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energy_methods Directory Reference
Directory dependency graph for energy_methods:
src/core/energy_methods

Files

file  AACompositionEnergy.cc
 
file  AACompositionEnergy.fwd.hh
 
file  AACompositionEnergy.hh
 
file  AACompositionEnergyCreator.hh
 
file  AARepeatEnergy.cc
 
file  AARepeatEnergy.fwd.hh
 
file  AARepeatEnergy.hh
 
file  AARepeatEnergyCreator.hh
 
file  AbegoEnergy.cc
 ABEGO energy method class implementation.
 
file  AbegoEnergy.fwd.hh
 ABEGO energy method class forward declaration.
 
file  AbegoEnergy.hh
 
file  AbegoEnergyCreator.hh
 
file  ArgCationPiEnergy.cc
 Cation pi term that specializes in bringing Arginine and rings together.
 
file  ArgCationPiEnergy.fwd.hh
 Cation pi term that specializes in bringing Arginine and rings together.
 
file  ArgCationPiEnergy.hh
 Cation pi term that specializes in bringing Arginine and rings together.
 
file  ArgCationPiEnergyCreator.hh
 
file  AromaticBackboneRestraintEnergy.cc
 Aramid backbone restraint energy method class implementation.
 
file  AromaticBackboneRestraintEnergy.fwd.hh
 Noncanonical ring closure energy method class forward declaration.
 
file  AromaticBackboneRestraintEnergy.hh
 Aromatic backbone restraint energy method class headers.
 
file  AromaticBackboneRestraintEnergyCreator.hh
 Declaration for the class that connects AromaticBackboneRestraintEnergy with the ScoringManager.
 
file  AspartimidePenaltyEnergy.cc
 
file  AspartimidePenaltyEnergy.fwd.hh
 Forward declarations for the AspartimidePenaltyEnergy.
 
file  AspartimidePenaltyEnergy.hh
 This is a score term that penalizes sequences that are likely to result in aspartimide formation during peptide synthesis.
 
file  AspartimidePenaltyEnergyCreator.hh
 Declaration for the class that connects AspartimidePenaltyEnergy with the ScoringManager.
 
file  BranchEnergy.cc
 Method definitions for BranchEnergyCreator and BranchEnergy classes.
 
file  BranchEnergy.fwd.hh
 
file  BranchEnergy.hh
 Method declarations and typedefs for BranchEnergy.
 
file  BranchEnergyCreator.hh
 Declaration for the class that connects BranchEnergy with the ScoringManager.
 
file  Burial_v2Energy.cc
 
file  Burial_v2Energy.hh
 energy term use for score burial of a specific residue
 
file  Burial_v2EnergyCreator.hh
 Declaration for the class that connects Burial_v2Energy with the ScoringManager.
 
file  BurialEnergy.cc
 
file  BurialEnergy.hh
 energy term use for scoring predicted burial
 
file  BurialEnergyCreator.hh
 Declaration for the class that connects BurialEnergy with the ScoringManager.
 
file  CartesianBondedEnergy.cc
 Harmonic bondangle/bondlength/torsion constraints.
 
file  CartesianBondedEnergy.fwd.hh
 
file  CartesianBondedEnergy.hh
 
file  CartesianBondedEnergyCreator.hh
 Declaration for the class that connects CartesianBondedEnergy with the ScoringManager.
 
file  CenHBEnergy.cc
 Smooth, differentiable version of centroid hbond term.
 
file  CenHBEnergy.fwd.hh
 
file  CenHBEnergy.hh
 Smooth, differentiable version of centroid hbond term.
 
file  CenHBEnergyCreator.hh
 Declaration for the class that connects CenHBEnergy with the ScoringManager.
 
