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methods Directory Reference
Directory dependency graph for methods:
src/core/scoring/methods

Directories

directory  dfire
 

Files

file  BurialEnergy.cc
 
file  BurialEnergy.hh
 energy term use for scoring predicted burial
 
file  BurialEnergyCreator.hh
 Declaration for the class that connects BurialEnergy with the ScoringManager.
 
file  CartBondedParameters.hh
 
file  CartesianBondedEnergy.cc
 Harmonic bondangle/bondlength/torsion constraints.
 
file  CartesianBondedEnergy.fwd.hh
 
file  CartesianBondedEnergy.hh
 
file  CartesianBondedEnergyCreator.hh
 Declaration for the class that connects CartesianBondedEnergy with the ScoringManager.
 
file  CenHBEnergy.cc
 Smooth, differentiable version of centroid hbond term.
 
file  CenHBEnergy.fwd.hh
 
file  CenHBEnergy.hh
 Smooth, differentiable version of centroid hbond term.
 
file  CenHBEnergyCreator.hh
 Declaration for the class that connects CenHBEnergy with the ScoringManager.
 
file  CenPairEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  CenPairEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  CenPairEnergyCreator.hh
 
file  chainbreak_util.cc
 Utility functions for scoring chainbreaks.
 
file  chainbreak_util.hh
 Utility functions for scoring chainbreaks.
 
file  ChainbreakEnergy.cc
 
file  ChainbreakEnergy.fwd.hh
 
file  ChainbreakEnergy.hh
 
file  ChainbreakEnergyCreator.hh
 Declaration for the class that connects ChainbreakEnergy with the ScoringManager.
 
file  ChemicalShiftAnisotropyEnergy.cc
 CSA energy - Orientation dependent chemical shift.
 
file  ChemicalShiftAnisotropyEnergy.fwd.hh
 
file  ChemicalShiftAnisotropyEnergy.hh
 CSP energy.
 
file  ChemicalShiftAnisotropyEnergyCreator.hh
 Declaration for the class that connects ChemicalShiftAnisotropyEnergy with the ScoringManager.
 
file  ContactOrderEnergy.cc
 calculates the contact order of a given conformation average sequence.
 
file  ContactOrderEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  ContactOrderEnergyCreator.hh
 Declaration for the class that connects ContactOrderEnergy with the ScoringManager.
 
file  ContextDependentLRTwoBodyEnergy.cc
 Context-Dependent, Long-Range, Two-Body Energy class implementation.
 
file  ContextDependentLRTwoBodyEnergy.fwd.hh
 Context-Dependent, Long-Range, Two-Body Energy Method class forward declaration.
 
file  ContextDependentLRTwoBodyEnergy.hh
 
file  ContextDependentOneBodyEnergy.cc
 
file  ContextDependentOneBodyEnergy.fwd.hh
 
file  ContextDependentOneBodyEnergy.hh
 
file  ContextDependentTwoBodyEnergy.cc
 Score function class.
 
file  ContextDependentTwoBodyEnergy.fwd.hh
 Forward declaration for the Context-Dependent (ShortRange) Two-Body EnergyMethod base class.
 
file  ContextDependentTwoBodyEnergy.hh
 
file  ContextIndependentLRTwoBodyEnergy.cc
 Context-Independent, Long-Range, Two-Body Energy class implementation.
 
file  ContextIndependentLRTwoBodyEnergy.fwd.hh
 Context-Independent, Long-Range, Two-Body Energy Method class forward declaration.
 
file  ContextIndependentLRTwoBodyEnergy.hh
 Context-Dependent, Long-Range, Two-Body Energy class declaration.
 
file  ContextIndependentOneBodyEnergy.cc
 
file  ContextIndependentOneBodyEnergy.fwd.hh
 
file  ContextIndependentOneBodyEnergy.hh
 
file  ContextIndependentTwoBodyEnergy.cc
 
file  ContextIndependentTwoBodyEnergy.fwd.hh
 
file  ContextIndependentTwoBodyEnergy.hh
 Short ranged, context-independent, two-body energy class declaration.
 
