offset = 220.0
core::Real const	LK_MATCHING_WEIGHT_OLD_EXACT = { 0.23968 }
Vector	dummy_deriv_vector_
core::Real const	MIN_OCC_ENERGY = { 0.01 }

Typedef Documentation

AACompositionEnergyOP

typedef utility::pointer::shared_ptr< AACompositionEnergy > core::energy_methods::AACompositionEnergyOP

AARepeatEnergyOP

typedef utility::pointer::shared_ptr< AARepeatEnergy > core::energy_methods::AARepeatEnergyOP

AbegoCOP

typedef utility::pointer::shared_ptr< Abego const > core::energy_methods::AbegoCOP

AbegoOP

typedef utility::pointer::shared_ptr< Abego > core::energy_methods::AbegoOP

all_water_weights_iterator

typedef std::map< core::scoring::hbonds::HBEvalType, WaterWeightGridSet::Grid >::const_iterator core::energy_methods::all_water_weights_iterator

ArgCationPiEnergyCOP

typedef utility::pointer::shared_ptr< ArgCationPiEnergy const > core::energy_methods::ArgCationPiEnergyCOP

ArgCationPiEnergyOP

typedef utility::pointer::shared_ptr< ArgCationPiEnergy > core::energy_methods::ArgCationPiEnergyOP

AromaticBackboneRestraintEnergyCOP

typedef utility::pointer::shared_ptr< AromaticBackboneRestraintEnergy const > core::energy_methods::AromaticBackboneRestraintEnergyCOP

AromaticBackboneRestraintEnergyOP

typedef utility::pointer::shared_ptr< AromaticBackboneRestraintEnergy > core::energy_methods::AromaticBackboneRestraintEnergyOP

AspartimidePenaltyEnergyAP

typedef utility::pointer::weak_ptr< AspartimidePenaltyEnergy > core::energy_methods::AspartimidePenaltyEnergyAP

AspartimidePenaltyEnergyCAP

typedef utility::pointer::weak_ptr< AspartimidePenaltyEnergy const > core::energy_methods::AspartimidePenaltyEnergyCAP

AspartimidePenaltyEnergyCOP

typedef utility::pointer::shared_ptr< AspartimidePenaltyEnergy const > core::energy_methods::AspartimidePenaltyEnergyCOP

AspartimidePenaltyEnergyOP

typedef utility::pointer::shared_ptr< AspartimidePenaltyEnergy > core::energy_methods::AspartimidePenaltyEnergyOP

CacheableSasaVectorCOP

typedef utility::pointer::shared_ptr< CacheableSasaVector const > core::energy_methods::CacheableSasaVectorCOP

CartesianBondedEnergyAP

typedef utility::pointer::weak_ptr< CartesianBondedEnergy > core::energy_methods::CartesianBondedEnergyAP

CartesianBondedEnergyCAP

typedef utility::pointer::weak_ptr< CartesianBondedEnergy const > core::energy_methods::CartesianBondedEnergyCAP

CartesianBondedEnergyCOP

typedef utility::pointer::shared_ptr< CartesianBondedEnergy const > core::energy_methods::CartesianBondedEnergyCOP

CartesianBondedEnergyOP

typedef utility::pointer::shared_ptr< CartesianBondedEnergy > core::energy_methods::CartesianBondedEnergyOP

CentroidDisulfideEnergyCOP

typedef utility::pointer::shared_ptr< CentroidDisulfideEnergy const > core::energy_methods::CentroidDisulfideEnergyCOP

CentroidDisulfideEnergyOP

typedef utility::pointer::shared_ptr< CentroidDisulfideEnergy > core::energy_methods::CentroidDisulfideEnergyOP

ChemicalShiftAnisotropyEnergyOP

typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropyEnergy > core::energy_methods::ChemicalShiftAnisotropyEnergyOP

DEEREnergyCOP

typedef utility::pointer::shared_ptr< DEEREnergy const > core::energy_methods::DEEREnergyCOP

DEEREnergyOP

typedef utility::pointer::shared_ptr< DEEREnergy > core::energy_methods::DEEREnergyOP

DipolarCouplingEnergyOP

typedef utility::pointer::shared_ptr< DipolarCouplingEnergy > core::energy_methods::DipolarCouplingEnergyOP

DisulfideMatchingEnergyCOP

typedef utility::pointer::shared_ptr< DisulfideMatchingEnergy const > core::energy_methods::DisulfideMatchingEnergyCOP

DisulfideMatchingEnergyOP

typedef utility::pointer::shared_ptr< DisulfideMatchingEnergy > core::energy_methods::DisulfideMatchingEnergyOP

DisulfMinDataCOP

using core::energy_methods::DisulfMinDataCOP = typedef utility::pointer::shared_ptr<const DisulfMinData>

DisulfMinDataOP

using core::energy_methods::DisulfMinDataOP = typedef utility::pointer::shared_ptr<DisulfMinData>

DNATorsionEnergyCOP

typedef utility::pointer::shared_ptr< DNATorsionEnergy const > core::energy_methods::DNATorsionEnergyCOP

DNATorsionEnergyOP

typedef utility::pointer::shared_ptr< DNATorsionEnergy > core::energy_methods::DNATorsionEnergyOP

DumpTrajectoryEnergyOP

typedef utility::pointer::shared_ptr< DumpTrajectoryEnergy > core::energy_methods::DumpTrajectoryEnergyOP

ElecDensAtomwiseEnergyCOP

typedef utility::pointer::shared_ptr< ElecDensAtomwiseEnergy const > core::energy_methods::ElecDensAtomwiseEnergyCOP

ElecDensAtomwiseEnergyOP

typedef utility::pointer::shared_ptr< ElecDensAtomwiseEnergy > core::energy_methods::ElecDensAtomwiseEnergyOP

ExactOccludedHbondSolEnergyCOP

typedef utility::pointer::shared_ptr< ExactOccludedHbondSolEnergy const> core::energy_methods::ExactOccludedHbondSolEnergyCOP

ExactOccludedHbondSolEnergyOP

typedef utility::pointer::shared_ptr< ExactOccludedHbondSolEnergy > core::energy_methods::ExactOccludedHbondSolEnergyOP

FA_GrpElecEnergyCOP

typedef utility::pointer::shared_ptr< FA_GrpElecEnergy const > core::energy_methods::FA_GrpElecEnergyCOP

FA_GrpElecEnergyOP

typedef utility::pointer::shared_ptr< FA_GrpElecEnergy > core::energy_methods::FA_GrpElecEnergyOP

Fa_MbenvEnergyOP

typedef utility::pointer::shared_ptr< Fa_MbenvEnergy > core::energy_methods::Fa_MbenvEnergyOP

FAElecContextDataCOP

typedef utility::pointer::shared_ptr< FAElecContextData const > core::energy_methods::FAElecContextDataCOP

FAElecContextDataOP

typedef utility::pointer::shared_ptr< FAElecContextData > core::energy_methods::FAElecContextDataOP

FaMPAsymEzCBEnergyCOP

typedef utility::pointer::shared_ptr< FaMPAsymEzCBEnergy const > core::energy_methods::FaMPAsymEzCBEnergyCOP

FaMPAsymEzCBEnergyOP

typedef utility::pointer::shared_ptr< FaMPAsymEzCBEnergy > core::energy_methods::FaMPAsymEzCBEnergyOP

FaMPAsymEzCGEnergyCOP

typedef utility::pointer::shared_ptr< FaMPAsymEzCGEnergy const > core::energy_methods::FaMPAsymEzCGEnergyCOP

FaMPAsymEzCGEnergyOP

typedef utility::pointer::shared_ptr< FaMPAsymEzCGEnergy > core::energy_methods::FaMPAsymEzCGEnergyOP

