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core::scoring::methods Namespace Reference

Namespaces

 carbohydrates
 
 dfire
 

Classes

class  Abego
 
class  AbegoEnergyCreator
 
class  ArgCationPiEnergy
 
class  ArgCationPiEnergyCreator
 
class  AromaticBackboneRestraintEnergy
 
class  AromaticBackboneRestraintEnergyCreator
 
class  AspartimidePenaltyEnergy
 
class  AspartimidePenaltyEnergyCreator
 
class  BBDepCartBondedParameters
 
class  BBIndepCartBondedParameters
 
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  CartBondedParameters
 
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  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  ContextDependentLRTwoBodyEnergy
 
class  ContextDependentOneBodyEnergy
 
class  ContextDependentTwoBodyEnergy
 
class  ContextIndependentLRTwoBodyEnergy
 
class  ContextIndependentOneBodyEnergy
 
class  ContextIndependentTwoBodyEnergy
 
class  CovalentLabelingEnergy
 
class  CovalentLabelingEnergyCreator
 
class  CovalentLabelingFAEnergy
 
class  CovalentLabelingFAEnergyCreator
 
class  CustomAtomPairEnergy
 
class  CustomAtomPairEnergyCreator
 
class  D2H_SA_Energy
 
class  D2H_SA_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  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  EnergyMethod
 base class for the energy method hierarchy More...
 
class  EnergyMethodCreator
 The EnergyMethodCreator class's responsibilities are to create on demand a new EnergyMethod class, and to tell the ScoringManager singleton which ScoreTypes the EnergyMethod it creates is responsible for. The EnergyMethodCreator must register itself with the ScoringManager at load time (before main() begins) so that the ScoringManager is ready to start creating EnergyMethods by the time the first ScoreFunction requests one. More...
 
class  EnergyMethodOptions
 
class  EnergyMethodRegistrator
 This templated class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  EnvEnergy
 
class  EnvEnergyCreator
 
class  EnvSmoothEnergy
 
class  EnvSmoothEnergyCreator
 
class  Fa_MbenvEnergy
 
class  Fa_MbenvEnergyCreator
 
class  Fa_MbsolvEnergy
 
class  Fa_MbsolvEnergyCreator
 
class  FACTSEnergy
 
class  FACTSEnergyCreator
 
class  FreeDOF_Energy
 
class  FreeDOF_EnergyCreator
 
class  FreeDOF_Options
 
class  GaussianOverlapEnergy
 
class  GaussianOverlapEnergyCreator
 
class  GenBornEnergy
 
class  GenBornEnergyCreator
 
class  GenericBondedEnergy
 
class  GenericBondedEnergyCreator
 
class  GoapEnergy
 
class  GoapEnergyCreator
 
class  GoapRsdType
 
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  LongRangeTwoBodyEnergy
 
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  MissingEnergy
 
class  MissingEnergyCreator
 
class  MMBondAngleEnergy
 
class  MMBondAngleEnergyCreator
 
class  MMBondLengthEnergy
 
class  MMBondLengthEnergyCreator
 
class  MMLJEnergyInter
 
class  MMLJEnergyInterCreator
 
class  MMLJEnergyIntra
 
class  MMLJEnergyIntraCreator
 
class  MMTorsionEnergy
 
class  MMTorsionEnergyCreator
 
class  MotifDockEnergy
 
class  MotifDockEnergyCreator
 
class  MultipoleElecEnergy
 
class  MultipoleElecEnergyCreator
 
class  MultipoleElecResPairMinData
 
class  NeighborListData
 
class  NMerPSSMEnergy
 
class  NMerPSSMEnergyCreator
 
class  NMerRefEnergy
 
class  NMerRefEnergyCreator
 
class  NMerSVMEnergy
 
class  NMerSVMEnergyCreator
 
class  OmegaTetherEnergy
 
class  OmegaTetherEnergyCreator
 
class  OneBodyEnergy
 
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  ProClosureEnergy
 
class  ProClosureEnergyCreator
 
class  ProQ_Energy
 
class  ProQ_EnergyCreator
 
class  PyEnergyMethodRegistrator
 This class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
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
 
struct  ResidueAtomOverlaps
 
class  ResidueCartBondedParameters
 
class  RG_Energy_Fast
 
class  RG_Energy_FastCreator
 
class  RG_Local_MinData
 
class  RG_LocalEnergy
 
class  RG_LocalEnergyCreator
 
class  RG_MinData
 
class  RingClosureEnergy
 
class  RingClosureEnergyCreator
 
class  RMS_Energy
 
class  RMS_EnergyCreator
 
class  SA_Energy
 
class  SA_EnergyCreator
 
class  SASAEnergy
 
class  SASAEnergyCreator
 
class  SecondaryStructureEnergy
 
class  SecondaryStructureEnergyCreator
 
class  SequenceDependentRefEnergy
 
class  SequenceDependentRefEnergyCreator
 
class  ShortRangeTwoBodyEnergy
 
class  SmoothCenPairEnergy
 
class  SmoothCenPairEnergyCreator
 
class  SmoothEnvEnergy
 
class  SmoothEnvEnergyCreator
 
class  SplitUnfoldedTwoBodyEnergy
 
class  SplitUnfoldedTwoBodyEnergyCreator
 
class  SSElementMotifContactEnergy
 
class  SSElementMotifContactEnergyCreator
 
class  SuckerEnergy
 
class  SuckerEnergyCreator
 
class  SymmetricLigandEnergy
 
class  SymmetricLigandEnergyCreator
 
class  TwoBodyEnergy
 
class  UnfoldedStateEnergy
 
class  UnfoldedStateEnergyCreator
 
class  VdWTinkerEnergy
 
class  VdWTinkerEnergyCreator
 
class  VdWTinkerResPairMinData
 
class  WaterAdductHBondEnergy
 
class  WaterAdductHBondEnergyCreator
 
class  WaterAdductIntraEnergy
 
class  WaterAdductIntraEnergyCreator
 
class  WaterSpecificEnergy
 
class  WaterSpecificEnergyCreator
 
class  WholeStructureEnergy
 Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...
 