file  CSD_TorsionEnergy.cc
 
file  CSD_TorsionEnergy.fwd.hh
 
file  CSD_TorsionEnergy.hh
 
file  CustomAtomPairEnergy.cc
 Simple EnergyMethod for calculating residue-residue constraints under some interaction cutoff.
 
file  CustomAtomPairEnergy.fwd.hh
 Statistically derived rotamer pair potential class forward declaration.
 
file  CustomAtomPairEnergy.hh
 
file  CustomAtomPairEnergyCreator.hh
 Declaration for the class that connects CustomAtomPairEnergy with the ScoringManager.
 
file  DipolarCouplingEnergy.cc
 DC energy - Orientation dependent chemical shift.
 
file  DipolarCouplingEnergy.fwd.hh
 
file  DipolarCouplingEnergy.hh
 CSP energy.
 
file  DipolarCouplingEnergyCreator.hh
 Declaration for the class that connects DipolarCouplingEnergy with the ScoringManager.
 
file  DirectReadoutEnergy.cc
 Statistically derived DNA contact potential class implementation.
 
file  DirectReadoutEnergy.fwd.hh
 
file  DirectReadoutEnergy.hh
 Statistically derived DNA contact potential class declaration.
 
file  DirectReadoutEnergyCreator.hh
 Declaration for the class that connects DirectReadoutEnergy with the ScoringManager.
 
file  DistanceChainbreakEnergy.cc
 
file  DistanceChainbreakEnergy.fwd.hh
 
file  DistanceChainbreakEnergy.hh
 
file  DistanceChainbreakEnergyCreator.hh
 Declaration for the class that connects DistanceChainbreakEnergy with the ScoringManager.
 
file  DNA_BaseEnergy.cc
 
file  DNA_BaseEnergy.fwd.hh
 
file  DNA_BaseEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  DNA_BaseEnergyCreator.hh
 Declaration for the class that connects DNA_BaseEnergy with the ScoringManager.
 
file  EnergyMethod.cc
 
file  EnergyMethod.fwd.hh
 Energy Method class forward declaration and EnergyMethodType enum definition.
 
file  EnergyMethod.hh
 
file  EnergyMethodCreator.fwd.hh
 Base class for EnergyMethod factory-registration and creation classes.
 
file  EnergyMethodCreator.hh
 Declaration of the base class for EnergyMethod factory registration and creation.
 
file  EnergyMethodOptions.cc
 
file  EnergyMethodOptions.fwd.hh
 
file  EnergyMethodOptions.hh
 
file  EnergyMethodRegistrator.hh
 Declaration of the base class for EnergyMethod factory registration and creation.
 
file  EnvEnergy.cc
 
file  EnvEnergy.hh
 EnergyMethod that evaluates env and cbeta energies.
 
file  EnvEnergyCreator.hh
 Declaration for the class that connects EnvEnergy with the ScoringManager.
 
file  EnvPairEnergy.fwd.hh
 
file  EnvSmoothEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  EnvSmoothEnergy.fwd.hh
 
file  EnvSmoothEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  EnvSmoothEnergyCreator.hh
 Declaration for the class that connects EnvSmoothEnergy with the ScoringManager.
 
file  Fa_MbenvEnergy.cc
 
file  Fa_MbenvEnergy.fwd.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
 
file  Fa_MbenvEnergy.hh
 
file  Fa_MbenvEnergyCreator.hh
 Declaration for the class that connects Fa_MbenvEnergy with the ScoringManager.
 
file  Fa_MbsolvEnergy.cc
 
file  Fa_MbsolvEnergy.fwd.hh
 
file  Fa_MbsolvEnergy.hh
 LK Solvation using hemisphere culling class forward declaration.
 