FaMPEnvEnergyCOP

typedef utility::pointer::shared_ptr< FaMPEnvEnergy const > core::energy_methods::FaMPEnvEnergyCOP

FaMPEnvEnergyOP

typedef utility::pointer::shared_ptr< FaMPEnvEnergy > core::energy_methods::FaMPEnvEnergyOP

FaMPEnvSmoothEnergyCOP

typedef utility::pointer::shared_ptr< FaMPEnvSmoothEnergy const > core::energy_methods::FaMPEnvSmoothEnergyCOP

FaMPEnvSmoothEnergyOP

typedef utility::pointer::shared_ptr< FaMPEnvSmoothEnergy > core::energy_methods::FaMPEnvSmoothEnergyOP

FaMPSolvEnergyCOP

typedef utility::pointer::shared_ptr< FaMPSolvEnergy const > core::energy_methods::FaMPSolvEnergyCOP

FaMPSolvEnergyOP

typedef utility::pointer::shared_ptr< FaMPSolvEnergy > core::energy_methods::FaMPSolvEnergyOP

FullatomDisulfideEnergyCOP

typedef utility::pointer::shared_ptr< FullatomDisulfideEnergy const > core::energy_methods::FullatomDisulfideEnergyCOP

FullatomDisulfideEnergyOP

typedef utility::pointer::shared_ptr< FullatomDisulfideEnergy > core::energy_methods::FullatomDisulfideEnergyOP

GenericBondedEnergyOP

typedef utility::pointer::shared_ptr< GenericBondedEnergy > core::energy_methods::GenericBondedEnergyOP

GoapEnergyOP

typedef utility::pointer::shared_ptr< GoapEnergy > core::energy_methods::GoapEnergyOP

GoapRsdTypeCOP

typedef utility::pointer::shared_ptr< GoapRsdType const > core::energy_methods::GoapRsdTypeCOP

GoapRsdTypeMap

typedef std::map< std::string, GoapRsdTypeOP > core::energy_methods::GoapRsdTypeMap

GoapRsdTypeOP

typedef utility::pointer::shared_ptr< GoapRsdType > core::energy_methods::GoapRsdTypeOP

HBondEnergyCAP

typedef utility::pointer::weak_ptr< HBondEnergy const > core::energy_methods::HBondEnergyCAP

HBondEnergyCOP

typedef utility::pointer::shared_ptr< HBondEnergy const > core::energy_methods::HBondEnergyCOP

HBondEnergyOP

typedef utility::pointer::shared_ptr< HBondEnergy > core::energy_methods::HBondEnergyOP

HydroxylTorsionEnergyOP

typedef utility::pointer::shared_ptr< HydroxylTorsionEnergy > core::energy_methods::HydroxylTorsionEnergyOP

IdealParametersDatabaseAP

typedef utility::pointer::weak_ptr< IdealParametersDatabase > core::energy_methods::IdealParametersDatabaseAP

IdealParametersDatabaseCAP

typedef utility::pointer::weak_ptr< IdealParametersDatabase const > core::energy_methods::IdealParametersDatabaseCAP

IdealParametersDatabaseCOP

typedef utility::pointer::shared_ptr< IdealParametersDatabase const > core::energy_methods::IdealParametersDatabaseCOP

IdealParametersDatabaseOP

typedef utility::pointer::shared_ptr< IdealParametersDatabase > core::energy_methods::IdealParametersDatabaseOP

ImplicitMembraneCoulombCOP

using core::energy_methods::ImplicitMembraneCoulombCOP = typedef utility::pointer::shared_ptr< ImplicitMembraneCoulomb const >

ImplicitMembraneCoulombOP

using core::energy_methods::ImplicitMembraneCoulombOP = typedef utility::pointer::shared_ptr< ImplicitMembraneCoulomb >

ImplicitMembraneElecEnergyCOP

using core::energy_methods::ImplicitMembraneElecEnergyCOP = typedef utility::pointer::shared_ptr< ImplicitMembraneElecEnergy const >

ImplicitMembraneElecEnergyOP

using core::energy_methods::ImplicitMembraneElecEnergyOP = typedef utility::pointer::shared_ptr< ImplicitMembraneElecEnergy >

Matrix

typedef numeric::xyzMatrix< Real > core::energy_methods::Matrix

MgEnergyCOP

typedef utility::pointer::shared_ptr< MgEnergy const > core::energy_methods::MgEnergyCOP

MgEnergyOP

typedef utility::pointer::shared_ptr< MgEnergy > core::energy_methods::MgEnergyOP

MHCEpitopeEnergyCOP

typedef utility::pointer::shared_ptr< MHCEpitopeEnergy const > core::energy_methods::MHCEpitopeEnergyCOP

MHCEpitopeEnergyOP

typedef utility::pointer::shared_ptr< MHCEpitopeEnergy > core::energy_methods::MHCEpitopeEnergyOP

MotifDockEnergyCOP

typedef utility::pointer::shared_ptr< MotifDockEnergy const> core::energy_methods::MotifDockEnergyCOP

MotifDockEnergyOP

typedef utility::pointer::shared_ptr< MotifDockEnergy > core::energy_methods::MotifDockEnergyOP

MPCbetaEnergyCOP

typedef utility::pointer::shared_ptr< MPCbetaEnergy const > core::energy_methods::MPCbetaEnergyCOP

MPCbetaEnergyOP

typedef utility::pointer::shared_ptr< MPCbetaEnergy > core::energy_methods::MPCbetaEnergyOP

MPEnvEnergyCOP

typedef utility::pointer::shared_ptr< MPEnvEnergy const > core::energy_methods::MPEnvEnergyCOP

MPEnvEnergyOP

typedef utility::pointer::shared_ptr< MPEnvEnergy > core::energy_methods::MPEnvEnergyOP

MPHelicalityEnergyCOP

typedef utility::pointer::shared_ptr< MPHelicalityEnergy const > core::energy_methods::MPHelicalityEnergyCOP

MPHelicalityEnergyOP

typedef utility::pointer::shared_ptr< MPHelicalityEnergy > core::energy_methods::MPHelicalityEnergyOP

MPPairEnergyCOP

typedef utility::pointer::shared_ptr< MPPairEnergy const > core::energy_methods::MPPairEnergyCOP

MPPairEnergyOP

typedef utility::pointer::shared_ptr< MPPairEnergy > core::energy_methods::MPPairEnergyOP

MPResidueLipophilicityEnergyCOP

typedef utility::pointer::shared_ptr< MPResidueLipophilicityEnergy const > core::energy_methods::MPResidueLipophilicityEnergyCOP

MPResidueLipophilicityEnergyOP

typedef utility::pointer::shared_ptr< MPResidueLipophilicityEnergy > core::energy_methods::MPResidueLipophilicityEnergyOP

MultipoleElecResPairMinDataCOP

using core::energy_methods::MultipoleElecResPairMinDataCOP = typedef utility::pointer::shared_ptr<const MultipoleElecResPairMinData>

MultipoleElecResPairMinDataOP

using core::energy_methods::MultipoleElecResPairMinDataOP = typedef utility::pointer::shared_ptr<MultipoleElecResPairMinData>

NetChargeEnergyOP

typedef utility::pointer::shared_ptr< NetChargeEnergy > core::energy_methods::NetChargeEnergyOP

OmegaTetherEnergyCOP

typedef utility::pointer::shared_ptr< OmegaTetherEnergy const > core::energy_methods::OmegaTetherEnergyCOP

OmegaTetherEnergyOP

typedef utility::pointer::shared_ptr< OmegaTetherEnergy > core::energy_methods::OmegaTetherEnergyOP

OtherPoseEnergyCOP

typedef utility::pointer::shared_ptr< OtherPoseEnergy const > core::energy_methods::OtherPoseEnergyCOP