class  YHHPlanarityEnergy
 
class  YHHPlanarityEnergyCreator
 

Typedefs

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,
CartBondedParametersCOP > > 
torsionparam_vector
 
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
< Fa_MbenvEnergy
Fa_MbenvEnergyOP
 
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
< MotifDockEnergy
MotifDockEnergyOP
 
typedef
utility::pointer::shared_ptr
< MotifDockEnergy const > 
MotifDockEnergyCOP
 
using MultipoleElecResPairMinDataOP = utility::pointer::shared_ptr< MultipoleElecResPairMinData >
 
using MultipoleElecResPairMinDataCOP = utility::pointer::shared_ptr< const MultipoleElecResPairMinData >
 
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
< SequenceDependentRefEnergy
SequenceDependentRefEnergyOP
 
typedef
utility::pointer::shared_ptr
< SequenceDependentRefEnergy
const > 
SequenceDependentRefEnergyCOP
 
typedef
utility::pointer::shared_ptr
< SplitUnfoldedTwoBodyEnergy
SplitUnfoldedTwoBodyEnergyOP
 
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
 
typedef
utility::pointer::weak_ptr
< CartBondedParameters
CartBondedParametersAP
 
typedef
utility::pointer::weak_ptr
< CartBondedParameters const > 
CartBondedParametersCAP
 
typedef
utility::pointer::shared_ptr
< CartBondedParameters
CartBondedParametersOP
 
typedef
utility::pointer::shared_ptr
< CartBondedParameters const > 
CartBondedParametersCOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentLRTwoBodyEnergy
ContextDependentLRTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentLRTwoBodyEnergy
const > 
ContextDependentLRTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentOneBodyEnergy
ContextDependentOneBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentTwoBodyEnergy
ContextDependentTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentTwoBodyEnergy
const > 
ContextDependentTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentLRTwoBodyEnergy
ContextIndependentLRTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentLRTwoBodyEnergy
const > 
ContextIndependentLRTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentOneBodyEnergy
ContextIndependentOneBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentOneBodyEnergy
const > 
ContextIndependentOneBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentTwoBodyEnergy
ContextIndependentTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentTwoBodyEnergy
const > 
ContextIndependentTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethod
EnergyMethodOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethod const > 
EnergyMethodCOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodCreator
EnergyMethodCreatorOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodCreator const > 
EnergyMethodCreatorCOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodOptions
EnergyMethodOptionsOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodOptions const > 
EnergyMethodOptionsCOP
 
typedef
utility::pointer::shared_ptr
< FreeDOF_Options
FreeDOF_OptionsOP
 
typedef
utility::pointer::shared_ptr
< FreeDOF_Options const > 
FreeDOF_OptionsCOP
 
typedef
utility::pointer::shared_ptr
< LongRangeTwoBodyEnergy
LongRangeTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< LongRangeTwoBodyEnergy const > 
LongRangeTwoBodyEnergyCOP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleEnergy
MMBondAngleEnergyAP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleEnergy const > 
MMBondAngleEnergyCAP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleEnergy
MMBondAngleEnergyOP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleEnergy const > 
MMBondAngleEnergyCOP
 
typedef
utility::pointer::weak_ptr
< MMBondLengthEnergy
MMBondLengthEnergyAP
 
typedef
utility::pointer::weak_ptr
< MMBondLengthEnergy const > 
MMBondLengthEnergyCAP
 
typedef
utility::pointer::shared_ptr
< MMBondLengthEnergy
MMBondLengthEnergyOP
 
typedef
utility::pointer::shared_ptr
< MMBondLengthEnergy const > 
MMBondLengthEnergyCOP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyInter
MMLJEnergyInterAP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyInter const > 
MMLJEnergyInterCAP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyInter
MMLJEnergyInterOP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyInter const > 
MMLJEnergyInterCOP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyIntra
MMLJEnergyIntraAP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyIntra const > 
MMLJEnergyIntraCAP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyIntra
MMLJEnergyIntraOP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyIntra const > 
MMLJEnergyIntraCOP
 
typedef
utility::pointer::shared_ptr
< NeighborListData
NeighborListDataOP
 
typedef
utility::pointer::shared_ptr
< NeighborListData const > 
NeighborListDataCOP
 
typedef std::pair
< mm::mm_torsion_atom_quad,
core::Real
mm_torsion_atom_quad_angle_pair
 
using mmtaqap_iter = utility::vector1< mm_torsion_atom_quad_angle_pair >::const_iterator
 
typedef
utility::pointer::weak_ptr
< MMTorsionEnergy
MMTorsionEnergyAP
 
typedef
utility::pointer::weak_ptr
< MMTorsionEnergy const > 
MMTorsionEnergyCAP
 
typedef
utility::pointer::shared_ptr
< MMTorsionEnergy
MMTorsionEnergyOP
 
typedef
utility::pointer::shared_ptr
< MMTorsionEnergy const > 
MMTorsionEnergyCOP
 
typedef
utility::pointer::shared_ptr
< OneBodyEnergy
OneBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< OneBodyEnergy const > 
OneBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ShortRangeTwoBodyEnergy
ShortRangeTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ShortRangeTwoBodyEnergy
const > 
ShortRangeTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< TwoBodyEnergy
TwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< TwoBodyEnergy const > 
TwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< WholeStructureEnergy
WholeStructureEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerPSSMEnergy
NMerPSSMEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerPSSMEnergy const > 
NMerPSSMEnergyCOP
 
typedef
utility::pointer::shared_ptr
< NMerRefEnergy
NMerRefEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerRefEnergy const > 
NMerRefEnergyCOP
 
typedef
utility::pointer::shared_ptr
< NMerSVMEnergy
NMerSVMEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerSVMEnergy const > 
NMerSVMEnergyCOP
 