file  Fa_MbsolvEnergyCreator.hh
 Declaration for the class that connects Fa_MbsolvEnergy with the ScoringManager.
 
file  FACTSEnergy.cc
 
file  FACTSEnergy.fwd.hh
 
file  FACTSEnergy.hh
 
file  FACTSEnergyCreator.hh
 
file  GaussianOverlapEnergy.cc
 Gaussian Overlap Energy.
 
file  GaussianOverlapEnergy.fwd.hh
 golap
 
file  GaussianOverlapEnergy.hh
 energy of overlaps
 
file  GaussianOverlapEnergyCreator.hh
 Declaration for the class that connects GaussianOverlapEnergy with the ScoringManager.
 
file  GenBornEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  GenBornEnergy.fwd.hh
 
file  GenBornEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  GenBornEnergyCreator.hh
 Declaration for the class that connects GenBornEnergy with the ScoringManager.
 
file  HybridVDW_Energy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  HybridVDW_Energy.fwd.hh
 
file  HybridVDW_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  HybridVDW_EnergyCreator.hh
 Declaration for the class that connects HybridVDW_Energy with the ScoringManager.
 
file  LinearChainbreakEnergy.cc
 
file  LinearChainbreakEnergy.fwd.hh
 
file  LinearChainbreakEnergy.hh
 
file  LinearChainbreakEnergyCreator.cc
 LinearChainbreakEnergyCreator implementation.
 
file  LinearChainbreakEnergyCreator.hh
 Declaration for the class that connects LinearChainbreakEnergy with the ScoringManager.
 
file  LK_BallEnergy.cc
 
file  LK_BallEnergy.fwd.hh
 
file  LK_BallEnergy.hh
 LK Solvation using hemisphere culling class declaration.
 
file  LK_BallEnergyCreator.hh
 Declaration for the class that connects LK_BallEnergy with the ScoringManager.
 
file  LK_BallInfo.cc
 
file  LK_BallInfo.hh
 
file  LK_CosThetaEnergy.cc
 
file  LK_CosThetaEnergy.fwd.hh
 
file  LK_CosThetaEnergy.hh
 LK Solvation using hemisphere culling class forward declaration.
 
file  LK_CosThetaEnergyCreator.hh
 Declaration for the class that connects LK_CosThetaEnergy with the ScoringManager.
 
file  LK_hack.cc
 
file  LK_hack.fwd.hh
 
file  LK_hack.hh
 LK Solvation using hemisphere culling class declaration.
 
file  LK_hackCreator.hh
 Declaration for the class that connects LK_hack with the ScoringManager.
 
file  LongRangeTwoBodyEnergy.cc
 Long-Range, Two-Body Energy class implementation.
 
file  LongRangeTwoBodyEnergy.fwd.hh
 Long range two body energy method class forward declaration.
 
file  LongRangeTwoBodyEnergy.hh
 Long range two body energy method class declaration.
 
file  MembraneCbetaEnergy.cc
 
file  MembraneCbetaEnergy.fwd.hh
 
file  MembraneCbetaEnergy.hh
 Membrane Environment Cbeta Energy.
 
file  MembraneCbetaEnergyCreator.hh
 Declaration for the class that connects MembraneCbetaEnergy with the ScoringManager.
 
file  MembraneCenPairEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  MembraneCenPairEnergy.fwd.hh
 
file  MembraneCenPairEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  MembraneCenPairEnergyCreator.hh
 Declaration for the class that connects MembraneCenPairEnergy with the ScoringManager.
 
file  MembraneEnvEnergy.cc
 
file  MembraneEnvEnergy.fwd.hh
 
file  MembraneEnvEnergy.hh
 Membrane Environment Cbeta Energy.
 
file  MembraneEnvEnergyCreator.hh
 Declaration for the class that connects MembraneEnvEnergy with the ScoringManager.
 