OtherPoseEnergyOP

typedef utility::pointer::shared_ptr< OtherPoseEnergy > core::energy_methods::OtherPoseEnergyOP

P_AA_EnergyOP

typedef utility::pointer::shared_ptr< P_AA_Energy > core::energy_methods::P_AA_EnergyOP

P_AA_pp_EnergyOP

typedef utility::pointer::shared_ptr< P_AA_pp_Energy > core::energy_methods::P_AA_pp_EnergyOP

P_AA_ss_EnergyOP

typedef utility::pointer::shared_ptr< P_AA_ss_Energy > core::energy_methods::P_AA_ss_EnergyOP

PBLifetimeCacheAP

typedef utility::pointer::weak_ptr< PBLifetimeCache > core::energy_methods::PBLifetimeCacheAP

PBLifetimeCacheCAP

typedef utility::pointer::weak_ptr< PBLifetimeCache const > core::energy_methods::PBLifetimeCacheCAP

PBLifetimeCacheCOP

typedef utility::pointer::shared_ptr< PBLifetimeCache const > core::energy_methods::PBLifetimeCacheCOP

PBLifetimeCacheOP

typedef utility::pointer::shared_ptr< PBLifetimeCache > core::energy_methods::PBLifetimeCacheOP

pHEnergyOP

typedef utility::pointer::shared_ptr< pHEnergy > core::energy_methods::pHEnergyOP

PointWaterEnergyCOP

typedef utility::pointer::shared_ptr< PointWaterEnergy const > core::energy_methods::PointWaterEnergyCOP

PointWaterEnergyOP

typedef utility::pointer::shared_ptr< PointWaterEnergy > core::energy_methods::PointWaterEnergyOP

PoissonBoltzmannEnergyAP

typedef utility::pointer::weak_ptr< PoissonBoltzmannEnergy > core::energy_methods::PoissonBoltzmannEnergyAP

PoissonBoltzmannEnergyCAP

typedef utility::pointer::weak_ptr< PoissonBoltzmannEnergy const > core::energy_methods::PoissonBoltzmannEnergyCAP

PoissonBoltzmannEnergyCOP

typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy const > core::energy_methods::PoissonBoltzmannEnergyCOP

PoissonBoltzmannEnergyOP

typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy > core::energy_methods::PoissonBoltzmannEnergyOP

PoseSequenceCOP

typedef std::shared_ptr< PoseSequence const > core::energy_methods::PoseSequenceCOP

PoseSequenceOP

typedef std::shared_ptr< PoseSequence > core::energy_methods::PoseSequenceOP

ProClosureEnergyCOP

typedef utility::pointer::shared_ptr< ProClosureEnergy const > core::energy_methods::ProClosureEnergyCOP

ProClosureEnergyOP

typedef utility::pointer::shared_ptr< ProClosureEnergy > core::energy_methods::ProClosureEnergyOP

RamachandranEnergy2BCOP

typedef utility::pointer::shared_ptr< RamachandranEnergy2B const > core::energy_methods::RamachandranEnergy2BCOP

RamachandranEnergy2BOP

typedef utility::pointer::shared_ptr< RamachandranEnergy2B > core::energy_methods::RamachandranEnergy2BOP

RamachandranEnergyCOP

typedef utility::pointer::shared_ptr< RamachandranEnergy const > core::energy_methods::RamachandranEnergyCOP

RamachandranEnergyOP

typedef utility::pointer::shared_ptr< RamachandranEnergy > core::energy_methods::RamachandranEnergyOP

RamaPreProEnergyAP

typedef utility::pointer::weak_ptr< RamaPreProEnergy > core::energy_methods::RamaPreProEnergyAP

RamaPreProEnergyCAP

typedef utility::pointer::weak_ptr< RamaPreProEnergy const > core::energy_methods::RamaPreProEnergyCAP

RamaPreProEnergyCOP

typedef utility::pointer::shared_ptr< RamaPreProEnergy const > core::energy_methods::RamaPreProEnergyCOP

RamaPreProEnergyOP

typedef utility::pointer::shared_ptr< RamaPreProEnergy > core::energy_methods::RamaPreProEnergyOP

ReferenceEnergyCOP

typedef utility::pointer::shared_ptr< ReferenceEnergy const > core::energy_methods::ReferenceEnergyCOP

ReferenceEnergyNoncanonicalCOP

typedef utility::pointer::shared_ptr< ReferenceEnergyNoncanonical const > core::energy_methods::ReferenceEnergyNoncanonicalCOP

ReferenceEnergyNoncanonicalOP

typedef utility::pointer::shared_ptr< ReferenceEnergyNoncanonical > core::energy_methods::ReferenceEnergyNoncanonicalOP

ReferenceEnergyOP

typedef utility::pointer::shared_ptr< ReferenceEnergy > core::energy_methods::ReferenceEnergyOP

ResidualDipolarCouplingEnergyOP

typedef utility::pointer::shared_ptr< ResidualDipolarCouplingEnergy > core::energy_methods::ResidualDipolarCouplingEnergyOP

ResidueCartBondedParametersAP

typedef utility::pointer::weak_ptr< ResidueCartBondedParameters > core::energy_methods::ResidueCartBondedParametersAP

ResidueCartBondedParametersCAP

typedef utility::pointer::weak_ptr< ResidueCartBondedParameters const > core::energy_methods::ResidueCartBondedParametersCAP

ResidueCartBondedParametersCOP

typedef utility::pointer::shared_ptr< ResidueCartBondedParameters const > core::energy_methods::ResidueCartBondedParametersCOP

ResidueCartBondedParametersOP

typedef utility::pointer::shared_ptr< ResidueCartBondedParameters > core::energy_methods::ResidueCartBondedParametersOP

RG_Local_MinDataOP

typedef utility::pointer::shared_ptr< RG_Local_MinData > core::energy_methods::RG_Local_MinDataOP

RG_MinDataOP

typedef utility::pointer::shared_ptr< RG_MinData > core::energy_methods::RG_MinDataOP

RingClosureEnergyCOP

typedef utility::pointer::shared_ptr< RingClosureEnergy const > core::energy_methods::RingClosureEnergyCOP

RingClosureEnergyOP

typedef utility::pointer::shared_ptr< RingClosureEnergy > core::energy_methods::RingClosureEnergyOP

RNA_ChemicalMappingEnergyCOP

typedef utility::pointer::shared_ptr< RNA_ChemicalMappingEnergy const > core::energy_methods::RNA_ChemicalMappingEnergyCOP

RNA_ChemicalMappingEnergyOP

typedef utility::pointer::shared_ptr< RNA_ChemicalMappingEnergy > core::energy_methods::RNA_ChemicalMappingEnergyOP

RNA_CoarseDistEnergyCOP

using core::energy_methods::RNA_CoarseDistEnergyCOP = typedef utility::pointer::shared_ptr< RNA_CoarseDistEnergy const >

RNA_CoarseDistEnergyOP

using core::energy_methods::RNA_CoarseDistEnergyOP = typedef utility::pointer::shared_ptr< RNA_CoarseDistEnergy >

RNA_FullAtomVDW_BasePhosphateCOP

typedef utility::pointer::shared_ptr< RNA_FullAtomVDW_BasePhosphate const > core::energy_methods::RNA_FullAtomVDW_BasePhosphateCOP

RNA_FullAtomVDW_BasePhosphateOP

typedef utility::pointer::shared_ptr< RNA_FullAtomVDW_BasePhosphate > core::energy_methods::RNA_FullAtomVDW_BasePhosphateOP

RNA_SugarCloseEnergyCOP

typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy const > core::energy_methods::RNA_SugarCloseEnergyCOP