Enumerations

enum  EnergyMethodType {
  ci_2b = 1, cd_2b, ci_lr_2b, cd_lr_2b,
  ci_1b, cd_1b, ws, n_energy_method_types = ws
}
 
enum  EnergyMethods {
  etable_method = 1, dunbrack_method, hbond_method, elec_method,
  lkball_method, mm_lj_energy_inter_method, pair_e_method, reference_e_method,
  vdw_method, ramachandran_method, n_energy_methods = ramachandran_method
}
 
enum  LongRangeEnergyType {
  constraints_lr = 1, gen_born_lr, multipole_elec_lr, vdw_tinker_lr,
  sasa_lr, epr_deer_lr, PB_elec_lr, cart_bonded_lr,
  gen_bonded_lr, rama2b_lr, ramaprepro_lr, aspartimide_penalty_lr,
  rna_suite_lr, tna_suite_lr, rna_stub_coord_lr, DFIRE,
  sym_bonus_lr, elec_dens_energy, elec_dens_fast_energy, elec_dens_cen_energy,
  elec_dens_allatom_cen_energy, elec_dens_atomwise_energy, patterson_corr_energy, fa_disulfide_energy,
  disulfide_matching_energy, centroid_disulfide_energy, n_long_range_types = centroid_disulfide_energy
}
 

Functions

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.scoring.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< DerivVectorPair > &atom_derivs)
 
static basic::Tracer TR ("core.scoring.AspartimidePenaltyEnergy")
 
static basic::Tracer tr ("core.scoring.methods.Branch", basic::t_info)
 
static basic::Tracer TR ("core.scoring.CartesianBondedEnergy")
 
static basic::Tracer GEOMETRIES ("core.scoring.CartesianBondedEnergy.GEOMETRIES")
 
std::string get_restag (core::chemical::ResidueType const &restype)
 helper function More...
 
static basic::Tracer TR ("core.scoring.CenPairMotifDegreeEnergy")
 
static basic::Tracer TR ("core.scoring.CenPairMotifEnergy")
 
static basic::Tracer tr ("core.scoring.methods.Chainbreak", basic::t_info)
 
static basic::Tracer tr ("core.scoring.methods.CustomAtomPairEnergy")
 
void swap_seqpos (core::Size &seqpos1, core::Size &seqpos2)
 
static basic::Tracer TR ("core.scoring.methods.D2H_SA_Energy.cc")
 
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 dna::retrieve_base_partner_from_pose More...
 
static basic::Tracer TR ("core.scoring.methods.DNA_DihedralEnergy")
 
static basic::Tracer TR ("core.scoring.methods.DNA_ReferenceEnergy")
 
Real sqr (Real x)
 
bool count_atom (int const &atype)
 
static basic::Tracer TR ("core.scoring.methods.GenericBondedEnergy")
 
static basic::Tracer TR ("core.scoring.GoapEnergy")
 
Real const vdw_scale_factor (0.8)
 
static basic::Tracer TR ("core.scoring.HydroxylTorsionEnergy")
 
static basic::Tracer tr ("core.scoring.methods.LinearBranch", basic::t_info)
 
static basic::Tracer tr ("core.scoring.methods.LinearChainbreak", basic::t_info)
 
MultipoleElecResidueInfo const & retrieve_mp_residue_info (pose::Pose const &pose, Size const seqpos)
 
MultipoleElecResidueInforetrieve_nonconst_mp_residue_info (pose::Pose &pose, Size const seqpos)
 
MultipoleElecResPairMinDataretrieve_nonconst_mp_pairdata (ResPairMinimizationData &pairdata)
 
MultipoleElecResPairMinData const & retrieve_mp_pairdata (ResPairMinimizationData const &pairdata)
 
MultipoleElecResidueInforetrieve_nonconst_mp_resdata (ResSingleMinimizationData &resdata)
 
MultipoleElecResidueInfo const & retrieve_mp_resdata (ResSingleMinimizationData const &resdata)
 
MultipoleElecResidueInfoCOP retrieve_mp_resdata_ptr (ResSingleMinimizationData const &resdata)
 
static basic::Tracer TR ("core.scoring.methods.ProQ_Energy.cc")
 
static basic::Tracer TR ("core.scoring.RamaPreProEnergy")
 
static basic::Tracer TR ("core.scoring.SSElementMotifContactEnergy")
 
VdWTinkerResidueInfo const & retrieve_vdw_residue_info (pose::Pose const &pose, Size const seqpos)
 
VdWTinkerResidueInforetrieve_nonconst_vdw_residue_info (pose::Pose &pose, Size const seqpos)
 
VdWTinkerResPairMinDataretrieve_nonconst_vdw_pairdata (ResPairMinimizationData &pairdata)
 
VdWTinkerResPairMinData const & retrieve_vdw_pairdata (ResPairMinimizationData const &pairdata)
 
VdWTinkerResidueInforetrieve_nonconst_vdw_resdata (ResSingleMinimizationData &resdata)
 
VdWTinkerResidueInfo const & retrieve_vdw_resdata (ResSingleMinimizationData const &resdata)
 
VdWTinkerResidueInfoCOP retrieve_vdw_resdata_ptr (ResSingleMinimizationData const &resdata)
 
void find_relevant_connections_onersd (pose::Pose const &pose, Size const seqpos, ResidueAtomOverlaps &branch_connection)
 
void find_relevant_connections (pose::Pose const &pose, utility::vector1< ResidueAtomOverlaps > &branch_connections)
 
bool is_lower_cutpoint (core::Size residue, core::pose::Pose const &pose)
 
bool is_upper_cutpoint (core::Size residue, core::pose::Pose const &pose)
 
void find_cutpoint_variants (core::pose::Pose const &pose, core::kinematics::FoldTree const &, utility::vector1< int > &cutpoints)
 
bool lower_upper_connected_across_cutpoint (core::conformation::Residue const &lower_rsd, core::conformation::Residue const &upper_rsd)
 Helper function for looking at residue connections to get lower/upper partners. More...
 