file  MembraneEnvPenalties.cc
 
file  MembraneEnvPenalties.fwd.hh
 
file  MembraneEnvPenalties.hh
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  MembraneEnvPenaltiesCreator.hh
 Declaration for the class that connects MembraneEnvPenalties with the ScoringManager.
 
file  MembraneEnvSmoothEnergy.cc
 Statistically derived smooth membrane environment potential class implementation.
 
file  MembraneEnvSmoothEnergy.fwd.hh
 
file  MembraneEnvSmoothEnergy.hh
 Statistically derived smooth membrane environment potential class declaration.
 
file  MembraneEnvSmoothEnergyCreator.hh
 Declaration for the class that connects MembraneEnvSmoothEnergy with the ScoringManager.
 
file  MembraneLipo.cc
 
file  MembraneLipo.fwd.hh
 
file  MembraneLipo.hh
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  MembraneLipoCreator.hh
 Declaration for the class that connects MembraneLipo with the ScoringManager.
 
file  MetalloPlacementEnergy.cc
 Low-res placement score for metal sites.
 
file  MetalloPlacementEnergy.fwd.hh
 
file  MetalloPlacementEnergy.hh
 Low-res placement score for metal sites.
 
file  Methods.hh
 Energy Method enumeration.
 
file  MMBondAngleEnergy.cc
 
file  MMBondAngleEnergy.fwd.hh
 molecular mechanics bond angle energy forward declaration
 
file  MMBondAngleEnergy.hh
 molecular mechanics bond angle energy
 
file  MMBondAngleEnergyCreator.hh
 Declaration for the class that connects MMBondAngleEnergy with the ScoringManager.
 
file  MMBondLengthEnergy.cc
 
file  MMBondLengthEnergy.fwd.hh
 Molecular mechanics bond length score class.
 
file  MMBondLengthEnergy.hh
 Molecular mechanics bond length score class.
 
file  MMBondLengthEnergyCreator.hh
 Molecular mechanics bond length score class.
 
file  MMLJEnergyInter.cc
 
file  MMLJEnergyInter.fwd.hh
 molecular mechanics lj energy forward declaration
 
file  MMLJEnergyInter.hh
 molecular mechanics lj energy
 
file  MMLJEnergyInterCreator.hh
 Declaration for the class that connects MMLJEnergyInter with the ScoringManager.
 
file  MMLJEnergyIntra.cc
 
file  MMLJEnergyIntra.fwd.hh
 molecular mechanics lj energy forward declaration
 
file  MMLJEnergyIntra.hh
 molecular mechanics lj energy
 
file  MMLJEnergyIntraCreator.hh
 Declaration for the class that connects MMLJEnergyIntra with the ScoringManager.
 
file  MMTorsionEnergy.cc
 
file  MMTorsionEnergy.fwd.hh
 molecular mechanics torsion energy forward declaration
 
file  MMTorsionEnergy.hh
 molecular mechanics torsion energy
 
file  MMTorsionEnergyCreator.hh
 Declaration for the class that connects MMTorsionEnergy with the ScoringManager.
 
file  NMerPSSMEnergy.cc
 
file  NMerPSSMEnergy.fwd.hh
 PSSMerence energy method forward declaration.
 
file  NMerPSSMEnergy.hh
 PSSMerence energy method implementation.
 
file  NMerPSSMEnergyCreator.hh
 Declaration for the class that connects NMerPSSMEnergy with the ScoringManager.
 
file  NMerRefEnergy.cc
 
file  NMerRefEnergy.fwd.hh
 Reference energy method forward declaration.
 
file  NMerRefEnergy.hh
 Reference energy method implementation.
 
file  NMerRefEnergyCreator.hh
 Declaration for the class that connects NMerRefEnergy with the ScoringManager.
 
file  OmegaTetherEnergy.cc
 OmegaTether energy method class implementation.
 