RNA_SugarCloseEnergyOP

typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy > core::energy_methods::RNA_SugarCloseEnergyOP

RNA_TorsionEnergyCOP

typedef utility::pointer::shared_ptr< RNA_TorsionEnergy const > core::energy_methods::RNA_TorsionEnergyCOP

RNA_TorsionEnergyOP

typedef utility::pointer::shared_ptr< RNA_TorsionEnergy > core::energy_methods::RNA_TorsionEnergyOP

ScoreCacheCOP

typedef utility::pointer::shared_ptr< ScoreCache const > core::energy_methods::ScoreCacheCOP

ScoreCacheOP

typedef utility::pointer::shared_ptr< ScoreCache > core::energy_methods::ScoreCacheOP

SequenceDependentRefEnergyCOP

typedef utility::pointer::shared_ptr< SequenceDependentRefEnergy const > core::energy_methods::SequenceDependentRefEnergyCOP

SequenceDependentRefEnergyOP

typedef utility::pointer::shared_ptr< SequenceDependentRefEnergy > core::energy_methods::SequenceDependentRefEnergyOP

SplitUnfoldedTwoBodyEnergyOP

typedef utility::pointer::shared_ptr<SplitUnfoldedTwoBodyEnergy> core::energy_methods::SplitUnfoldedTwoBodyEnergyOP

SugarBackboneEnergyCOP

typedef utility::pointer::shared_ptr< SugarBackboneEnergy const> core::energy_methods::SugarBackboneEnergyCOP

SugarBackboneEnergyOP

typedef utility::pointer::shared_ptr< SugarBackboneEnergy > core::energy_methods::SugarBackboneEnergyOP

sum_water_weights_iterator

typedef std::map< core::scoring::hbonds::HBEvalType, core::Real >::const_iterator core::energy_methods::sum_water_weights_iterator

torsionparam_vector

typedef utility::vector1< std::pair< atm_name_quad, core::scoring::methods::CartBondedParametersCOP > > core::energy_methods::torsionparam_vector

UnfoldedStateEnergyOP

typedef utility::pointer::shared_ptr< UnfoldedStateEnergy > core::energy_methods::UnfoldedStateEnergyOP

VdWTinkerResPairMinDataCOP

using core::energy_methods::VdWTinkerResPairMinDataCOP = typedef utility::pointer::shared_ptr<const VdWTinkerResPairMinData>

VdWTinkerResPairMinDataOP

using core::energy_methods::VdWTinkerResPairMinDataOP = typedef utility::pointer::shared_ptr<VdWTinkerResPairMinData>

Vector

typedef numeric::xyzVector< core::Real > core::energy_methods::Vector

WaterAdductIntraEnergyOP

typedef utility::pointer::shared_ptr< WaterAdductIntraEnergy > core::energy_methods::WaterAdductIntraEnergyOP

WaterSpecificEnergyOP

typedef utility::pointer::shared_ptr< WaterSpecificEnergy > core::energy_methods::WaterSpecificEnergyOP

YHHPlanarityEnergyOP

typedef utility::pointer::shared_ptr< YHHPlanarityEnergy > core::energy_methods::YHHPlanarityEnergyOP

Function Documentation

aa2idx()

core::Size core::energy_methods::aa2idx

(

core::chemical::AA

aa

)

References protocols::cluster::calibur::aa, core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::aa_val.

Referenced by core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), and core::energy_methods::FastSAXSEnergy::setup_for_scoring().

add_to_individual_sol_energies()

void core::energy_methods::add_to_individual_sol_energies	(	pose::Pose &	input_pose,
		core::Size const	polar_resnum,
		core::Size const	polar_atomno,
		core::scoring::etable::EtableOP	etable_ptr,
		GridInfo const &	grid_info,
		core::Real const &	grid_constant,
		std::vector< std::vector< std::vector< core::Real > > > const &	water_weights,
		std::vector< std::vector< std::vector< bool > > > &	occluded_sites,
		bool const	hydrogens_can_occlude,
		bool const	pairwise_additive,
		bool const	pairwise_additive_output,
		utility::vector1< core::Real > &	residue_energies
	)

References core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_type_index(), core::pose::Pose::energies(), geosol_kT, core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), TR(), core::energy_methods::GridInfo::xnum_points(), core::energy_methods::GridInfo::xorigin(), core::energy_methods::GridInfo::xstep(), core::conformation::Atom::xyz(), core::energy_methods::GridInfo::ynum_points(), core::energy_methods::GridInfo::yorigin(), core::energy_methods::GridInfo::ystep(), core::energy_methods::GridInfo::znum_points(), core::energy_methods::GridInfo::zorigin(), and core::energy_methods::GridInfo::zstep().

Referenced by compute_exact_geosol().

assign_rna_atom_type()

RNAAtomType core::energy_methods::assign_rna_atom_type	(	conformation::Residue const &	rsd,
		Size const	i
	)

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), BASE, core::conformation::Residue::first_sidechain_atom(), is_phosphate_2(), PHOSPHATE, and SUGAR.

Referenced by core::energy_methods::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), and core::energy_methods::RNA_FA_ElecEnergy::score_atom_pair().

atom_is_aro()

bool core::energy_methods::atom_is_aro	(	conformation::Residue const &	rsd,
		Size const	i
	)

References core::conformation::Residue::atom_type(), and core::chemical::AtomType::name().

Referenced by core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), and core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro().

atom_is_aro2()

bool core::energy_methods::atom_is_aro2	(	conformation::Residue const &	rsd,
		Size const	i
	)

References core::conformation::Residue::atom_type(), and core::chemical::AtomType::name().

Referenced by core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), and core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro().

chi2_torsion_atom_index()

Size core::energy_methods::chi2_torsion_atom_index

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::chi_atoms().

Referenced by core::energy_methods::HackAroEnergy::eval_atom_derivative().

compute_exact_geosol()

core::Real core::energy_methods::compute_exact_geosol	(	pose::Pose &	input_pose,
		bool const	hydrogens_can_occlude,
		bool const	pairwise_additive,
		bool const	pairwise_additive_output,
		utility::vector1< core::Real > &	residue_energies
	)

References core::conformation::Residue::accpt_pos(), add_to_individual_sol_energies(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::chemical::FA_STANDARD, geosol_kT, core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::hbonds::hbacc_H2O, core::scoring::hbonds::hbdon_H2O, core::conformation::Residue::Hpos_polar(), core::conformation::Residue::is_lower_terminus(), LK_MATCHING_WEIGHT_OLD_EXACT, core::pose::Pose::residue(), core::scoring::hbonds::seq_sep_other, core::pose::Pose::size(), and TR().

count_atom()

bool core::energy_methods::count_atom ( int const &  atype )

inline

Referenced by core::energy_methods::SuckerEnergy::eval_atom_derivative(), and core::energy_methods::SuckerEnergy::residue_pair_energy().

count_pair_bs()

bool core::energy_methods::count_pair_bs ( Size const  pos1, Size const  pos2, BasePartner const &  partner  )

inline

ordered!!!! requires pos1<pos2

Referenced by core::energy_methods::DNA_BaseEnergy::eval_atom_derivative(), and core::energy_methods::DNA_BaseEnergy::residue_pair_energy().

create_ExactSHOEnergy_from_cmdline()

ExactOccludedHbondSolEnergyOP core::energy_methods::create_ExactSHOEnergy_from_cmdline

(

core::scoring::methods::EnergyMethodOptions const &

options

)

creates an ExactOccludedHbondSolEnergy object according to command-line options

Parameters

[in]

options

options not from the command line

References core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation(), core::scoring::methods::EnergyMethodOptions::etable_options(), core::scoring::etable::EtableOptions::no_lk_polar_desolvation, and core::scoring::etable::EtableOptions::proline_N_is_lk_nonpolar.