Size get_upper_cutpoint_partner_for_lower (pose::Pose const &pose, Size const lower_res)
 
Size get_lower_cutpoint_partner_for_upper (pose::Pose const &pose, Size const upper_res)
 
core::Size get_upper_cutpoint_partner_for_lower (core::pose::Pose const &pose, core::Size const lower_res)
 Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper. More...
 
core::Size get_lower_cutpoint_partner_for_upper (core::pose::Pose const &pose, core::Size const upper_res)
 Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper. More...
 
bool operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator== More...
 
bool operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator== More...
 
std::ostream & operator<< (std::ostream &out, EnergyMethodOptions const &options)
 
bool operator== (FreeDOF_Options const &a, FreeDOF_Options const &b)
 
std::ostream & operator<< (std::ostream &out, const FreeDOF_Options &options)
 
static basic::Tracer TR ("core.mm.MMBondAngleEnergy")
 
static basic::Tracer TR ("core.mm.MMBondLengthEnergy")
 
static basic::Tracer TR ("core.scoring.methods.MMTorsionEnergy")
 
static basic::Tracer TR ("core.scoring.methods.OneBodyEnergy")
 
static basic::Tracer TR ("core.scoring.methods.TwoBodyEnergy")
 
static basic::Tracer tr ("core.scoring.methods")
 
core::Real get_residue_weight_by_ss (const char ss)
 
bool residues_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::Real const interaction_cutoff)
 
bool atoms_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::id::AtomID const &id1, core::id::AtomID const &id2, core::Real const interaction_cutoff)
 
void determine_lo_and_hi_residues (core::pose::Pose const &pose, core::Size const rsd1, core::Size const rsd2, bool &res1_is_lo, bool &res2_is_lo)
 Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper. More...
 
void create_long_range_energy_container (core::pose::Pose &pose, core::scoring::ScoreType const scoretype, core::scoring::methods::LongRangeEnergyType const lr_type)
 Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary. More...
 

