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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  CartesianBondedEnergy
 
class  CartesianBondedEnergyCreator
 
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
 
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  DisulfMinData
 
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  ElecDensAtomwiseEnergy
 
class  ElecDensAtomwiseEnergyCreator
 
class  ElecDensCenEnergy
 
class  ElecDensCenEnergyCreator
 
class  ElecDensEnergy
 
class  ElecDensEnergyCreator
 
class  EnvEnergy
 
class  EnvEnergyCreator
 
class  EnvSmoothEnergy
 
class  EnvSmoothEnergyCreator
 
class  ExactOccludedHbondSolEnergy
 
class  ExactOccludedHbondSolEnergyCreator
 
class  FA_ElecEnergyAroAll
 
class  FA_ElecEnergyAroAllCreator
 
class  FA_ElecEnergyAroAro
 
class  FA_ElecEnergyAroAroCreator
 
class  FA_GrpElecEnergy
 
class  FA_GrpElecEnergyCreator
 
class  Fa_MbenvEnergy
 
class  Fa_MbenvEnergyCreator
 
class  Fa_MbsolvEnergy
 
class  Fa_MbsolvEnergyCreator
 
class  FACTSEnergy
 
class  FACTSEnergyCreator
 
class  FAElecContextData
 
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  FullatomDisulfideEnergy
 
class  FullatomDisulfideEnergyCreator
 
class  GaussianOverlapEnergy
 
class  GaussianOverlapEnergyCreator
 
class  GenBornEnergy
 
class  GenBornEnergyCreator
 
class  GenericBondedEnergy
 
class  GenericBondedEnergyCreator
 
class  GoapEnergy
 
class  GoapEnergyCreator
 
class  GoapRsdType
 
class  GridInfo
 
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  IdealParametersDatabase
 
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_hack
 
class  LK_hackCreator
 
class  LK_PolarNonPolarEnergy
 
class  LK_PolarNonPolarEnergyCreator
 
class  LK_SigmoidalFunc
 
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  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  MultipoleElecEnergy
 
class  MultipoleElecEnergyCreator
 
class  MultipoleElecResPairMinData
 
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  PBLifetimeCache
 
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  PoissonBoltzmannEnergy
 
class  PoissonBoltzmannEnergyCreator
 
class  PoseSequence
 
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  ResidueCartBondedParameters
 
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  RG_MinData
 
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  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  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  VdWTinkerEnergy
 
class  VdWTinkerEnergyCreator
 
class  VdWTinkerResPairMinData
 
class  WaterAdductHBondEnergy
 
class  WaterAdductHBondEnergyCreator
 
class  WaterAdductIntraEnergy
 
class  WaterAdductIntraEnergyCreator
 
class  WaterSpecificEnergy
 
class  WaterSpecificEnergyCreator
 
class  WaterWeightGridSet
 
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
< 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
< 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
 
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::shared_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.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::MultipoleElecResidueInforetrieve_nonconst_mp_residue_info (pose::Pose &pose, Size const seqpos)
 
MultipoleElecResPairMinDataretrieve_nonconst_mp_pairdata (core::scoring::ResPairMinimizationData &pairdata)
 
MultipoleElecResPairMinData const & retrieve_mp_pairdata (core::scoring::ResPairMinimizationData const &pairdata)
 
core::scoring::MultipoleElecResidueInforetrieve_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::VdWTinkerResidueInforetrieve_nonconst_vdw_residue_info (pose::Pose &pose, Size const seqpos)
 
VdWTinkerResPairMinDataretrieve_nonconst_vdw_pairdata (core::scoring::ResPairMinimizationData &pairdata)
 
VdWTinkerResPairMinData const & retrieve_vdw_pairdata (core::scoring::ResPairMinimizationData const &pairdata)
 
core::scoring::VdWTinkerResidueInforetrieve_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 }
 