file  CenPairEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  CenPairEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  CenPairEnergyCreator.hh
 
file  CenPairMotifDegreeEnergy.cc
 
file  CenPairMotifDegreeEnergy.hh
 
file  CenPairMotifDegreeEnergyCreator.hh
 
file  CenPairMotifEnergy.cc
 
file  CenPairMotifEnergy.hh
 
file  CenPairMotifEnergyCreator.hh
 
file  CenRotEnvEnergy.cc
 CenRot version of centroid env.
 
file  CenRotEnvEnergy.hh
 
file  CenRotEnvEnergyCreator.hh
 
file  CenRotPairEnergy.cc
 CenRot version of cen pair.
 
file  CenRotPairEnergy.hh
 
file  CenRotPairEnergyCreator.hh
 
file  CentroidDisulfideEnergy.cc
 Centroid Disulfide Energy class implementation.
 
file  CentroidDisulfideEnergy.fwd.hh
 Centroid Disulfide Energy class forward declaration.
 
file  CentroidDisulfideEnergy.hh
 Centroid Disulfide Energy class declaration.
 
file  CentroidDisulfideEnergyCreator.hh
 Declaration for the class that connects CentroidDisulfideEnergy with the ScoringManager.
 
file  ChainbreakEnergy.cc
 Method definitions for ChainbreakEnergyCreator and ChainbreakEnergy classes.
 
file  ChainbreakEnergy.fwd.hh
 
file  ChainbreakEnergy.hh
 Method declarations and typedefs for ChainbreakEnergy.
 
file  ChainbreakEnergyCreator.hh
 Declaration for the class that connects ChainbreakEnergy with the ScoringManager.
 
file  ChemicalShiftAnisotropyEnergy.cc
 CSA energy - Orientation dependent chemical shift.
 
file  ChemicalShiftAnisotropyEnergy.fwd.hh
 
file  ChemicalShiftAnisotropyEnergy.hh
 CSP energy.
 
file  ChemicalShiftAnisotropyEnergyCreator.hh
 Declaration for the class that connects ChemicalShiftAnisotropyEnergy with the ScoringManager.
 
file  ContactOrderEnergy.cc
 calculates the contact order of a given conformation average sequence.
 
file  ContactOrderEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  ContactOrderEnergyCreator.hh
 Declaration for the class that connects ContactOrderEnergy with the ScoringManager.
 
file  ContextDependentGeometricSolEnergy.cc
 
file  ContextDependentGeometricSolEnergy.fwd.hh
 
file  ContextDependentGeometricSolEnergy.hh
 
file  ContextDependentGeometricSolEnergyCreator.hh
 Declaration for the class that connects GeometricSolEnergy with the ScoringManager.
 
file  ContextIndependentGeometricSolEnergy.cc
 
file  ContextIndependentGeometricSolEnergy.fwd.hh
 
file  ContextIndependentGeometricSolEnergy.hh
 
file  ContextIndependentGeometricSolEnergyCreator.hh
 
file  CovalentLabelingEnergy.cc
 
file  CovalentLabelingEnergy.fwd.hh
 
file  CovalentLabelingEnergy.hh
 energy term use for scoring predicted CovalentLabeling
 
file  CovalentLabelingEnergyCreator.hh
 Declaration for the class that connects CovalentLabelingEnergy with the ScoringManager.
 
file  CovalentLabelingFAEnergy.cc
 
file  CovalentLabelingFAEnergy.fwd.hh
 
file  CovalentLabelingFAEnergy.hh
 energy term use for scoring predicted CovalentLabelingFA
 
file  CovalentLabelingFAEnergyCreator.hh
 Declaration for the class that connects CovalentLabelingFAEnergy with the ScoringManager.
 
file  CustomAtomPairEnergy.cc
 Simple EnergyMethod for calculating residue-residue constraints under some interaction cutoff.
 
file  CustomAtomPairEnergy.fwd.hh
 Statistically derived rotamer pair potential class forward declaration.
 
file  CustomAtomPairEnergy.hh
 
file  CustomAtomPairEnergyCreator.hh
 Declaration for the class that connects CustomAtomPairEnergy with the ScoringManager.
 