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
 

Typedef Documentation

typedef utility::pointer::shared_ptr< Abego const > core::scoring::methods::AbegoCOP
typedef utility::pointer::shared_ptr< Abego > core::scoring::methods::AbegoOP
typedef utility::pointer::shared_ptr< ArgCationPiEnergy const > core::scoring::methods::ArgCationPiEnergyCOP
typedef utility::pointer::shared_ptr< ArgCationPiEnergy > core::scoring::methods::ArgCationPiEnergyOP
typedef utility::pointer::weak_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCAP
typedef utility::pointer::shared_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCOP
typedef utility::pointer::weak_ptr< CartesianBondedEnergy const > core::scoring::methods::CartesianBondedEnergyCAP
typedef utility::pointer::shared_ptr< CartesianBondedEnergy const > core::scoring::methods::CartesianBondedEnergyCOP
typedef utility::pointer::shared_ptr< DEEREnergy const > core::scoring::methods::DEEREnergyCOP
typedef utility::pointer::shared_ptr< DEEREnergy > core::scoring::methods::DEEREnergyOP
typedef utility::pointer::shared_ptr< EnergyMethod const > core::scoring::methods::EnergyMethodCOP
typedef utility::pointer::shared_ptr< EnergyMethodCreator const > core::scoring::methods::EnergyMethodCreatorCOP
typedef utility::pointer::shared_ptr< EnergyMethodCreator > core::scoring::methods::EnergyMethodCreatorOP
typedef utility::pointer::shared_ptr< EnergyMethod > core::scoring::methods::EnergyMethodOP
typedef utility::pointer::shared_ptr< EnergyMethodOptions const > core::scoring::methods::EnergyMethodOptionsCOP
typedef utility::pointer::shared_ptr< EnergyMethodOptions > core::scoring::methods::EnergyMethodOptionsOP
typedef utility::pointer::shared_ptr< Fa_MbenvEnergy > core::scoring::methods::Fa_MbenvEnergyOP
typedef utility::pointer::shared_ptr< FreeDOF_Options const > core::scoring::methods::FreeDOF_OptionsCOP
typedef utility::pointer::shared_ptr< FreeDOF_Options > core::scoring::methods::FreeDOF_OptionsOP
typedef utility::pointer::shared_ptr< GenericBondedEnergy > core::scoring::methods::GenericBondedEnergyOP
typedef utility::pointer::shared_ptr< GoapEnergy > core::scoring::methods::GoapEnergyOP
typedef utility::pointer::shared_ptr< GoapRsdType const > core::scoring::methods::GoapRsdTypeCOP
typedef std::map< std::string, GoapRsdTypeOP > core::scoring::methods::GoapRsdTypeMap
typedef utility::pointer::shared_ptr< GoapRsdType > core::scoring::methods::GoapRsdTypeOP
typedef utility::pointer::shared_ptr< IdealParametersDatabase const > core::scoring::methods::IdealParametersDatabaseCOP
typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy const > core::scoring::methods::LongRangeTwoBodyEnergyCOP
typedef utility::pointer::weak_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyAP
typedef utility::pointer::weak_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCAP
typedef utility::pointer::shared_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCOP
typedef utility::pointer::shared_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyOP
typedef utility::pointer::weak_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCAP
typedef utility::pointer::shared_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCOP
typedef utility::pointer::shared_ptr< MMBondLengthEnergy > core::scoring::methods::MMBondLengthEnergyOP
typedef utility::pointer::weak_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterAP
typedef utility::pointer::weak_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCAP
typedef utility::pointer::shared_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCOP
typedef utility::pointer::shared_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterOP
typedef utility::pointer::weak_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraAP
typedef utility::pointer::weak_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCAP
typedef utility::pointer::shared_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCOP
typedef utility::pointer::shared_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraOP
using core::scoring::methods::mmtaqap_iter = typedef utility::vector1<mm_torsion_atom_quad_angle_pair>::const_iterator
typedef utility::pointer::weak_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyAP
typedef utility::pointer::weak_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCAP
typedef utility::pointer::shared_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCOP
typedef utility::pointer::shared_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyOP
typedef utility::pointer::shared_ptr< MotifDockEnergy const> core::scoring::methods::MotifDockEnergyCOP
typedef utility::pointer::shared_ptr< MotifDockEnergy > core::scoring::methods::MotifDockEnergyOP
using core::scoring::methods::MultipoleElecResPairMinDataCOP = typedef utility::pointer::shared_ptr<const MultipoleElecResPairMinData>
typedef utility::pointer::shared_ptr< NeighborListData const > core::scoring::methods::NeighborListDataCOP
typedef utility::pointer::shared_ptr< NeighborListData > core::scoring::methods::NeighborListDataOP
typedef utility::pointer::shared_ptr< NMerPSSMEnergy const > core::scoring::methods::NMerPSSMEnergyCOP
typedef utility::pointer::shared_ptr< NMerPSSMEnergy > core::scoring::methods::NMerPSSMEnergyOP
typedef utility::pointer::shared_ptr< NMerRefEnergy const > core::scoring::methods::NMerRefEnergyCOP
typedef utility::pointer::shared_ptr< NMerRefEnergy > core::scoring::methods::NMerRefEnergyOP
typedef utility::pointer::shared_ptr< NMerSVMEnergy const > core::scoring::methods::NMerSVMEnergyCOP
typedef utility::pointer::shared_ptr< NMerSVMEnergy > core::scoring::methods::NMerSVMEnergyOP
typedef utility::pointer::shared_ptr< OmegaTetherEnergy const > core::scoring::methods::OmegaTetherEnergyCOP
typedef utility::pointer::shared_ptr< OmegaTetherEnergy > core::scoring::methods::OmegaTetherEnergyOP
typedef utility::pointer::shared_ptr< OneBodyEnergy const > core::scoring::methods::OneBodyEnergyCOP
typedef utility::pointer::shared_ptr< OneBodyEnergy > core::scoring::methods::OneBodyEnergyOP
typedef utility::pointer::shared_ptr< OtherPoseEnergy const > core::scoring::methods::OtherPoseEnergyCOP
typedef utility::pointer::shared_ptr< OtherPoseEnergy > core::scoring::methods::OtherPoseEnergyOP
typedef utility::pointer::shared_ptr< P_AA_Energy > core::scoring::methods::P_AA_EnergyOP
typedef utility::pointer::shared_ptr< P_AA_pp_Energy > core::scoring::methods::P_AA_pp_EnergyOP
typedef utility::pointer::shared_ptr< P_AA_ss_Energy > core::scoring::methods::P_AA_ss_EnergyOP
typedef utility::pointer::weak_ptr< PBLifetimeCache > core::scoring::methods::PBLifetimeCacheAP
typedef utility::pointer::weak_ptr< PBLifetimeCache const > core::scoring::methods::PBLifetimeCacheCAP
typedef utility::pointer::shared_ptr< PBLifetimeCache const > core::scoring::methods::PBLifetimeCacheCOP
typedef utility::pointer::shared_ptr< PBLifetimeCache > core::scoring::methods::PBLifetimeCacheOP
typedef utility::pointer::shared_ptr< pHEnergy > core::scoring::methods::pHEnergyOP
typedef utility::pointer::shared_ptr< PointWaterEnergy const > core::scoring::methods::PointWaterEnergyCOP
typedef utility::pointer::shared_ptr< PointWaterEnergy > core::scoring::methods::PointWaterEnergyOP
typedef utility::pointer::shared_ptr< PoissonBoltzmannEnergy const > core::scoring::methods::PoissonBoltzmannEnergyCOP
typedef utility::pointer::shared_ptr< ProClosureEnergy const > core::scoring::methods::ProClosureEnergyCOP
typedef utility::pointer::shared_ptr< ProClosureEnergy > core::scoring::methods::ProClosureEnergyOP
typedef utility::pointer::shared_ptr< RamachandranEnergy2B const > core::scoring::methods::RamachandranEnergy2BCOP
typedef utility::pointer::shared_ptr< RamachandranEnergy const > core::scoring::methods::RamachandranEnergyCOP
typedef utility::pointer::shared_ptr< RamachandranEnergy > core::scoring::methods::RamachandranEnergyOP
typedef utility::pointer::weak_ptr< RamaPreProEnergy > core::scoring::methods::RamaPreProEnergyAP
typedef utility::pointer::weak_ptr< RamaPreProEnergy const > core::scoring::methods::RamaPreProEnergyCAP
typedef utility::pointer::shared_ptr< RamaPreProEnergy const > core::scoring::methods::RamaPreProEnergyCOP
typedef utility::pointer::shared_ptr< RamaPreProEnergy > core::scoring::methods::RamaPreProEnergyOP
typedef utility::pointer::shared_ptr< ReferenceEnergy const > core::scoring::methods::ReferenceEnergyCOP
typedef utility::pointer::shared_ptr< ReferenceEnergy > core::scoring::methods::ReferenceEnergyOP
typedef utility::pointer::shared_ptr< RG_Local_MinData > core::scoring::methods::RG_Local_MinDataOP
typedef utility::pointer::shared_ptr< RG_MinData > core::scoring::methods::RG_MinDataOP
typedef utility::pointer::shared_ptr< RingClosureEnergy const > core::scoring::methods::RingClosureEnergyCOP
typedef utility::pointer::shared_ptr< RingClosureEnergy > core::scoring::methods::RingClosureEnergyOP
typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy const > core::scoring::methods::ShortRangeTwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< TwoBodyEnergy const > core::scoring::methods::TwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< TwoBodyEnergy > core::scoring::methods::TwoBodyEnergyOP
typedef utility::pointer::shared_ptr< UnfoldedStateEnergy > core::scoring::methods::UnfoldedStateEnergyOP
using core::scoring::methods::VdWTinkerResPairMinDataCOP = typedef utility::pointer::shared_ptr<const VdWTinkerResPairMinData>
using core::scoring::methods::VdWTinkerResPairMinDataOP = typedef utility::pointer::shared_ptr<VdWTinkerResPairMinData>
typedef utility::pointer::shared_ptr< WaterSpecificEnergy > core::scoring::methods::WaterSpecificEnergyOP
typedef utility::pointer::shared_ptr< YHHPlanarityEnergy > core::scoring::methods::YHHPlanarityEnergyOP