Referenced by core::energy_methods::ExactOccludedHbondSolEnergyCreator::create_energy_method().

dna_deriv_atom()

std::string const core::energy_methods::dna_deriv_atom

(

" C5 "

)

the atom through which the knowledge based potential applies a force

Referenced by core::energy_methods::DNA_BaseEnergy::eval_atom_derivative().

eval()

void core::energy_methods::eval	(	Real const	phi0,
		Real const	weight,
		Size const	rt1,
		Size const	rt2,
		Size const	rt3,
		Size const	rt4,
		conformation::Residue const &	rsd,
		utility::vector1< core::scoring::DerivVectorPair > &	atom_derivs
	)

References core::conformation::Residue::xyz().

Referenced by protocols::evaluation::EvaluatorFactory::add_all_evaluators(), protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::abinitio::AbrelaxApplication::add_evaluation(), protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(), protocols::constraints_additional::CombinedConstraintEvaluatorCreator::add_evaluators(), protocols::constraints_additional::ConstraintEvaluatorCreator::add_evaluators(), protocols::simple_filters::CamShiftEvaluatorCreator::add_evaluators(), protocols::simple_filters::ChiWellRmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::ContactMapEvaluatorCreator::add_evaluators(), protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), protocols::simple_filters::JScoreEvaluatorCreator::add_evaluators(), protocols::simple_filters::JumpNrEvaluatorCreator::add_evaluators(), protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), protocols::simple_filters::PalesEvaluatorCreator::add_evaluators(), protocols::simple_filters::PoolEvaluatorCreator::add_evaluators(), protocols::simple_filters::PredictedBurialFnEvaluatorCreator::add_evaluators(), protocols::simple_filters::RdcEvaluatorCreator::add_evaluators(), protocols::simple_filters::RdcTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::StructureSimilarityEvaluatorCreator::add_evaluators(), protocols::topology_broker::ConstraintEvaluatorWrapperCreator::add_evaluators(), protocols::sparta::ChemicalShiftEvaluatorCreator::add_evaluators(), protocols::evaluation::EvaluatorFactory::add_evaluators(), core::fragment::picking_old::vall::VallLibrarian::add_fragment_eval(), protocols::indexed_structure_store::search::bind_QueryDatabase(), protocols::indexed_structure_store::bind_StructureStore(), protocols::abinitio::IterativeBase::compute_cores(), core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), protocols::evaluation::evaluate_pose(), protocols::abinitio::get_core(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), and core::scoring::Ramachandran::read_rama_map_file().

fit_layer_lines_with_splines()

utility::pointer::shared_ptr< numeric::interpolation::spline::Interpolator > core::energy_methods::fit_layer_lines_with_splines	(	ObjexxFCL::FArray1D< float >	xvals,
		ObjexxFCL::FArray1D< float >	yvals
	)

Referenced by core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring().

GEOMETRIES()

static basic::Tracer core::energy_methods::GEOMETRIES ( "core.energy_methods.CartesianBondedEnergy.GEOMETRIES"  )

static

get_restag()

std::string core::energy_methods::get_restag

(

core::chemical::ResidueType const &

restype

)

helper function

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_unk, core::chemical::aa_unp, core::chemical::get_L_equivalent(), core::chemical::is_canonical_D_aa(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueTypeBase::na_analogue(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name3(), core::chemical::name_from_aa(), and core::chemical::PATCH_LINKER.

Referenced by core::energy_methods::IdealParametersDatabase::create_parameters_for_restype(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::energy_methods::IdealParametersDatabase::generate_impropers_map_res(), core::energy_methods::IdealParametersDatabase::lookup_angle(), core::energy_methods::IdealParametersDatabase::lookup_improper(), and core::energy_methods::IdealParametersDatabase::lookup_length().

get_seq()

std::string core::energy_methods::get_seq	(	utility::vector1< core::conformation::ResidueCOP > const &	reslist,
		utility::vector1< core::Size > &	symm_multipliers
	)

Helper for testing – returns the AA sequence, with X for noncanonical and space between chains.

References core::chemical::num_canonical_aas, protocols::loops::start, and protocols::loops::stop.

Referenced by core::energy_methods::MHCEpitopeEnergy::full_rescore(), and core::energy_methods::MHCEpitopeEnergy::update_score().

gnl_R_qfht()

void core::energy_methods::gnl_R_qfht	(	ObjexxFCL::FArray3D< float > &	fourier_in,
		utility::vector0< utility::vector0< int > >::iterator &	nvals,
		core::Size &	lmax,
		core::Real &	max_r_value,
		double &	qfht_K1,
		double &	qfht_K2,
		ObjexxFCL::FArray3D< std::complex< float > > &	Gnl
	)

References core::scoring::fiber_diffraction::ft_nfft(), core::scoring::fiber_diffraction::hankel_free(), core::scoring::fiber_diffraction::hankel_make_input(), core::scoring::fiber_diffraction::hankel_trans_no_lec(), and protocols::hybridization::val.

Referenced by core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring().

is_base_2()

bool core::energy_methods::is_base_2	(	conformation::Residue const &	rsd,
		Size const	i
	)

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), is_phosphate_2(), and is_sugar_2().

Referenced by core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), and core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy().

is_phosphate_2()

bool core::energy_methods::is_phosphate_2	(	conformation::Residue const &	rsd,
		Size const	i
	)

References core::conformation::Residue::atom_base(), and core::conformation::Residue::atom_is_hydrogen().

Referenced by assign_rna_atom_type(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), is_base_2(), and is_sugar_2().

is_sugar_2()

bool core::energy_methods::is_sugar_2	(	conformation::Residue const &	rsd,
		Size const	i
	)

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::first_sidechain_atom(), and is_phosphate_2().

Referenced by core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), and is_base_2().

load_fastsax_spectrum()

void core::energy_methods::load_fastsax_spectrum	(	core::Size &	nq,
		utility::vector1< core::Real >::iterator &	q,
		utility::vector1< core::Real >::iterator &	i_obs,
		utility::vector1< core::Real >::iterator &	i_sig
	)

References core::chemical::rings::q, ref_spectrum, and TR().

Referenced by core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), and core::energy_methods::FastSAXSEnergy::setup_for_scoring().

load_form_factors()

void core::energy_methods::load_form_factors	(	core::Size	nq,
		utility::vector1< core::Real >::iterator &	q_in,
		utility::vector1< utility::vector1< core::Real > >::iterator &	spectrum
	)

References ref_spectrum, and TR().

Referenced by core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), and core::energy_methods::FastSAXSEnergy::setup_for_scoring().

parcs_ccs()

core::Real core::energy_methods::parcs_ccs	(	core::pose::Pose &	mypose,
		core::Size const	nrot,
		core::Real const	prad
	)

References core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::atom_type(), HEAVY_ATOM_EFFECTIVE_RADIUS, HYDROGEN_ATOM_EFFECTIVE_RADIUS, core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::is_virtual(), core::scoring::motif::random_rotation(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::Pose::total_atoms(), and core::conformation::Residue::xyz().

Referenced by core::energy_methods::CCS_IMMSEnergy::finalize_total_energy().

point_line_distance()

Real core::energy_methods::point_line_distance	(	numeric::xyzVector< Real > const &	point,
		numeric::xyzVector< Real > const &	line_base,
		numeric::xyzVector< Real > const &	line_ray
	)

Referenced by core::energy_methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), and core::energy_methods::ArgCationPiEnergy::residue_pair_energy().

polymeric_termini_incomplete()

bool core::energy_methods::polymeric_termini_incomplete ( conformation::Residue  res )

inline

References core::conformation::Residue::connection_incomplete(), and core::conformation::Residue::n_polymeric_residue_connections().

retrieve_base_partner_from_pose_inline()

BasePartner const & core::energy_methods::retrieve_base_partner_from_pose_inline ( pose::Pose const &  pose )

inline

same as core::scoring::dna::retrieve_base_partner_from_pose

References core::pose::datacache::CacheableDataType::BASE_PARTNER, and core::pose::Pose::data().