file  D2H_SA_Energy.cc
 sa energy function definition.
 
file  D2H_SA_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  D2H_SA_EnergyCreator.hh
 Declaration for the class that connects D2H_SA_Energy with the ScoringManager.
 
file  DEEREnergy.cc
 Score term for data obtained with double electron-electron resonance (DEER)
 
file  DEEREnergy.fwd.hh
 
file  DEEREnergy.hh
 Score term for data obtained with double electron-electron resonance (DEER)
 
file  DEEREnergyCreator.hh
 Parent class for DEEREnergy structure.
 
file  DFIRE_Energy.cc
 
file  DFIRE_Energy.fwd.hh
 
file  DFIRE_Energy.hh
 
file  DFIRE_EnergyCreator.hh
 
file  DipolarCouplingEnergy.cc
 DC energy - Orientation dependent chemical shift.
 
file  DipolarCouplingEnergy.fwd.hh
 
file  DipolarCouplingEnergy.hh
 CSP energy.
 
file  DipolarCouplingEnergyCreator.hh
 Declaration for the class that connects DipolarCouplingEnergy with the ScoringManager.
 
file  DirectReadoutEnergy.cc
 Statistically derived DNA contact potential class implementation.
 
file  DirectReadoutEnergy.fwd.hh
 
file  DirectReadoutEnergy.hh
 Statistically derived DNA contact potential class declaration.
 
file  DirectReadoutEnergyCreator.hh
 Declaration for the class that connects DirectReadoutEnergy with the ScoringManager.
 
file  DistanceChainbreakEnergy.cc
 
file  DistanceChainbreakEnergy.fwd.hh
 
file  DistanceChainbreakEnergy.hh
 
file  DistanceChainbreakEnergyCreator.hh
 Declaration for the class that connects DistanceChainbreakEnergy with the ScoringManager.
 
file  DisulfideMatchingEnergy.cc
 Centroid Disulfide Energy class implementation.
 
file  DisulfideMatchingEnergy.fwd.hh
 Centroid Disulfide Energy class forward declaration.
 
file  DisulfideMatchingEnergy.hh
 Centroid Disulfide Energy class declaration.
 
file  DisulfideMatchingEnergyCreator.hh
 Declaration for the class that connects DisulfideMatchingEnergy with the ScoringManager.
 
file  DNA_BaseEnergy.cc
 
file  DNA_BaseEnergy.fwd.hh
 
file  DNA_BaseEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  DNA_BaseEnergyCreator.hh
 Declaration for the class that connects DNA_BaseEnergy with the ScoringManager.
 
file  DNA_DihedralEnergy.cc
 dna scoring
 
file  DNA_DihedralEnergy.fwd.hh
 dna scoring
 
file  DNA_DihedralEnergy.hh
 dna scoring
 
file  DNA_DihedralEnergyCreator.hh
 dna scoring
 
file  DNA_EnvPairEnergy.cc
 dna scoring
 
file  DNA_EnvPairEnergy.fwd.hh
 dna scoring
 
file  DNA_EnvPairEnergy.hh
 dna scoring
 
file  DNA_EnvPairEnergyCreator.hh
 dna scoring
 
file  DNA_ReferenceEnergy.cc
 dna scoring
 
file  DNA_ReferenceEnergy.fwd.hh
 dna scoring
 
file  DNA_ReferenceEnergy.hh
 dna scoring
 
file  DNA_ReferenceEnergyCreator.hh
 dna scoring
 
file  DNAChiEnergy.cc
 
file  DNAChiEnergy.fwd.hh
 
file  DNAChiEnergy.hh
 
file  DNAChiEnergyCreator.hh
 Declaration for the class that connects DNAChiEnergy with the ScoringManager.
 
file  DNATorsionEnergy.cc
 DNATorsion energy method class implementation.
 
file  DNATorsionEnergy.fwd.hh
 
file  DNATorsionEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  DNATorsionEnergyCreator.hh
 Declaration for the class that connects DNATorsionEnergy with the ScoringManager.
 