Enumeration Type Documentation

Enumerator
etable_method 
dunbrack_method 
hbond_method 
elec_method 
lkball_method 
mm_lj_energy_inter_method 
pair_e_method 
reference_e_method 
vdw_method 
ramachandran_method 
n_energy_methods 
Enumerator
ci_2b 
cd_2b 
ci_lr_2b 
cd_lr_2b 
ci_1b 
cd_1b 
ws 
n_energy_method_types 
Enumerator
constraints_lr 
gen_born_lr 
multipole_elec_lr 
vdw_tinker_lr 
sasa_lr 
epr_deer_lr 
PB_elec_lr 
cart_bonded_lr 
gen_bonded_lr 
rama2b_lr 
ramaprepro_lr 
aspartimide_penalty_lr 
rna_suite_lr 
tna_suite_lr 
rna_stub_coord_lr 
DFIRE 
sym_bonus_lr 
elec_dens_energy 
elec_dens_fast_energy 
elec_dens_cen_energy 
elec_dens_allatom_cen_energy 
elec_dens_atomwise_energy 
patterson_corr_energy 
fa_disulfide_energy 
disulfide_matching_energy 
centroid_disulfide_energy 
n_long_range_types 

Function Documentation

bool core::scoring::methods::atoms_interact ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
core::id::AtomID const &  id1,
core::id::AtomID const &  id2,
core::Real const  interaction_cutoff 
)
bool core::scoring::methods::count_atom ( int const &  atype)
inline
bool core::scoring::methods::count_pair_bs ( Size const  pos1,
Size const  pos2,
BasePartner const &  partner 
)
inline
void core::scoring::methods::create_long_range_energy_container ( core::pose::Pose pose,
core::scoring::ScoreType const  scoretype,
core::scoring::methods::LongRangeEnergyType const  lr_type 
)

Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pose::Pose::energies().

Referenced by core::scoring::methods::RamaPreProEnergy::setup_for_scoring(), and core::scoring::methods::AspartimidePenaltyEnergy::setup_for_scoring().

void core::scoring::methods::determine_lo_and_hi_residues ( core::pose::Pose const &  pose,
core::Size const  rsd1,
core::Size const  rsd2,
bool res1_is_lo,
bool res2_is_lo 
)

Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper.

Inputs are rsd1 and rsd2; outputs are rsd1_is_lo and rsd2_is_lo. Both will be false if the residues aren't connected (s.t. the C of one connected to some connection of the other).

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::conformation::Residue::has_upper_connect(), core::chemical::ResidueConnection::index(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::upper_connect().

Referenced by core::scoring::methods::RamaPreProEnergy::defines_residue_pair_energy(), core::scoring::methods::AspartimidePenaltyEnergy::defines_residue_pair_energy(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), and core::scoring::methods::AspartimidePenaltyEnergy::residue_pair_energy().

std::string const core::scoring::methods::dna_deriv_atom ( " C5 "  )

the atom through which the knowledge based potential applies a force

Referenced by core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative().

void core::scoring::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< DerivVectorPair > &  atom_derivs 
)
void core::scoring::methods::find_cutpoint_variants ( core::pose::Pose const &  pose,
core::kinematics::FoldTree const &  ,
utility::vector1< int > &  cutpoints 
)
void core::scoring::methods::find_relevant_connections ( pose::Pose const &  pose,
utility::vector1< ResidueAtomOverlaps > &  branch_connections 
)
void core::scoring::methods::find_relevant_connections_onersd ( pose::Pose const &  pose,
Size const  seqpos,
ResidueAtomOverlaps &  branch_connection 
)
static basic::Tracer core::scoring::methods::GEOMETRIES ( "core.scoring.CartesianBondedEnergy.GEOMETRIES"  )
static
core::Size core::scoring::methods::get_lower_cutpoint_partner_for_upper ( core::pose::Pose const &  pose,
core::Size const  upper_res 
)

Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper.

Size core::scoring::methods::get_lower_cutpoint_partner_for_upper ( pose::Pose const &  pose,
Size const  upper_res 
)
core::Real core::scoring::methods::get_residue_weight_by_ss ( const char  ss)
std::string core::scoring::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::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_improper(), and core::scoring::methods::IdealParametersDatabase::lookup_length().

core::Size core::scoring::methods::get_upper_cutpoint_partner_for_lower ( core::pose::Pose const &  pose,
core::Size const  lower_res 
)

Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper.

Size core::scoring::methods::get_upper_cutpoint_partner_for_lower ( pose::Pose const &  pose,
Size const  lower_res 
)
bool core::scoring::methods::is_lower_cutpoint ( core::Size  residue,
core::pose::Pose const &  pose 
)
bool core::scoring::methods::is_upper_cutpoint ( core::Size  residue,
core::pose::Pose const &  pose 
)
bool core::scoring::methods::lower_upper_connected_across_cutpoint ( core::conformation::Residue const &  lower_rsd,
core::conformation::Residue const &  upper_rsd 
)
bool core::scoring::methods::operator!= ( EnergyMethodOptions const &  a,
EnergyMethodOptions const &  b 
)
std::ostream& core::scoring::methods::operator<< ( std::ostream &  out,
const FreeDOF_Options &  options 
)
std::ostream & core::scoring::methods::operator<< ( std::ostream &  out,
EnergyMethodOptions const &  options 
)
bool core::scoring::methods::operator== ( FreeDOF_Options const &  a,
FreeDOF_Options const &  b 
)
bool core::scoring::methods::operator== ( EnergyMethodOptions const &  a,
EnergyMethodOptions const &  b 
)