file  OmegaTetherEnergy.fwd.hh
 OmegaTether energy method class forward declaration.
 
file  OmegaTetherEnergy.hh
 OmegaTether energy method class declaration.
 
file  OmegaTetherEnergyCreator.hh
 Declaration for the class that connects OmegaTetherEnergy with the ScoringManager.
 
file  OneBodyEnergy.cc
 
file  OneBodyEnergy.fwd.hh
 
file  OneBodyEnergy.hh
 
file  P_AA_Energy.cc
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method implementation.
 
file  P_AA_Energy.fwd.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
 
file  P_AA_Energy.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method declaration.
 
file  P_AA_EnergyCreator.hh
 Declaration for the class that connects P_AA_Energy with the ScoringManager.
 
file  P_AA_pp_Energy.cc
 
file  P_AA_pp_Energy.fwd.hh
 
file  P_AA_pp_Energy.hh
 Probability of observing an amino acid, given its phi/psi energy method declaration.
 
file  P_AA_pp_EnergyCreator.hh
 Declaration for the class that connects P_AA_pp_Energy with the ScoringManager.
 
file  PackStatEnergy.cc
 Radius of gyration energy function definition. Returns -1 * RG for a given Pose.
 
file  PackStatEnergy.hh
 
file  PackStatEnergyCreator.hh
 Declaration for the class that connects PackStatEnergy with the ScoringManager.
 
file  PairEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  PairEnergy.fwd.hh
 Statistically derived rotamer pair potential class forward declaration.
 
file  PairEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  PairEnergyCreator.hh
 Declaration for the class that connects PairEnergy with the ScoringManager.
 
file  PeptideBondEnergy.cc
 
file  PeptideBondEnergy.fwd.hh
 
file  PeptideBondEnergy.hh
 scoring method that defines ideal bond lengths between carbonyl carbon of residue N and nitrogen of residue N+1.
 
file  PeptideBondEnergyCreator.hh
 Declaration for the class that connects PeptideBondEnergy with the ScoringManager.
 
file  pHEnergy.cc
 Energy due to ionization state of the residue at a particular pH (see pHEnergy.hh for a detailed description)
 
file  pHEnergy.fwd.hh
 pH energy forward declaration
 
file  pHEnergy.hh
 pH Score (kT = 0.59 at 298 K) based on the chemical potential of the protonated/deprotonated residues. It indirectly contributes to a change in rotamer probabilities of protonated/deprotonated residues in the Dunbrack energy depending on the value of pH
 
file  pHEnergyCreator.hh
 Declaration for the class that connects pHEnergy with the ScoringManager.
 
file  PoissonBoltzmannEnergy.cc
 Ramachandran energy method class implementation.
 
file  PoissonBoltzmannEnergy.fwd.hh
 Ramachandran energy method class forward declaration.
 
file  PoissonBoltzmannEnergy.hh
 Membrane Environment Cbeta Energy.
 
file  PoissonBoltzmannEnergyCreator.hh
 
file  ProClosureEnergy.cc
 Proline ring closure energy method class implementation.
 
file  ProClosureEnergy.fwd.hh
 Proline ring closure energy method class forward declaration.
 
file  ProClosureEnergy.hh
 Proline ring closure energy method class declaration.
 
file  ProClosureEnergyCreator.hh
 Declaration for the class that connects ProClosureEnergy with the ScoringManager.
 
file  PyEnergy.hh
 Various Energy classes for subclassing in PyRosetta.
 
file  PyEnergyMethodRegisterer.hh
 EnergyMethod factory registration and creation in PyRosetta.
 
file  RamachandranEnergy.cc
 Ramachandran energy method class implementation.
 
file  RamachandranEnergy.fwd.hh
 Ramachandran energy method class forward declaration.
 
file  RamachandranEnergy.hh
 Ramachandran energy method class declaration.
 