file  DumpTrajectoryEnergy.cc
 An EnergyMethod that dumps trajectories to file.
 
file  DumpTrajectoryEnergy.fwd.hh
 Forward declarations for an EnergyMethod that dumps trajectories to file.
 
file  DumpTrajectoryEnergy.hh
 Headers for an EnergyMethod that dumps trajectories to file.
 
file  DumpTrajectoryEnergyCreator.hh
 Creator for an EnergyMethod that dump trajectories to file.
 
file  ElecDensAllAtomCenEnergy.cc
 
file  ElecDensAllAtomCenEnergy.hh
 
file  ElecDensAllAtomCenEnergyCreator.hh
 Declaration for the class that connects ElecDensAllAtomCenEnergy with the ScoringManager.
 
file  ElecDensAtomwiseEnergy.cc
 elec_dens_atomwise scoring method implementation
 
file  ElecDensAtomwiseEnergy.fwd.hh
 
file  ElecDensAtomwiseEnergy.hh
 Declaration for elec_dens_atomwise scoring method.
 
file  ElecDensAtomwiseEnergyCreator.hh
 
file  ElecDensCenEnergy.cc
 
file  ElecDensCenEnergy.hh
 
file  ElecDensCenEnergyCreator.hh
 Declaration for the class that connects ElecDensCenEnergy with the ScoringManager.
 
file  ElecDensEnergy.cc
 
file  ElecDensEnergy.hh
 
file  ElecDensEnergyCreator.hh
 Declaration for the class that connects ElecDensEnergy with the ScoringManager.
 
file  EnvEnergy.cc
 
file  EnvEnergy.hh
 EnergyMethod that evaluates env and cbeta energies.
 
file  EnvEnergyCreator.hh
 Declaration for the class that connects EnvEnergy with the ScoringManager.
 
file  EnvSmoothEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  EnvSmoothEnergy.fwd.hh
 
file  EnvSmoothEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  EnvSmoothEnergyCreator.hh
 Declaration for the class that connects EnvSmoothEnergy with the ScoringManager.
 
file  ExactOccludedHbondSolEnergy.cc
 
file  ExactOccludedHbondSolEnergy.fwd.hh
 
file  ExactOccludedHbondSolEnergy.hh
 
file  ExactOccludedHbondSolEnergyCreator.hh
 Declaration for the class that connects ExactOccludedHbondSolEnergy with the ScoringManager.
 
file  FA_ElecEnergyAroAll.cc
 Electrostatics energy method for aromatic side chain (stand-in for pi/pi interactions).
 
file  FA_ElecEnergyAroAll.fwd.hh
 Electrostatics for RNA class forward declaration.
 
file  FA_ElecEnergyAroAll.hh
 
file  FA_ElecEnergyAroAllCreator.hh
 Declaration for the class that connects FA_ElecEnergyAroAll with the ScoringManager.
 
file  FA_ElecEnergyAroAro.cc
 Electrostatics energy method for aromatic side chain (stand-in for pi/pi interactions).
 
file  FA_ElecEnergyAroAro.fwd.hh
 Electrostatics for RNA class forward declaration.
 
file  FA_ElecEnergyAroAro.hh
 
file  FA_ElecEnergyAroAroCreator.hh
 Declaration for the class that connects FA_ElecEnergyAroAro with the ScoringManager.
 
file  FA_GrpElecEnergy.cc
 
file  FA_GrpElecEnergy.fwd.hh
 
file  FA_GrpElecEnergy.hh
 
file  FA_GrpElecEnergyCreator.hh
 Declaration for the class that connects FA_ElecEnergy with the ScoringManager.
 
file  Fa_MbenvEnergy.cc
 
file  Fa_MbenvEnergy.fwd.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
 
file  Fa_MbenvEnergy.hh
 
file  Fa_MbenvEnergyCreator.hh
 Declaration for the class that connects Fa_MbenvEnergy with the ScoringManager.
 