Referenced by core::energy_methods::DNA_BaseEnergy::eval_atom_derivative(), core::energy_methods::DNA_BaseEnergy::residue_pair_energy(), and core::energy_methods::DNA_ReferenceEnergy::residue_pair_energy().

retrieve_mp_pairdata()

MultipoleElecResPairMinData const& core::energy_methods::retrieve_mp_pairdata ( core::scoring::ResPairMinimizationData const &  pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), and core::scoring::mp_respair_data.

retrieve_mp_resdata()

core::scoring::MultipoleElecResidueInfo const& core::energy_methods::retrieve_mp_resdata ( core::scoring::ResSingleMinimizationData const &  resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data_ref(), and core::scoring::mp_res_data.

Referenced by core::energy_methods::MultipoleElecEnergy::eval_intrares_derivatives(), and core::energy_methods::MultipoleElecEnergy::eval_intrares_energy_ext().

retrieve_mp_resdata_ptr()

core::scoring::MultipoleElecResidueInfoCOP core::energy_methods::retrieve_mp_resdata_ptr ( core::scoring::ResSingleMinimizationData const &  resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), and core::scoring::mp_res_data.

Referenced by core::energy_methods::MultipoleElecEnergy::setup_for_minimizing_for_residue_pair().

retrieve_mp_residue_info()

core::scoring::MultipoleElecResidueInfo const& core::energy_methods::retrieve_mp_residue_info ( pose::Pose const &  pose, Size const  seqpos  )

inline

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, and core::scoring::MultipoleElecPoseInfo::residue_info().

Referenced by core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::MultipoleElecEnergy::residue_pair_energy(), and core::energy_methods::MultipoleElecEnergy::residue_pair_energy_ext().

retrieve_nonconst_mp_pairdata()

MultipoleElecResPairMinData& core::energy_methods::retrieve_nonconst_mp_pairdata ( core::scoring::ResPairMinimizationData &  pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::mp_respair_data, and core::scoring::ResPairMinimizationData::set_data().

Referenced by core::energy_methods::MultipoleElecEnergy::setup_for_minimizing_for_residue_pair().

retrieve_nonconst_mp_resdata()

core::scoring::MultipoleElecResidueInfo& core::energy_methods::retrieve_nonconst_mp_resdata ( core::scoring::ResSingleMinimizationData &  resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), core::scoring::mp_res_data, and core::scoring::ResSingleMinimizationData::set_data().

Referenced by core::energy_methods::MultipoleElecEnergy::setup_for_scoring_for_residue().

retrieve_nonconst_mp_residue_info()

core::scoring::MultipoleElecResidueInfo& core::energy_methods::retrieve_nonconst_mp_residue_info ( pose::Pose &  pose, Size const  seqpos  )

inline

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, and core::scoring::MultipoleElecPoseInfo::residue_info().

retrieve_nonconst_vdw_pairdata()

VdWTinkerResPairMinData& core::energy_methods::retrieve_nonconst_vdw_pairdata ( core::scoring::ResPairMinimizationData &  pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::set_data(), and core::scoring::vdw_respair_data.

Referenced by core::energy_methods::VdWTinkerEnergy::setup_for_minimizing_for_residue_pair().

retrieve_nonconst_vdw_resdata()

core::scoring::VdWTinkerResidueInfo& core::energy_methods::retrieve_nonconst_vdw_resdata ( core::scoring::ResSingleMinimizationData &  resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), core::scoring::ResSingleMinimizationData::set_data(), and core::scoring::vdw_res_data.

Referenced by core::energy_methods::VdWTinkerEnergy::setup_for_scoring_for_residue().

retrieve_nonconst_vdw_residue_info()

core::scoring::VdWTinkerResidueInfo& core::energy_methods::retrieve_nonconst_vdw_residue_info ( pose::Pose &  pose, Size const  seqpos  )

inline

References core::pose::Pose::data(), core::scoring::VdWTinkerPoseInfo::residue_info(), and core::pose::datacache::CacheableDataType::VDWTINKER_POSE_INFO.

retrieve_vdw_pairdata()

VdWTinkerResPairMinData const& core::energy_methods::retrieve_vdw_pairdata ( core::scoring::ResPairMinimizationData const &  pairdata )

inline

References core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), and core::scoring::vdw_respair_data.

retrieve_vdw_resdata()

core::scoring::VdWTinkerResidueInfo const& core::energy_methods::retrieve_vdw_resdata ( core::scoring::ResSingleMinimizationData const &  resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data_ref(), and core::scoring::vdw_res_data.

Referenced by core::energy_methods::VdWTinkerEnergy::eval_intrares_derivatives(), core::energy_methods::VdWTinkerEnergy::eval_intrares_energy_ext(), and core::energy_methods::VdWTinkerEnergy::eval_residue_pair_derivatives().

retrieve_vdw_resdata_ptr()

core::scoring::VdWTinkerResidueInfoCOP core::energy_methods::retrieve_vdw_resdata_ptr ( core::scoring::ResSingleMinimizationData const &  resdata )

inline

References core::scoring::ResSingleMinimizationData::get_data(), and core::scoring::vdw_res_data.

Referenced by core::energy_methods::VdWTinkerEnergy::setup_for_minimizing_for_residue_pair().

retrieve_vdw_residue_info()

core::scoring::VdWTinkerResidueInfo const& core::energy_methods::retrieve_vdw_residue_info ( pose::Pose const &  pose, Size const  seqpos  )

inline

References core::pose::Pose::data(), core::scoring::VdWTinkerPoseInfo::residue_info(), and core::pose::datacache::CacheableDataType::VDWTINKER_POSE_INFO.

Referenced by core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::VdWTinkerEnergy::residue_pair_energy(), and core::energy_methods::VdWTinkerEnergy::residue_pair_energy_ext().

rna_elec_weight()

Real core::energy_methods::rna_elec_weight	(	core::scoring::EnergyMap const &	weights,
		bool const	b1,
		bool const	s1,
		bool const	p1,
		bool const	b2,
		bool const	s2,
		bool const	p2
	)

References core::scoring::fa_elec_rna_base_base, core::scoring::fa_elec_rna_phos_base, core::scoring::fa_elec_rna_phos_phos, core::scoring::fa_elec_rna_phos_sugr, core::scoring::fa_elec_rna_sugr_base, and core::scoring::fa_elec_rna_sugr_sugr.

Referenced by core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives().

SQ()

core::Real core::energy_methods::SQ ( core::Real  N )

inline

References core::chemical::element::N.