file  RamachandranEnergy2B.cc
 
file  RamachandranEnergy2B.fwd.hh
 
file  RamachandranEnergy2B.hh
 Ramachandran energy method class declaration.
 
file  RamachandranEnergy2BCreator.hh
 Declaration for the class that connects RamachandranEnergy2B with the ScoringManager.
 
file  RamachandranEnergyCreator.hh
 Declaration for the class that connects RamachandranEnergy with the ScoringManager.
 
file  ReferenceEnergy.cc
 
file  ReferenceEnergy.fwd.hh
 Reference energy method forward declaration.
 
file  ReferenceEnergy.hh
 Reference energy method implementation.
 
file  ReferenceEnergyCreator.hh
 Declaration for the class that connects ReferenceEnergy with the ScoringManager.
 
file  ReferenceEnergyNoncanonical.cc
 Reference energy method implementation.
 
file  ReferenceEnergyNoncanonical.fwd.hh
 Reference energy method forward declaration.
 
file  ReferenceEnergyNoncanonical.hh
 Reference energy method declaration.
 
file  ReferenceEnergyNoncanonicalCreator.hh
 Declaration for the class that connects ReferenceEnergyNoncanonical with the ScoringManager.
 
file  ResidualDipolarCouplingEnergy.cc
 RDC energy - comparing experimental RDC values to calculated values.
 
file  ResidualDipolarCouplingEnergy.fwd.hh
 
file  ResidualDipolarCouplingEnergy.hh
 RDC energy - comparing experimental RDC values to calculated values.
 
file  ResidualDipolarCouplingEnergy_Rohl.cc
 RDC energy - comparing experimental RDC values to calculated values.
 
file  ResidualDipolarCouplingEnergy_Rohl.hh
 
file  ResidualDipolarCouplingEnergy_RohlCreator.hh
 Declaration for the class that connects ResidualDipolarCouplingEnergy_Rohl with the ScoringManager.
 
file  ResidualDipolarCouplingEnergyCreator.hh
 Declaration for the class that connects ResidualDipolarCouplingEnergy with the ScoringManager.
 
file  ResidualDipolarCouplingEnergyRigidSegments.cc
 RDC energy - comparing experimental RDC values to calculated values.
 
file  ResidualDipolarCouplingEnergyRigidSegments.fwd.hh
 
file  ResidualDipolarCouplingEnergyRigidSegments.hh
 RDC energy - comparing experimental RDC values to calculated values.
 
file  RG_Energy.cc
 Radius of gyration energy function definition. Returns -1 * RG for a given Pose.
 
file  RG_Energy.hh
 
file  RG_Energy_Fast.cc
 Radius of gyration energy function definition.
 
file  RG_Energy_Fast.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RG_Energy_FastCreator.hh
 Declaration for the class that connects RG_Energy_Fast with the ScoringManager.
 
file  RMS_Energy.cc
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  RMS_Energy.hh
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  RMS_EnergyCreator.hh
 Declaration for the class that connects RMS_Energy with the ScoringManager.
 
file  SA_Energy.cc
 sa energy function definition.
 
file  SA_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  SA_EnergyCreator.hh
 
file  SecondaryStructureEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  SecondaryStructureEnergy.fwd.hh
 
file  SecondaryStructureEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  SecondaryStructureEnergyCreator.hh
 Declaration for the class that connects SecondaryStructureEnergy with the ScoringManager.
 
file  SequenceDependentRefEnergy.cc
 
file  SequenceDependentRefEnergy.fwd.hh
 Reference energy method forward declaration.
 
file  SequenceDependentRefEnergy.hh
 Reference energy method implementation.
 
file  SequenceDependentRefEnergyCreator.hh
 Declaration for the class that connects SequenceDependentRefEnergy with the ScoringManager.
 
file  ShortRangeTwoBodyEnergy.cc
 Short-Range, Two-Body Energy Method base class implementation.
 
file  ShortRangeTwoBodyEnergy.fwd.hh
 Short Range Two Body Energy Method base class forward declaration.
 