used inside ScoreFunctionInfo::operator==

References core::scoring::methods::EnergyMethodOptions::aa_composition_setup_files_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_assume_const_backbone_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_atomic_depth_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_probe_radius_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_resolution_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_cross_chain_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_energy_threshold_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_natural_corrections1_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_oversat_penalty_, core::scoring::methods::EnergyMethodOptions::arg_cation_pi_his_can_be_pi_, core::scoring::methods::EnergyMethodOptions::aspartimide_penalty_value_, core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name_, core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score_, core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set_, core::scoring::methods::EnergyMethodOptions::cartbonded_ang_, core::scoring::methods::EnergyMethodOptions::cartbonded_improper_, core::scoring::methods::EnergyMethodOptions::cartbonded_len_, core::scoring::methods::EnergyMethodOptions::cartbonded_linear_, core::scoring::methods::EnergyMethodOptions::cartbonded_proton_, core::scoring::methods::EnergyMethodOptions::cartbonded_skip_cutpoints_, core::scoring::methods::EnergyMethodOptions::cartbonded_tors_, core::scoring::methods::EnergyMethodOptions::count_pair_full_, core::scoring::methods::EnergyMethodOptions::count_pair_hybrid_, core::scoring::methods::EnergyMethodOptions::covalent_labeling_fa_input_, core::scoring::methods::EnergyMethodOptions::covalent_labeling_input_, core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep_, core::scoring::methods::EnergyMethodOptions::dump_trajectory_gz_, core::scoring::methods::EnergyMethodOptions::dump_trajectory_prefix_, core::scoring::methods::EnergyMethodOptions::dump_trajectory_stride_, core::scoring::methods::EnergyMethodOptions::elec_die_, core::scoring::methods::EnergyMethodOptions::elec_group_file_, core::scoring::methods::EnergyMethodOptions::elec_max_dis_, core::scoring::methods::EnergyMethodOptions::elec_min_dis_, core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_D0_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_D_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_S_, core::scoring::methods::EnergyMethodOptions::envsmooth_zero_negatives_, core::scoring::methods::EnergyMethodOptions::etable_options_, core::scoring::methods::EnergyMethodOptions::eval_intrares_elec_ST_only_, core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA_, core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein_, core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec_, core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec_, core::scoring::methods::EnergyMethodOptions::exclude_RNA_protein_fa_elec_, core::scoring::methods::EnergyMethodOptions::exclude_RNA_RNA_fa_elec_, core::scoring::methods::EnergyMethodOptions::fastdens_perres_weights_, core::scoring::methods::EnergyMethodOptions::free_dof_options_, core::scoring::methods::EnergyMethodOptions::genbonded_score_full_, core::scoring::methods::EnergyMethodOptions::genbonded_score_hybrid_, core::scoring::methods::EnergyMethodOptions::geom_sol_interres_path_distance_cutoff_, core::scoring::methods::EnergyMethodOptions::geom_sol_intrares_path_distance_cutoff_, core::scoring::methods::EnergyMethodOptions::grp_cpfxn_, core::scoring::methods::EnergyMethodOptions::grpelec_context_dependent_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_hbond_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_param1_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_param2_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_type_, core::scoring::methods::EnergyMethodOptions::hbnet_bonus_ramping_function_, core::scoring::methods::EnergyMethodOptions::hbnet_max_network_size_, core::scoring::methods::EnergyMethodOptions::hbond_options_, core::scoring::methods::EnergyMethodOptions::hrf_dynamics_input_, core::scoring::methods::EnergyMethodOptions::method_weights_, core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_files_, core::scoring::methods::EnergyMethodOptions::netcharge_setup_files_, core::scoring::methods::EnergyMethodOptions::nmer_ref_seq_length_, core::scoring::methods::EnergyMethodOptions::nmer_svm_, core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_, core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_avg_rank_as_energy_, core::scoring::methods::EnergyMethodOptions::nmer_svm_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_list_, core::scoring::methods::EnergyMethodOptions::nmer_svm_list_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_pssm_feat_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_, core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_term_length_, core::scoring::methods::EnergyMethodOptions::ordered_pt_wat_penalty_, core::scoring::methods::EnergyMethodOptions::ordered_wat_penalty_, core::scoring::methods::EnergyMethodOptions::pb_bound_tag_, core::scoring::methods::EnergyMethodOptions::pb_unbound_tag_, core::scoring::methods::EnergyMethodOptions::protein_dielectric_, core::scoring::methods::EnergyMethodOptions::put_intra_into_total_, core::scoring::methods::EnergyMethodOptions::rna_options_, core::scoring::methods::EnergyMethodOptions::smooth_fa_elec_, core::scoring::methods::EnergyMethodOptions::split_unfolded_label_type_, core::scoring::methods::EnergyMethodOptions::split_unfolded_value_type_, core::scoring::methods::EnergyMethodOptions::ss_weights_, core::scoring::methods::EnergyMethodOptions::target_clash_pdb_, core::scoring::methods::EnergyMethodOptions::unfolded_energies_type_, core::scoring::methods::EnergyMethodOptions::use_gen_kirkwood_, core::scoring::methods::EnergyMethodOptions::use_polarization_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_distance_cutoff_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_dotproduct_cutoff_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_containing_cones_cutoff_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_disabled_except_during_packing_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_grid_padding_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_size_, and core::scoring::methods::EnergyMethodOptions::water_dielectric_.