Referenced by core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), and core::energy_methods::ElecDensEnergy::eval_atom_derivative().

sqr()

Real core::energy_methods::sqr ( Real  x )

inline

Referenced by core::energy_methods::EnvSmoothEnergy::sigmoidish_neighbor(), core::energy_methods::FaMPEnvSmoothEnergy::sigmoidish_neighbor(), and core::energy_methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor().

swap_seqpos()

void core::energy_methods::swap_seqpos	(	core::Size &	seqpos1,
		core::Size &	seqpos2
	)

TR() [1/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AACompositionEnergy"  )

static

Referenced by core::energy_methods::AACompositionEnergy::AACompositionEnergy(), add_to_individual_sol_energies(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::energy_methods::CenHBEnergy::CenHBEnergy(), core::energy_methods::AACompositionEnergy::clean_up_residuearrayannealableenergy_after_packing(), core::energy_methods::MPSpanInsertionEnergy::compute(), compute_exact_geosol(), core::energy_methods::MPCbetaEnergy::compute_mpcbeta_score(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::energy_methods::MPSpanInsertionEnergy::create_updated_span(), core::energy_methods::D2H_SA_Energy::D2H_SA_Energy(), core::energy_methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::energy_methods::MHCEpitopeEnergy::difference_btw_cached_and_full_rescore(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::GenericBondedEnergy::eval_intrares_energy(), core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::energy_methods::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::energy_methods::RNA_PartitionEnergy::exec_cmd(), core::energy_methods::AACompositionEnergy::finalize_after_minimizing(), core::energy_methods::MHCEpitopeEnergy::finalize_after_minimizing(), core::energy_methods::MHCEpitopeEnergy::finalize_total_energy(), core::energy_methods::Abego::finalize_total_energy(), core::energy_methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifEnergy::finalize_total_energy(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), core::energy_methods::MPSpanAngleEnergy::finalize_total_energy(), core::energy_methods::RNA_PartitionEnergy::finalize_total_energy(), core::energy_methods::ProQ_Energy::finalize_total_energy(), core::energy_methods::MHCEpitopeEnergy::full_rescore(), core::energy_methods::IdealParametersDatabase::generate_impropers_map_res(), core::energy_methods::MHCEpitopeEnergy::get_helpers_from_pose(), core::energy_methods::RNA_PartitionEnergy::get_partition_score(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::energy_methods::WaterWeightGridSet::get_sum_water_weight_grid(), core::energy_methods::WaterWeightGridSet::get_water_weight_grid(), core::energy_methods::FaMPEnvEnergy::init(), core::energy_methods::FaMPSolvEnergy::init(), core::energy_methods::IdealParametersDatabase::init(), core::energy_methods::ProQ_Energy::initialize(), load_fastsax_spectrum(), load_form_factors(), core::energy_methods::AARepeatEnergy::load_penalty_table_from_file(), core::energy_methods::IdealParametersDatabase::lookup_angle(), core::energy_methods::IdealParametersDatabase::lookup_length(), core::energy_methods::MHCEpitopeEnergy::MHCEpitopeEnergy(), core::energy_methods::NetChargeEnergy::NetChargeEnergy(), core::energy_methods::MPResidueLipophilicityEnergy::parse_elazar_spline_table(), core::energy_methods::SASAEnergy::prepare_rotamers_for_packing(), core::energy_methods::WaterWeightGridSet::print_water_weight_grid_xz_plane(), core::energy_methods::IdealParametersDatabase::read_angle_database(), core::energy_methods::GoapEnergy::read_angle_definitions(), core::energy_methods::IdealParametersDatabase::read_improper_database(), core::energy_methods::IdealParametersDatabase::read_length_database(), core::energy_methods::GoapEnergy::read_potential_values(), core::energy_methods::ProQ_Energy::read_profiles_and_entropy(), core::energy_methods::IdealParametersDatabase::read_torsion_database(), core::energy_methods::AACompositionEnergy::report(), core::energy_methods::MHCEpitopeEnergy::report(), core::energy_methods::NetChargeEnergy::report(), core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy(), core::energy_methods::RNA_CoarseDistEnergy::score_atom_pair(), core::energy_methods::AACompositionEnergy::set_up_residuearrayannealableenergy_for_packing(), core::energy_methods::MHCEpitopeEnergy::set_up_residuearrayannealableenergy_for_packing(), core::energy_methods::NetChargeEnergy::set_up_residuearrayannealableenergy_for_packing(), core::energy_methods::ExactOccludedHbondSolEnergy::setup_for_derivatives(), core::energy_methods::ElecDensEnergy::setup_for_derivatives(), core::energy_methods::FiberDiffractionEnergy::setup_for_derivatives(), core::energy_methods::ExactOccludedHbondSolEnergy::setup_for_minimizing(), core::energy_methods::AACompositionEnergy::setup_for_minimizing(), core::energy_methods::MHCEpitopeEnergy::setup_for_minimizing(), core::energy_methods::SASAEnergy::setup_for_packing(), core::energy_methods::Abego::setup_for_scoring(), core::energy_methods::CartesianBondedEnergy::setup_for_scoring(), core::energy_methods::DNA_DihedralEnergy::setup_for_scoring(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensAtomwiseEnergy::setup_for_scoring(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensEnergy::setup_for_scoring(), core::energy_methods::FastDensEnergy::setup_for_scoring(), core::energy_methods::GoapEnergy::setup_for_scoring(), core::energy_methods::ImplicitMembraneElecEnergy::setup_for_scoring(), core::energy_methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), core::energy_methods::FiberDiffractionEnergy::setup_for_scoring(), core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring(), core::energy_methods::GenericBondedEnergy::setup_for_scoring(), core::energy_methods::MHCEpitopeEnergy::setup_symmetry(), core::energy_methods::DumpTrajectoryEnergy::start_new_activity(), core::energy_methods::IdealParametersDatabase::symmetrize_tables(), core::energy_methods::UnfoldedStateEnergy::UnfoldedStateEnergy(), core::energy_methods::MHCEpitopeEnergy::update_score(), and core::energy_methods::WaterWeightGridSet::WaterWeightGridSet().

TR() [2/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AARepeatEnergy"  )

static

TR() [3/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AromaticBackboneRestraintEnergy"  )

static

TR() [4/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AspartimidePenaltyEnergy"  )

static

tr() [1/6]

static basic::Tracer core::energy_methods::tr ( "core.energy_methods.BranchEnergy"  )

static

Referenced by core::energy_methods::OccludedHbondSolEnergy_onebody::atomic_interaction_cutoff(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar(), core::energy_methods::OccludedHbondSolEnergy::eval_intrares_energy(), core::energy_methods::DistanceChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearChainbreakEnergy::finalize_total_energy(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::OccludedHbondSolEnergy(), core::energy_methods::OccludedHbondSolEnergy_onebody::OccludedHbondSolEnergy_onebody(), core::energy_methods::OccludedHbondSolEnergy::residue_pair_energy(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::setup_for_derivatives(), core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), core::energy_methods::OccludedHbondSolEnergy_onebody::setup_for_minimizing(), and core::energy_methods::CustomAtomPairEnergy::setup_for_scoring().

TR() [5/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CartesianBondedEnergy"  )

static

tr() [2/6]

static basic::Tracer core::energy_methods::tr ( "core.energy_methods.CCS_IMMSEnergy"  )

static

TR() [6/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CenHBEnergy"  )

static

TR() [7/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CenPairMotifDegreeEnergy"  )

static

TR() [8/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CenPairMotifEnergy"  )

static

TR() [9/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CentroidDisulfideEnergy"  )

static

tr() [3/6]

static basic::Tracer core::energy_methods::tr ( "core.energy_methods.ChainbreakEnergy"  )

static

tr() [4/6]

static basic::Tracer core::energy_methods::tr ( "core.energy_methods.CustomAtomPairEnergy"  )

static

TR() [10/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.D2H_SA_Energy"  )

static

TR() [11/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DEEREnergy"  )

static

Tracer used for error messages.