file  ShortRangeTwoBodyEnergy.hh
 Short Range Two Body Energy Method base class declaration.
 
file  SmoothCenPairEnergy.cc
 Smooth, differentiable, version of cenpair.
 
file  SmoothCenPairEnergy.hh
 
file  SmoothCenPairEnergyCreator.hh
 
file  SmoothEnvCenPairEnergy.fwd.hh
 
file  SmoothEnvEnergy.cc
 Smooth, differentiable, version of centroid env.
 
file  SmoothEnvEnergy.hh
 
file  SmoothEnvEnergyCreator.hh
 
file  SuckerEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  SuckerEnergy.fwd.hh
 Statistically derived rotamer pair potential class forward declaration.
 
file  SuckerEnergy.hh
 energy attracting atoms to sucker atoms
 
file  SuckerEnergyCreator.hh
 Declaration for the class that connects SuckerEnergy with the ScoringManager.
 
file  SymmetricLigandEnergy.cc
 Dunbrack energy method implementation.
 
file  SymmetricLigandEnergy.fwd.hh
 Dunbrack energy method forward declaration.
 
file  SymmetricLigandEnergy.hh
 score for implicit ligand interactions from symmetric geometry
 
file  SymmetricLigandEnergyCreator.hh
 
file  TwoBodyEnergy.cc
 Two Body Energy Method base class implementation.
 
file  TwoBodyEnergy.fwd.hh
 Two Body Energy Method base class forward declaration.
 
file  TwoBodyEnergy.hh
 Two Body Energy Method base class declaration.
 
file  UnfoldedStateEnergy.cc
 Unfolded state energy method implementation; energies based on eneriges of residues in fragments.
 
file  UnfoldedStateEnergy.fwd.hh
 Unfolded state energy method, forward declaration.
 
file  UnfoldedStateEnergy.hh
 Unfolded state energy declaration header file.
 
file  UnfoldedStateEnergyCreator.hh
 Declaration for the class that connects UnfoldedStateEnergy with the ScoringManager.
 
file  util.cc
 utility methods for scoring.
 
file  util.hh
 utility methods for scoring.
 
file  VDW_Energy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  VDW_Energy.fwd.hh
 
file  VDW_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  VDW_EnergyCreator.hh
 Declaration for the class that connects VDW_Energy with the ScoringManager.
 
file  WaterAdductHBondEnergy.cc
 
file  WaterAdductHBondEnergy.fwd.hh
 
file  WaterAdductHBondEnergy.hh
 Energy potential for water mediated hydrogen bonds involving adduct-placed water molecules.
 
file  WaterAdductHBondEnergyCreator.hh
 Declaration for the class that connects WaterAdductHBondEnergy with the ScoringManager.
 
file  WaterAdductIntraEnergy.cc
 
file  WaterAdductIntraEnergy.fwd.hh
 
file  WaterAdductIntraEnergy.hh
 Energetic offset/cost for placing a water adduct on an amino or nucleic acid.
 
file  WaterAdductIntraEnergyCreator.hh
 Declaration for the class that connects WaterAdductIntraEnergy with the ScoringManager.
 
file  WholeStructureEnergy.cc
 Implementation of the EnergyMethod that applies to a whole structure and not on a residue-by-residue basis.
 
file  WholeStructureEnergy.fwd.hh
 EnergyMethod that applies to a whole structure and not on a residue-by-residue basis.
 
file  WholeStructureEnergy.hh
 EnergyMethod that applies to a whole structure and not on a residue-by-residue basis.
 
file  YHHPlanarityEnergy.cc
 
file  YHHPlanarityEnergy.fwd.hh
 
file  YHHPlanarityEnergy.hh
 Term for chi3 on tyrosine residues to prefer the hydrogen lie in the plane of the ring.
 
file  YHHPlanarityEnergyCreator.hh