file  Fa_MbsolvEnergy.cc
 
file  Fa_MbsolvEnergy.fwd.hh
 
file  Fa_MbsolvEnergy.hh
 LK Solvation using hemisphere culling class forward declaration.
 
file  Fa_MbsolvEnergyCreator.hh
 Declaration for the class that connects Fa_MbsolvEnergy with the ScoringManager.
 
file  FACTSEnergy.cc
 
file  FACTSEnergy.fwd.hh
 
file  FACTSEnergy.hh
 
file  FACTSEnergyCreator.hh
 
file  FaMPEnvEnergy.cc
 
file  FaMPEnvEnergy.fwd.hh
 
file  FaMPEnvEnergy.hh
 LK-Type Membrane Environment Energy.
 
file  FaMPEnvEnergyCreator.hh
 
file  FaMPEnvSmoothEnergy.cc
 
file  FaMPEnvSmoothEnergy.fwd.hh
 
file  FaMPEnvSmoothEnergy.hh
 Fullatom Smoothed Membrane Environment Energy.
 
file  FaMPEnvSmoothEnergyCreator.hh
 
file  FaMPSolvEnergy.cc
 LK-Type Membrane Solvation Energy.
 
file  FaMPSolvEnergy.fwd.hh
 
file  FaMPSolvEnergy.hh
 LK-Type Membrane Solvation Energy.
 
file  FaMPSolvEnergyCreator.hh
 
file  FastDensEnergy.cc
 
file  FastDensEnergy.hh
 
file  FastDensEnergyCreator.hh
 Declaration for the class that connects FastDensEnergy with the ScoringManager.
 
file  FastSAXSEnergy.cc
 
file  FastSAXSEnergy.hh
 
file  FastSAXSEnergyCreator.hh
 Energy Creator for FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010)
 
file  FiberDiffractionEnergy.cc
 
file  FiberDiffractionEnergy.hh
 
file  FiberDiffractionEnergyCreator.hh
 Energy Creator for FiberDiffractionEnergy.
 
file  FiberDiffractionEnergyDens.cc
 
file  FiberDiffractionEnergyDens.hh
 
file  FiberDiffractionEnergyDensCreator.hh
 Energy Creator for FiberDiffractionEnergyDens.
 
file  FiberDiffractionEnergyGpu.cc
 
file  FiberDiffractionEnergyGpu.hh
 
file  FiberDiffractionEnergyGpuCreator.hh
 
file  FreeDOF_Energy.cc
 FreeMoiety energy method implementation.
 
file  FreeDOF_Energy.fwd.hh
 FreeMoiety energy method forward declaration.
 
file  FreeDOF_Energy.hh
 Score function class.
 
file  FreeDOF_EnergyCreator.hh
 Declaration for the class that connects FreeDOF_Energy with the ScoringManager.
 
file  FullatomDisulfideEnergy.cc
 
file  FullatomDisulfideEnergy.fwd.hh
 
file  FullatomDisulfideEnergy.hh
 
file  FullatomDisulfideEnergyCreator.hh
 Declaration for the class that connects FullatomDisulfideEnergy with the ScoringManager.
 
file  GaussianOverlapEnergy.cc
 Gaussian Overlap Energy.
 
file  GaussianOverlapEnergy.fwd.hh
 golap
 
file  GaussianOverlapEnergy.hh
 energy of overlaps
 
file  GaussianOverlapEnergyCreator.hh
 Declaration for the class that connects GaussianOverlapEnergy with the ScoringManager.
 
file  GenBornEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  GenBornEnergy.fwd.hh
 
file  GenBornEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  GenBornEnergyCreator.hh
 Declaration for the class that connects GenBornEnergy with the ScoringManager.
 
file  GenericBondedEnergy.cc
 A "generic" (atom-type-only-based) torsional potential.
 