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

typedef utility::pointer::shared_ptr< AACompositionEnergy > core::energy_methods::AACompositionEnergyOP
typedef utility::pointer::shared_ptr< AARepeatEnergy > core::energy_methods::AARepeatEnergyOP
typedef utility::pointer::shared_ptr< Abego const > core::energy_methods::AbegoCOP
typedef utility::pointer::shared_ptr< Abego > core::energy_methods::AbegoOP
typedef utility::pointer::shared_ptr< ArgCationPiEnergy const > core::energy_methods::ArgCationPiEnergyCOP
typedef utility::pointer::shared_ptr< ArgCationPiEnergy > core::energy_methods::ArgCationPiEnergyOP
typedef utility::pointer::shared_ptr< AspartimidePenaltyEnergy const > core::energy_methods::AspartimidePenaltyEnergyCOP
typedef utility::pointer::weak_ptr< CartesianBondedEnergy const > core::energy_methods::CartesianBondedEnergyCAP
typedef utility::pointer::shared_ptr< CartesianBondedEnergy const > core::energy_methods::CartesianBondedEnergyCOP
typedef utility::pointer::shared_ptr< CentroidDisulfideEnergy const > core::energy_methods::CentroidDisulfideEnergyCOP
typedef utility::pointer::shared_ptr< DEEREnergy const > core::energy_methods::DEEREnergyCOP
typedef utility::pointer::shared_ptr< DEEREnergy > core::energy_methods::DEEREnergyOP
typedef utility::pointer::shared_ptr< DisulfideMatchingEnergy const > core::energy_methods::DisulfideMatchingEnergyCOP
using core::energy_methods::DisulfMinDataCOP = typedef utility::pointer::shared_ptr<const DisulfMinData>
using core::energy_methods::DisulfMinDataOP = typedef utility::pointer::shared_ptr<DisulfMinData>
typedef utility::pointer::shared_ptr< DNATorsionEnergy const > core::energy_methods::DNATorsionEnergyCOP
typedef utility::pointer::shared_ptr< DNATorsionEnergy > core::energy_methods::DNATorsionEnergyOP
typedef utility::pointer::shared_ptr< DumpTrajectoryEnergy > core::energy_methods::DumpTrajectoryEnergyOP
typedef utility::pointer::shared_ptr< ElecDensAtomwiseEnergy const > core::energy_methods::ElecDensAtomwiseEnergyCOP
typedef utility::pointer::shared_ptr< FA_GrpElecEnergy const > core::energy_methods::FA_GrpElecEnergyCOP
typedef utility::pointer::shared_ptr< FA_GrpElecEnergy > core::energy_methods::FA_GrpElecEnergyOP
typedef utility::pointer::shared_ptr< Fa_MbenvEnergy > core::energy_methods::Fa_MbenvEnergyOP
typedef utility::pointer::shared_ptr< FAElecContextData const > core::energy_methods::FAElecContextDataCOP
typedef utility::pointer::shared_ptr< FAElecContextData > core::energy_methods::FAElecContextDataOP
typedef utility::pointer::shared_ptr< FaMPEnvEnergy const > core::energy_methods::FaMPEnvEnergyCOP
typedef utility::pointer::shared_ptr< FaMPEnvEnergy > core::energy_methods::FaMPEnvEnergyOP
typedef utility::pointer::shared_ptr< FaMPEnvSmoothEnergy const > core::energy_methods::FaMPEnvSmoothEnergyCOP
typedef utility::pointer::shared_ptr< FaMPEnvSmoothEnergy > core::energy_methods::FaMPEnvSmoothEnergyOP
typedef utility::pointer::shared_ptr< FaMPSolvEnergy const > core::energy_methods::FaMPSolvEnergyCOP
typedef utility::pointer::shared_ptr< FaMPSolvEnergy > core::energy_methods::FaMPSolvEnergyOP
typedef utility::pointer::shared_ptr< FullatomDisulfideEnergy const > core::energy_methods::FullatomDisulfideEnergyCOP
typedef utility::pointer::shared_ptr< GenericBondedEnergy > core::energy_methods::GenericBondedEnergyOP
typedef utility::pointer::shared_ptr< GoapEnergy > core::energy_methods::GoapEnergyOP
typedef utility::pointer::shared_ptr< GoapRsdType const > core::energy_methods::GoapRsdTypeCOP
typedef std::map< std::string, GoapRsdTypeOP > core::energy_methods::GoapRsdTypeMap