Real core::scoring::methods::point_line_distance ( numeric::xyzVector< Real > const &  point,
numeric::xyzVector< Real > const &  line_base,
numeric::xyzVector< Real > const &  line_ray 
)
bool core::scoring::methods::residues_interact ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
core::Real const  interaction_cutoff 
)
BasePartner const & core::scoring::methods::retrieve_base_partner_from_pose_inline ( pose::Pose const &  pose)
inline
MultipoleElecResPairMinData const& core::scoring::methods::retrieve_mp_pairdata ( ResPairMinimizationData const &  pairdata)
inline
MultipoleElecResidueInfo const& core::scoring::methods::retrieve_mp_resdata ( ResSingleMinimizationData const &  resdata)
inline
MultipoleElecResidueInfoCOP core::scoring::methods::retrieve_mp_resdata_ptr ( ResSingleMinimizationData const &  resdata)
inline
MultipoleElecResidueInfo const& core::scoring::methods::retrieve_mp_residue_info ( pose::Pose const &  pose,
Size const  seqpos 
)
inline
MultipoleElecResPairMinData& core::scoring::methods::retrieve_nonconst_mp_pairdata ( ResPairMinimizationData &  pairdata)
inline
MultipoleElecResidueInfo& core::scoring::methods::retrieve_nonconst_mp_resdata ( ResSingleMinimizationData &  resdata)
inline
MultipoleElecResidueInfo& core::scoring::methods::retrieve_nonconst_mp_residue_info ( pose::Pose pose,
Size const  seqpos 
)
inline
VdWTinkerResPairMinData& core::scoring::methods::retrieve_nonconst_vdw_pairdata ( ResPairMinimizationData &  pairdata)
inline
VdWTinkerResidueInfo& core::scoring::methods::retrieve_nonconst_vdw_resdata ( ResSingleMinimizationData &  resdata)
inline
VdWTinkerResidueInfo& core::scoring::methods::retrieve_nonconst_vdw_residue_info ( pose::Pose pose,
Size const  seqpos 
)
inline
VdWTinkerResPairMinData const& core::scoring::methods::retrieve_vdw_pairdata ( ResPairMinimizationData const &  pairdata)
inline
VdWTinkerResidueInfo const& core::scoring::methods::retrieve_vdw_resdata ( ResSingleMinimizationData const &  resdata)
inline
VdWTinkerResidueInfoCOP core::scoring::methods::retrieve_vdw_resdata_ptr ( ResSingleMinimizationData const &  resdata)
inline
VdWTinkerResidueInfo const& core::scoring::methods::retrieve_vdw_residue_info ( pose::Pose const &  pose,
Size const  seqpos 
)
inline
Real core::scoring::methods::sqr ( Real  x)
inline
void core::scoring::methods::swap_seqpos ( core::Size seqpos1,
core::Size seqpos2 
)
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.OneBodyEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.HydroxylTorsionEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.TwoBodyEnergy"  )
static
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods.Branch"  ,
basic::t_info   
)
static
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods.Chainbreak"  ,
basic::t_info   
)
static
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods"  )
static
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods.LinearBranch"  ,
basic::t_info   
)
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.DNA_ReferenceEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.AromaticBackboneRestraintEnergy"  )
static

Referenced by core::scoring::methods::D2H_SA_Energy::D2H_SA_Energy(), core::scoring::methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::methods::TwoBodyEnergy::eval_intrares_energy_ext(), core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::methods::Abego::finalize_total_energy(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::methods::ProQ_Energy::finalize_total_energy(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::methods::IdealParametersDatabase::init(), core::scoring::methods::ProQ_Energy::initialize(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_length(), core::scoring::methods::SASAEnergy::prepare_rotamers_for_packing(), core::scoring::methods::IdealParametersDatabase::read_angle_database(), core::scoring::methods::GoapEnergy::read_angle_definitions(), core::scoring::methods::IdealParametersDatabase::read_improper_database(), core::scoring::methods::IdealParametersDatabase::read_length_database(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssms_from_options(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svms_from_options(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), core::scoring::methods::NMerRefEnergy::read_nmer_table_list(), core::scoring::methods::NMerRefEnergy::read_nmer_tables_from_options(), core::scoring::methods::GoapEnergy::read_potential_values(), core::scoring::methods::ProQ_Energy::read_profiles_and_entropy(), core::scoring::methods::IdealParametersDatabase::read_torsion_database(), core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::TwoBodyEnergy::residue_pair_energy_ext(), core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(), core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(), core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue_pair(), core::scoring::methods::SASAEnergy::setup_for_packing(), core::scoring::methods::Abego::setup_for_scoring(), core::scoring::methods::GenericBondedEnergy::setup_for_scoring(), core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue(), core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue_pair(), core::scoring::methods::IdealParametersDatabase::symmetrize_tables(), and core::scoring::methods::UnfoldedStateEnergy::UnfoldedStateEnergy().

static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.D2H_SA_Energy.cc"  )
static
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods.LinearChainbreak"  ,
basic::t_info   
)
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.CenPairMotifDegreeEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.CenPairMotifEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.GenericBondedEnergy"  )
static
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods.CustomAtomPairEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.GoapEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.DNA_DihedralEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.SSElementMotifContactEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.MMTorsionEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondLengthEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.ProQ_Energy.cc"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondAngleEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.AspartimidePenaltyEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.RamaPreProEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.CartesianBondedEnergy"  )
static
Real const core::scoring::methods::vdw_scale_factor ( 0.  8)

Variable Documentation

Distance const core::scoring::methods::end_sig = 10.2
DistanceSquared const core::scoring::methods::end_sig2 = end_sig*end_sig
const Real core::scoring::methods::K_ANGLE =80.0
static
const Real core::scoring::methods::K_LENGTH =300.0
static
const Real core::scoring::methods::K_TORSION =80.0
static
const Real core::scoring::methods::K_TORSION_IMPROPER =80.0
static
const Real core::scoring::methods::K_TORSION_PROTON =10.0
static
Distance const core::scoring::methods::start_sig = 9.8
DistanceSquared const core::scoring::methods::start_sig2 = start_sig*start_sig