file  GenericBondedEnergy.fwd.hh
 
file  GenericBondedEnergy.hh
 A "generic" (atom-type-only-based) torsional potential.
 
file  GenericBondedEnergyCreator.hh
 Declaration for the class that connects GenericBondedEnergy with the ScoringManager.
 
file  GoapEnergy.cc
 C++ implementaion of GOAP(Generalized Orientation-dependent, All-atom statistical Potential) by Zhou H & Skolnick J, Biophys J 2011, 101(8):2043-52.
 
file  GoapEnergy.fwd.hh
 
file  GoapEnergy.hh
 
file  GoapEnergyCreator.hh
 
file  HackAroEnergy.cc
 
file  HackAroEnergy.fwd.hh
 
file  HackAroEnergy.hh
 
file  HackAroEnergyCreator.hh
 Declaration for the class that connects HackAroEnergy with the ScoringManager.
 
file  HolesEnergy.cc
 
file  HolesEnergy.hh
 
file  HolesEnergyCreator.hh
 Declaration for the class that connects HolesEnergy with the ScoringManager.
 
file  HRF_MSLabelingEnergy.cc
 
file  HRF_MSLabelingEnergy.fwd.hh
 
file  HRF_MSLabelingEnergy.hh
 energy term use for scoring predicted HRF_MSLabeling
 
file  HRF_MSLabelingEnergyCreator.hh
 Declaration for the class that connects HRF_MSLabelingEnergy with the ScoringManager.
 
file  HRFDynamicsEnergy.cc
 Score term calculated based upon neighbor count agreement with hydroxyl radical footprinting labeling data. In a manuscript to be published in 2020.
 
file  HRFDynamicsEnergy.fwd.hh
 
file  HRFDynamicsEnergy.hh
 Score term based off mass spectrometry HRF data.
 
file  HRFDynamicsEnergyCreator.hh
 Declaration for the class that connects HRFDynamicsEnergy with the ScoringManager.
 
file  HybridVDW_Energy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  HybridVDW_Energy.fwd.hh
 
file  HybridVDW_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  HybridVDW_EnergyCreator.hh
 Declaration for the class that connects HybridVDW_Energy with the ScoringManager.
 
file  HydroxylTorsionEnergy.cc
 
file  HydroxylTorsionEnergy.fwd.hh
 
file  HydroxylTorsionEnergy.hh
 Term for proton_chi on Ser/Thr/Tyr residues.
 
file  HydroxylTorsionEnergyCreator.hh
 
file  IntermolEnergy.cc
 Cost of bringing two chains together.
 
file  IntermolEnergy.hh
 Radius of gyration score for METHODS, to match Rosetta++.
 
file  IntermolEnergyCreator.hh
 Declaration for the class that connects IntermolEnergy with the ScoringManager.
 
file  LinearBranchEnergy.cc
 Atom pair energy functions.
 
file  LinearBranchEnergy.fwd.hh
 
file  LinearBranchEnergy.hh
 
file  LinearBranchEnergyCreator.cc
 LinearBranchEnergyCreator implementation.
 
file  LinearBranchEnergyCreator.hh
 Declaration for the class that connects LinearBranchEnergy with the ScoringManager.
 
file  LinearChainbreakEnergy.cc
 Atom pair energy functions.
 
file  LinearChainbreakEnergy.fwd.hh
 
file  LinearChainbreakEnergy.hh
 
file  LinearChainbreakEnergyCreator.cc
 LinearChainbreakEnergyCreator implementation.
 
file  LinearChainbreakEnergyCreator.hh
 Declaration for the class that connects LinearChainbreakEnergy with the ScoringManager.
 
file  LK_hack.cc
 
file  LK_hack.fwd.hh
 
file  LK_hack.hh
 LK Solvation using hemisphere culling class declaration.
 
file  LK_hackCreator.hh
 Declaration for the class that connects LK_hack with the ScoringManager.
 