typedef utility::pointer::shared_ptr< GoapRsdType > core::energy_methods::GoapRsdTypeOP
typedef utility::pointer::shared_ptr< HBondEnergy const > core::energy_methods::HBondEnergyCAP
typedef utility::pointer::shared_ptr< HBondEnergy const > core::energy_methods::HBondEnergyCOP
typedef utility::pointer::shared_ptr< HBondEnergy > core::energy_methods::HBondEnergyOP
typedef utility::pointer::shared_ptr< IdealParametersDatabase const > core::energy_methods::IdealParametersDatabaseCOP
typedef numeric::xyzMatrix< Real > core::energy_methods::Matrix
typedef utility::pointer::shared_ptr< MgEnergy const > core::energy_methods::MgEnergyCOP
typedef utility::pointer::shared_ptr< MgEnergy > core::energy_methods::MgEnergyOP
typedef utility::pointer::shared_ptr< MHCEpitopeEnergy const > core::energy_methods::MHCEpitopeEnergyCOP
typedef utility::pointer::shared_ptr< MHCEpitopeEnergy > core::energy_methods::MHCEpitopeEnergyOP
typedef utility::pointer::shared_ptr< MotifDockEnergy const> core::energy_methods::MotifDockEnergyCOP
typedef utility::pointer::shared_ptr< MotifDockEnergy > core::energy_methods::MotifDockEnergyOP
typedef utility::pointer::shared_ptr< MPCbetaEnergy const > core::energy_methods::MPCbetaEnergyCOP
typedef utility::pointer::shared_ptr< MPCbetaEnergy > core::energy_methods::MPCbetaEnergyOP
typedef utility::pointer::shared_ptr< MPEnvEnergy const > core::energy_methods::MPEnvEnergyCOP
typedef utility::pointer::shared_ptr< MPEnvEnergy > core::energy_methods::MPEnvEnergyOP
typedef utility::pointer::shared_ptr< MPHelicalityEnergy const > core::energy_methods::MPHelicalityEnergyCOP
typedef utility::pointer::shared_ptr< MPHelicalityEnergy > core::energy_methods::MPHelicalityEnergyOP
typedef utility::pointer::shared_ptr< MPPairEnergy const > core::energy_methods::MPPairEnergyCOP
typedef utility::pointer::shared_ptr< MPPairEnergy > core::energy_methods::MPPairEnergyOP
using core::energy_methods::MultipoleElecResPairMinDataCOP = typedef utility::pointer::shared_ptr<const MultipoleElecResPairMinData>
typedef utility::pointer::shared_ptr< NetChargeEnergy > core::energy_methods::NetChargeEnergyOP
typedef utility::pointer::shared_ptr< OmegaTetherEnergy const > core::energy_methods::OmegaTetherEnergyCOP
typedef utility::pointer::shared_ptr< OmegaTetherEnergy > core::energy_methods::OmegaTetherEnergyOP
typedef utility::pointer::shared_ptr< OtherPoseEnergy const > core::energy_methods::OtherPoseEnergyCOP
typedef utility::pointer::shared_ptr< OtherPoseEnergy > core::energy_methods::OtherPoseEnergyOP
typedef utility::pointer::shared_ptr< P_AA_Energy > core::energy_methods::P_AA_EnergyOP
typedef utility::pointer::shared_ptr< P_AA_pp_Energy > core::energy_methods::P_AA_pp_EnergyOP
typedef utility::pointer::shared_ptr< P_AA_ss_Energy > core::energy_methods::P_AA_ss_EnergyOP
typedef utility::pointer::weak_ptr< PBLifetimeCache > core::energy_methods::PBLifetimeCacheAP
typedef utility::pointer::weak_ptr< PBLifetimeCache const > core::energy_methods::PBLifetimeCacheCAP
typedef utility::pointer::shared_ptr< PBLifetimeCache const > core::energy_methods::PBLifetimeCacheCOP
typedef utility::pointer::shared_ptr< PBLifetimeCache > core::energy_methods::PBLifetimeCacheOP
typedef utility::pointer::shared_ptr< pHEnergy > core::energy_methods::pHEnergyOP
typedef utility::pointer::shared_ptr< PointWaterEnergy const > core::energy_methods::PointWaterEnergyCOP
typedef utility::pointer::shared_ptr< PointWaterEnergy > core::energy_methods::PointWaterEnergyOP