Global to avoid re-instantiating tracer with every new object

TR() [12/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DisulfideMatchingEnergy"  )

static

TR() [13/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DNA_DihedralEnergy"  )

static

TR() [14/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DNA_ReferenceEnergy"  )

static

TR() [15/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DumpTrajectoryEnergy"  )

static

TR() [16/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensAllAtomCenEnergy"  )

static

TR() [17/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensAtomwiseEnergy"  )

static

TR() [18/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensCenEnergy"  )

static

TR() [19/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensEnergy"  )

static

TR() [20/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FastDensEnergy"  )

static

TR() [21/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FastSAXSEnergy"  )

static

TR() [22/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FiberDiffractionEnergy"  )

static

TR() [23/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FiberDiffractionEnergyDens"  )

static

TR() [24/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.GenericBondedEnergy"  )

static

TR() [25/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.GoapEnergy"  )

static

TR() [26/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.HydroxylTorsionEnergy"  )

static

tr() [5/6]

static basic::Tracer core::energy_methods::tr ( "core.energy_methods.LinearBranchEnergy"  )

static

tr() [6/6]

static basic::Tracer core::energy_methods::tr ( "core.energy_methods.LinearChainbreakEnergy"  )

static

TR() [27/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.MHCEpitopeEnergy"  )

static

TR() [28/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.NetChargeEnergy"  )

static

TR() [29/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ProQ_Energy"  )

static

TR() [30/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.RamaPreProEnergy"  )

static

TR() [31/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.SSElementMotifContactEnergy"  )

static

TR() [32/32]

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.XtalMLEnergy"  )

static

trSAXSEnergy()

static basic::Tracer core::energy_methods::trSAXSEnergy ( "core.energy_methods.SAXSEnergy"  )

static

Referenced by core::energy_methods::SAXSEnergy::compute_chi(), core::energy_methods::SAXSEnergy::compute_chi_with_fit(), core::energy_methods::SAXSEnergy::compute_L1(), core::energy_methods::SAXSEnergy::init_ff(), core::energy_methods::SAXSEnergy::read_spectrum(), core::energy_methods::SAXSEnergy::rehash_form_factors(), core::energy_methods::SAXSEnergy::SAXSEnergy(), and core::energy_methods::SAXSEnergy::set_up_q().

vdw_scale_factor()

Real const core::energy_methods::vdw_scale_factor

(

0.

8

)

Referenced by core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), and core::energy_methods::HybridVDW_Energy::residue_pair_energy().

Variable Documentation

ASYMEZ_TABLE_BINS [1/2]

const core::Real core::energy_methods::ASYMEZ_TABLE_BINS = 61

static

Referenced by core::energy_methods::FaMPAsymEzCBEnergy::FaMPAsymEzCBEnergy(), and core::energy_methods::FaMPAsymEzCGEnergy::FaMPAsymEzCGEnergy().

ASYMEZ_TABLE_BINS [2/2]

const core::Real core::energy_methods::ASYMEZ_TABLE_BINS = 61

static

dummy_deriv_vector_

Vector core::energy_methods::dummy_deriv_vector_

end_sig

Distance const core::energy_methods::end_sig = 10.2

Referenced by core::energy_methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::FaMPEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::EnvSmoothEnergy::sigmoidish_neighbor(), core::energy_methods::FaMPEnvSmoothEnergy::sigmoidish_neighbor(), and core::energy_methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor().

end_sig2

DistanceSquared const core::energy_methods::end_sig2 = end_sig*end_sig

Referenced by core::energy_methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::FaMPEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::EnvSmoothEnergy::sigmoidish_neighbor(), core::energy_methods::FaMPEnvSmoothEnergy::sigmoidish_neighbor(), and core::energy_methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor().

geosol_kT

core::Real const core::energy_methods::geosol_kT = { 0.593 }

Referenced by add_to_individual_sol_energies(), compute_exact_geosol(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_grid_constant(), and core::energy_methods::WaterWeightGridSet::fill_water_grid().

K_ANGLE

const Real core::energy_methods::K_ANGLE =80.0

static

Referenced by core::energy_methods::IdealParametersDatabase::IdealParametersDatabase().

K_LENGTH

const Real core::energy_methods::K_LENGTH =300.0

static

Referenced by core::energy_methods::IdealParametersDatabase::IdealParametersDatabase().

K_TORSION

const Real core::energy_methods::K_TORSION =80.0

static

Referenced by core::energy_methods::IdealParametersDatabase::IdealParametersDatabase().

K_TORSION_IMPROPER

const Real core::energy_methods::K_TORSION_IMPROPER =80.0

static

Referenced by core::energy_methods::IdealParametersDatabase::IdealParametersDatabase().

K_TORSION_PROTON

const Real core::energy_methods::K_TORSION_PROTON =10.0

static

Referenced by core::energy_methods::IdealParametersDatabase::IdealParametersDatabase().

LK_MATCHING_INTERCEPT

core::Real const core::energy_methods::LK_MATCHING_INTERCEPT = { 0 }

Referenced by core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), and core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy().

LK_MATCHING_SLOPE

core::Real const core::energy_methods::LK_MATCHING_SLOPE = { 0.4775 }

Referenced by core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), and core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy().

LK_MATCHING_WEIGHT_OLD_EXACT

core::Real const core::energy_methods::LK_MATCHING_WEIGHT_OLD_EXACT = { 0.23968 }

Referenced by compute_exact_geosol().

MAX_AA [1/2]

const core::Real core::energy_methods::MAX_AA = 20

static

Referenced by core::energy_methods::FaMPAsymEzCBEnergy::FaMPAsymEzCBEnergy(), and core::energy_methods::FaMPAsymEzCGEnergy::FaMPAsymEzCGEnergy().

MAX_AA [2/2]

const core::Real core::energy_methods::MAX_AA = 20

static

MAX_Z_POSITION [1/2]

const core::Real core::energy_methods::MAX_Z_POSITION = 30.5

static

Referenced by core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), and core::energy_methods::FaMPAsymEzCGEnergy::residue_energy().

MAX_Z_POSITION [2/2]

const core::Real core::energy_methods::MAX_Z_POSITION = 30.5

static

MIN_OCC_ENERGY

core::Real const core::energy_methods::MIN_OCC_ENERGY = { 0.01 }

offset_12

Real const core::energy_methods::offset_12 = 475.0

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

offset_6

Real const core::energy_methods::offset_6 = 20.0

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

ref_spectrum

core::Real core::energy_methods::ref_spectrum[][21]

Referenced by protocols::abinitio::AbrelaxApplication::check_filters(), protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(), load_fastsax_spectrum(), load_form_factors(), and core::energy_methods::SAXSEnergy::SAXSEnergy().

sixA_offset

Real const core::energy_methods::sixA_offset = 20

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

sixA_slope

Real const core::energy_methods::sixA_slope = 0.15

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

slope_12

Real const core::energy_methods::slope_12 = 0.5

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

slope_6

Real const core::energy_methods::slope_6 = 0.15

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

start_sig

Distance const core::energy_methods::start_sig = 9.8

Referenced by core::energy_methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::FaMPEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::EnvSmoothEnergy::sigmoidish_neighbor(), core::energy_methods::FaMPEnvSmoothEnergy::sigmoidish_neighbor(), and core::energy_methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor().

start_sig2

DistanceSquared const core::energy_methods::start_sig2 = start_sig*start_sig

Referenced by core::energy_methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::FaMPEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::EnvSmoothEnergy::sigmoidish_neighbor(), core::energy_methods::FaMPEnvSmoothEnergy::sigmoidish_neighbor(), and core::energy_methods::MembraneEnvSmoothEnergy::sigmoidish_neighbor().

twelveA_offset

Real const core::energy_methods::twelveA_offset = 220.0

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

twelveA_slope

Real const core::energy_methods::twelveA_slope = 5

Referenced by core::energy_methods::MPHelicalityEnergy::calc_residue_burial(), core::energy_methods::MPResidueLipophilicityEnergy::calc_residue_burial(), and core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv().

Z_BIN_SHIFT [1/2]

const core::Real core::energy_methods::Z_BIN_SHIFT = 31

static

Referenced by core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), and core::energy_methods::FaMPAsymEzCGEnergy::residue_energy().

Z_BIN_SHIFT [2/2]

const core::Real core::energy_methods::Z_BIN_SHIFT = 31

static