file  LK_PolarNonPolarEnergy.cc
 
file  LK_PolarNonPolarEnergy.fwd.hh
 
file  LK_PolarNonPolarEnergy.hh
 LK Solvation using hemisphere culling class forward declaration.
 
file  LK_PolarNonPolarEnergyCreator.hh
 Declaration for the class that connects LK_PolarNonPolarEnergy with the ScoringManager.
 
file  LoopCloseEnergy.cc
 Cost of bringing two chains together.
 
file  LoopCloseEnergy.hh
 
file  LoopCloseEnergyCreator.hh
 Declaration for the class that connects LoopCloseEnergy with the ScoringManager.
 
file  MembraneCbetaEnergy.cc
 
file  MembraneCbetaEnergy.fwd.hh
 
file  MembraneCbetaEnergy.hh
 Membrane Environment Cbeta Energy.
 
file  MembraneCbetaEnergyCreator.hh
 Declaration for the class that connects MembraneCbetaEnergy with the ScoringManager.
 
file  MembraneCenPairEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  MembraneCenPairEnergy.fwd.hh
 
file  MembraneCenPairEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  MembraneCenPairEnergyCreator.hh
 Declaration for the class that connects MembraneCenPairEnergy with the ScoringManager.
 
file  MembraneEnvEnergy.cc
 
file  MembraneEnvEnergy.fwd.hh
 
file  MembraneEnvEnergy.hh
 Membrane Environment Cbeta Energy.
 
file  MembraneEnvEnergyCreator.hh
 Declaration for the class that connects MembraneEnvEnergy with the ScoringManager.
 
file  MembraneEnvPenalties.cc
 
file  MembraneEnvPenalties.fwd.hh
 
file  MembraneEnvPenalties.hh
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  MembraneEnvPenaltiesCreator.hh
 Declaration for the class that connects MembraneEnvPenalties with the ScoringManager.
 
file  MembraneEnvSmoothEnergy.cc
 Statistically derived smooth membrane environment potential class implementation.
 
file  MembraneEnvSmoothEnergy.fwd.hh
 
file  MembraneEnvSmoothEnergy.hh
 Statistically derived smooth membrane environment potential class declaration.
 
file  MembraneEnvSmoothEnergyCreator.hh
 Declaration for the class that connects MembraneEnvSmoothEnergy with the ScoringManager.
 
file  MembraneLipo.cc
 
file  MembraneLipo.fwd.hh
 
file  MembraneLipo.hh
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  MembraneLipoCreator.hh
 Declaration for the class that connects MembraneLipo with the ScoringManager.
 
file  MgEnergy.cc
 
file  MgEnergy.fwd.hh
 
file  MgEnergy.hh
 
file  MgEnergyCreator.hh
 Declaration for the class that connects MgEnergy with the ScoringManager.
 
file  MHCEpitopeEnergy.cc
 
file  MHCEpitopeEnergy.fwd.hh
 
file  MHCEpitopeEnergy.hh
 
file  MHCEpitopeEnergyCreator.hh
 
file  MissingEnergy.cc
 Cost of failing to close loops.
 
file  MissingEnergy.hh
 Cost of failing to close loops.
 
file  MissingEnergyCreator.hh
 Declaration for the class that connects MissingEnergy with the ScoringManager.
 
file  MotifDockEnergy.cc
 Adaptation of Motif score for Docking.
 
file  MotifDockEnergy.fwd.hh
 
file  MotifDockEnergy.hh
 Adaptation of Motif score for Docking.
 
file  MotifDockEnergyCreator.hh
 Adaptation of Motif score for Docking.
 
file  MPCBetaEnergy.cc
 
file  MPCBetaEnergy.fwd.hh
 
file  MPCBetaEnergy.hh
 
file  MPCBetaEnergyCreator.hh
 
file  MPEnvEnergy.cc
 Membrane Environemnt Energy.
 
file  MPEnvEnergy.fwd.hh
 Membrane Environemnt Energy.
 
file  MPEnvEnergy.hh
 Membrane Environemnt Energy.
 