typedef utility::pointer::weak_ptr< PoissonBoltzmannEnergy const > core::energy_methods::PoissonBoltzmannEnergyCAP
typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy const > core::energy_methods::PoissonBoltzmannEnergyCOP
typedef std::shared_ptr< PoseSequence const > core::energy_methods::PoseSequenceCOP
typedef utility::pointer::shared_ptr< ProClosureEnergy const > core::energy_methods::ProClosureEnergyCOP
typedef utility::pointer::shared_ptr< ProClosureEnergy > core::energy_methods::ProClosureEnergyOP
typedef utility::pointer::shared_ptr< RamachandranEnergy2B const > core::energy_methods::RamachandranEnergy2BCOP
typedef utility::pointer::shared_ptr< RamachandranEnergy2B > core::energy_methods::RamachandranEnergy2BOP
typedef utility::pointer::shared_ptr< RamachandranEnergy const > core::energy_methods::RamachandranEnergyCOP
typedef utility::pointer::shared_ptr< RamachandranEnergy > core::energy_methods::RamachandranEnergyOP
typedef utility::pointer::weak_ptr< RamaPreProEnergy > core::energy_methods::RamaPreProEnergyAP
typedef utility::pointer::weak_ptr< RamaPreProEnergy const > core::energy_methods::RamaPreProEnergyCAP
typedef utility::pointer::shared_ptr< RamaPreProEnergy const > core::energy_methods::RamaPreProEnergyCOP
typedef utility::pointer::shared_ptr< RamaPreProEnergy > core::energy_methods::RamaPreProEnergyOP
typedef utility::pointer::shared_ptr< ReferenceEnergy const > core::energy_methods::ReferenceEnergyCOP
typedef utility::pointer::shared_ptr< ReferenceEnergy > core::energy_methods::ReferenceEnergyOP
typedef utility::pointer::shared_ptr< RG_Local_MinData > core::energy_methods::RG_Local_MinDataOP
typedef utility::pointer::shared_ptr< RG_MinData > core::energy_methods::RG_MinDataOP
typedef utility::pointer::shared_ptr< RingClosureEnergy const > core::energy_methods::RingClosureEnergyCOP
typedef utility::pointer::shared_ptr< RingClosureEnergy > core::energy_methods::RingClosureEnergyOP
using core::energy_methods::RNA_CoarseDistEnergyCOP = typedef utility::pointer::shared_ptr< RNA_CoarseDistEnergy const >
using core::energy_methods::RNA_CoarseDistEnergyOP = typedef utility::pointer::shared_ptr< RNA_CoarseDistEnergy >
typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy const > core::energy_methods::RNA_SugarCloseEnergyCOP
typedef utility::pointer::shared_ptr< RNA_SugarCloseEnergy > core::energy_methods::RNA_SugarCloseEnergyOP
typedef utility::pointer::shared_ptr< RNA_TorsionEnergy const > core::energy_methods::RNA_TorsionEnergyCOP
typedef utility::pointer::shared_ptr< RNA_TorsionEnergy > core::energy_methods::RNA_TorsionEnergyOP
typedef utility::pointer::shared_ptr< ScoreCache const > core::energy_methods::ScoreCacheCOP
typedef utility::pointer::shared_ptr< ScoreCache > core::energy_methods::ScoreCacheOP
typedef utility::pointer::shared_ptr< SugarBackboneEnergy const> core::energy_methods::SugarBackboneEnergyCOP
typedef utility::pointer::shared_ptr< SugarBackboneEnergy > core::energy_methods::SugarBackboneEnergyOP
typedef utility::pointer::shared_ptr< UnfoldedStateEnergy > core::energy_methods::UnfoldedStateEnergyOP
using core::energy_methods::VdWTinkerResPairMinDataCOP = typedef utility::pointer::shared_ptr<const VdWTinkerResPairMinData>
using core::energy_methods::VdWTinkerResPairMinDataOP = typedef utility::pointer::shared_ptr<VdWTinkerResPairMinData>
typedef numeric::xyzVector< core::Real > core::energy_methods::Vector
typedef utility::pointer::shared_ptr< WaterSpecificEnergy > core::energy_methods::WaterSpecificEnergyOP
typedef utility::pointer::shared_ptr< YHHPlanarityEnergy > core::energy_methods::YHHPlanarityEnergyOP

Function Documentation

core::Size core::energy_methods::aa2idx ( core::chemical::AA  aa)
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 
)
RNAAtomType core::energy_methods::assign_rna_atom_type ( conformation::Residue const &  rsd,
Size const  i 
)
bool core::energy_methods::atom_is_aro ( conformation::Residue const &  rsd,
Size const  i 
)
bool core::energy_methods::atom_is_aro2 ( conformation::Residue const &  rsd,
Size const  i 
)
Size core::energy_methods::chi2_torsion_atom_index ( conformation::Residue const &  rsd)
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 
)
bool core::energy_methods::count_atom ( int const &  atype)
inline
bool core::energy_methods::count_pair_bs ( Size const  pos1,
Size const  pos2,
BasePartner const &  partner 
)
inline
ExactOccludedHbondSolEnergyOP core::energy_methods::create_ExactSHOEnergy_from_cmdline ( core::scoring::methods::EnergyMethodOptions const &  options)
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().

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 
)
utility::pointer::shared_ptr< numeric::interpolation::spline::Interpolator > core::energy_methods::fit_layer_lines_with_splines ( ObjexxFCL::FArray1D< float >  xvals,
ObjexxFCL::FArray1D< float >  yvals 
)
static basic::Tracer core::energy_methods::GEOMETRIES ( "core.energy_methods.CartesianBondedEnergy.GEOMETRIES"  )
static
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().

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().

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 
)
bool core::energy_methods::is_base_2 ( conformation::Residue const &  rsd,
Size const  i 
)
bool core::energy_methods::is_phosphate_2 ( conformation::Residue const &  rsd,
Size const  i 
)
bool core::energy_methods::is_sugar_2 ( conformation::Residue const &  rsd,
Size const  i 
)
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 
)
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 
)
Real core::energy_methods::point_line_distance ( numeric::xyzVector< Real > const &  point,
numeric::xyzVector< Real > const &  line_base,
numeric::xyzVector< Real > const &  line_ray 
)
bool core::energy_methods::polymeric_termini_incomplete ( conformation::Residue  res)
inline
BasePartner const & core::energy_methods::retrieve_base_partner_from_pose_inline ( pose::Pose const &  pose)
inline
MultipoleElecResPairMinData const& core::energy_methods::retrieve_mp_pairdata ( core::scoring::ResPairMinimizationData const &  pairdata)
inline
core::scoring::MultipoleElecResidueInfo const& core::energy_methods::retrieve_mp_resdata ( core::scoring::ResSingleMinimizationData const &  resdata)
inline
core::scoring::MultipoleElecResidueInfoCOP core::energy_methods::retrieve_mp_resdata_ptr ( core::scoring::ResSingleMinimizationData const &  resdata)
inline
core::scoring::MultipoleElecResidueInfo const& core::energy_methods::retrieve_mp_residue_info ( pose::Pose const &  pose,
Size const  seqpos 
)
inline
MultipoleElecResPairMinData& core::energy_methods::retrieve_nonconst_mp_pairdata ( core::scoring::ResPairMinimizationData pairdata)
inline
core::scoring::MultipoleElecResidueInfo& core::energy_methods::retrieve_nonconst_mp_resdata ( core::scoring::ResSingleMinimizationData resdata)
inline
core::scoring::MultipoleElecResidueInfo& core::energy_methods::retrieve_nonconst_mp_residue_info ( pose::Pose pose,
Size const  seqpos 
)
inline
VdWTinkerResPairMinData& core::energy_methods::retrieve_nonconst_vdw_pairdata ( core::scoring::ResPairMinimizationData pairdata)
inline
core::scoring::VdWTinkerResidueInfo& core::energy_methods::retrieve_nonconst_vdw_resdata ( core::scoring::ResSingleMinimizationData resdata)
inline
core::scoring::VdWTinkerResidueInfo& core::energy_methods::retrieve_nonconst_vdw_residue_info ( pose::Pose pose,
Size const  seqpos 
)
inline
VdWTinkerResPairMinData const& core::energy_methods::retrieve_vdw_pairdata ( core::scoring::ResPairMinimizationData const &  pairdata)
inline
core::scoring::VdWTinkerResidueInfo const& core::energy_methods::retrieve_vdw_resdata ( core::scoring::ResSingleMinimizationData const &  resdata)
inline
core::scoring::VdWTinkerResidueInfoCOP core::energy_methods::retrieve_vdw_resdata_ptr ( core::scoring::ResSingleMinimizationData const &  resdata)
inline
core::scoring::VdWTinkerResidueInfo const& core::energy_methods::retrieve_vdw_residue_info ( pose::Pose const &  pose,
Size const  seqpos 
)
inline
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 
)
core::Real core::energy_methods::SQ ( core::Real  N)
inline
Real core::energy_methods::sqr ( Real  x)
inline
void core::energy_methods::swap_seqpos ( core::Size seqpos1,
core::Size seqpos2 
)
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.HydroxylTorsionEnergy"  )
static
static basic::Tracer core::energy_methods::tr ( "core.energy_methods.BranchEnergy"  )
static
static basic::Tracer core::energy_methods::tr ( "core.energy_methods.ChainbreakEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DumpTrajectoryEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CenHBEnergy"  )
static
static basic::Tracer core::energy_methods::tr ( "core.energy_methods.LinearBranchEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DNA_ReferenceEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AromaticBackboneRestraintEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensAtomwiseEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AARepeatEnergy"  )
static
static basic::Tracer core::energy_methods::tr ( "core.energy_methods.LinearChainbreakEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.D2H_SA_Energy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CenPairMotifEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.GenericBondedEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CenPairMotifDegreeEnergy"  )
static
static basic::Tracer core::energy_methods::tr ( "core.energy_methods.CustomAtomPairEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.GoapEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.NetChargeEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AACompositionEnergy"  )
static

Referenced by add_to_individual_sol_energies(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::energy_methods::CenHBEnergy::CenHBEnergy(), 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::MHCEpitopeEnergy::finalize_after_minimizing(), 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::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::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::NetChargeEnergy::report(), core::energy_methods::MHCEpitopeEnergy::report(), core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy(), core::energy_methods::RNA_CoarseDistEnergy::score_atom_pair(), core::energy_methods::NetChargeEnergy::set_up_residuearrayannealableenergy_for_packing(), core::energy_methods::MHCEpitopeEnergy::set_up_residuearrayannealableenergy_for_packing(), core::energy_methods::FiberDiffractionEnergy::setup_for_derivatives(), core::energy_methods::ElecDensEnergy::setup_for_derivatives(), core::energy_methods::ExactOccludedHbondSolEnergy::setup_for_derivatives(), core::energy_methods::DEEREnergy::setup_for_derivatives(), core::energy_methods::MHCEpitopeEnergy::setup_for_minimizing(), core::energy_methods::ExactOccludedHbondSolEnergy::setup_for_minimizing(), core::energy_methods::SASAEnergy::setup_for_packing(), core::energy_methods::DNA_DihedralEnergy::setup_for_scoring(), core::energy_methods::Abego::setup_for_scoring(), core::energy_methods::GenericBondedEnergy::setup_for_scoring(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), core::energy_methods::FiberDiffractionEnergy::setup_for_scoring(), core::energy_methods::ElecDensEnergy::setup_for_scoring(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::FastDensEnergy::setup_for_scoring(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring(), core::energy_methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::energy_methods::GoapEnergy::setup_for_scoring(), core::energy_methods::ElecDensAtomwiseEnergy::setup_for_scoring(), core::energy_methods::CartesianBondedEnergy::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().

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.SSElementMotifContactEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FastDensEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FastSAXSEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DisulfideMatchingEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.MHCEpitopeEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.DNA_DihedralEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ProQ_Energy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CentroidDisulfideEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.XtalMLEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FiberDiffractionEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.AspartimidePenaltyEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.RamaPreProEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensAllAtomCenEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensCenEnergy"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.FiberDiffractionEnergyDens"  )
static
static basic::Tracer core::energy_methods::TR ( "core.energy_methods.ElecDensEnergy"  )
static
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

static basic::Tracer core::energy_methods::TR ( "core.energy_methods.CartesianBondedEnergy"  )
static
static basic::Tracer core::energy_methods::trSAXSEnergy ( "core.energy_methods.SAXSEnergy"  )
static
Real const core::energy_methods::vdw_scale_factor ( 0.  8)

Variable Documentation

Vector core::energy_methods::dummy_deriv_vector_
Distance const core::energy_methods::end_sig = 10.2
DistanceSquared const core::energy_methods::end_sig2 = end_sig*end_sig
core::Real const core::energy_methods::geosol_kT = { 0.593 }
const Real core::energy_methods::K_ANGLE =80.0
static
const Real core::energy_methods::K_LENGTH =300.0
static
const Real core::energy_methods::K_TORSION =80.0
static
const Real core::energy_methods::K_TORSION_IMPROPER =80.0
static
const Real core::energy_methods::K_TORSION_PROTON =10.0
static
core::Real const core::energy_methods::LK_MATCHING_INTERCEPT = { 0 }
core::Real const core::energy_methods::LK_MATCHING_SLOPE = { 0.4775 }
core::Real const core::energy_methods::LK_MATCHING_WEIGHT_OLD_EXACT = { 0.23968 }

Referenced by compute_exact_geosol().

core::Real const core::energy_methods::MIN_OCC_ENERGY = { 0.01 }
Real const core::energy_methods::offset_12 = 475.0
Real const core::energy_methods::offset_6 = 20.0
core::Real core::energy_methods::ref_spectrum[][21]
Real const core::energy_methods::sixA_offset = 20
Real const core::energy_methods::sixA_slope = 0.15
Real const core::energy_methods::slope_12 = 0.5
Real const core::energy_methods::slope_6 = 0.15
Distance const core::energy_methods::start_sig = 9.8
DistanceSquared const core::energy_methods::start_sig2 = start_sig*start_sig
Real const core::energy_methods::twelveA_offset = 220.0
Real const core::energy_methods::twelveA_slope = 5