file  MPEnvEnergyCreator.hh
 
file  MPHelicalityEnergy.cc
 Fullatom and centroid level smooth membrane non-helicality penalty.
 
file  MPHelicalityEnergy.fwd.hh
 
file  MPHelicalityEnergy.hh
 Fullatom and centroid level smooth membrane non-helicality penalty.
 
file  MPHelicalityEnergyCreator.hh
 
file  MPPairEnergy.cc
 Membrane Residue Pair Energy Term.
 
file  MPPairEnergy.fwd.hh
 
file  MPPairEnergy.hh
 Membrane Residue Pair Energy Term.
 
file  MPPairEnergyCreator.hh
 
file  MPResidueLipophilicityEnergy.cc
 Fullatom Smoothed Membrane Environment Energy.
 
file  MPResidueLipophilicityEnergy.fwd.hh
 
file  MPResidueLipophilicityEnergy.hh
 Fullatom Smoothed Membrane Environment Energy.
 
file  MPResidueLipophilicityEnergyCreator.hh
 
file  MPSpanAngleEnergy.cc
 penalize spans with unnatural dG of insertion
 
file  MPSpanAngleEnergy.hh
 
file  MPSpanAngleEnergyCreator.hh
 
file  MPSpanInsertionEnergy.cc
 penalize spans with unnatural dG of insertion
 
file  MPSpanInsertionEnergy.hh
 
file  MPSpanInsertionEnergyCreator.hh
 
file  MultipoleElecEnergy.cc
 Fixed multipole electrostatics using Jay Ponder's approach in Tinker/Amoeba.
 
file  MultipoleElecEnergy.fwd.hh
 
file  MultipoleElecEnergy.hh
 Fixed multipole electrostatics using Jay Ponder's approach in Tinker/Amoeba.
 
file  MultipoleElecEnergyCreator.hh
 Declaration for the class that connects MultipoleElecEnergy with the ScoringManager.
 
file  NetChargeEnergy.cc
 
file  NetChargeEnergy.fwd.hh
 
file  NetChargeEnergy.hh
 
file  NetChargeEnergyCreator.hh
 
file  non_scorefxn_exact_model.cc
 
file  non_scorefxn_exact_model.hh
 
file  NPDHBondEnergy.cc
 
file  NPDHBondEnergy.fwd.hh
 
file  NPDHBondEnergy.hh
 
file  NPDHBondEnergyCreator.hh
 Declaration for the class that connects NPDHBondEnergy with the ScoringManager.
 
file  OccludedHbondSolEnergy.cc
 
file  OccludedHbondSolEnergy.fwd.hh
 
file  OccludedHbondSolEnergy.hh
 
file  OccludedHbondSolEnergy_onebody.cc
 
file  OccludedHbondSolEnergy_onebody.fwd.hh
 
file  OccludedHbondSolEnergy_onebody.hh
 
file  OccludedHbondSolEnergy_onebodyCreator.hh
 Declaration for the class that connects OccludedHbondSolEnergy_onebody with the ScoringManager.
 
file  OccludedHbondSolEnergyCreator.hh
 Declaration for the class that connects OccludedHbondSolEnergy 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  OtherPoseEnergy.cc
 Way to handle scoring of a collection of poses, allowing shift of focus between poses.
 
file  OtherPoseEnergy.fwd.hh
 
file  OtherPoseEnergy.hh
 
file  OtherPoseEnergyCreator.hh
 Declaration for the class that connects OtherPoseEnergy with the ScoringManager.
 
file  P_AA_Energy.cc
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method implementation.
 
file  P_AA_Energy.fwd.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
 
file  P_AA_Energy.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method declaration.
 
file  P_AA_EnergyCreator.hh
 Declaration for the class that connects P_AA_Energy with the ScoringManager.
 
file  P_AA_pp_Energy.cc
 Probability of observing an amino acid, given its phi/psi energy method declaration.
 
file  P_AA_pp_Energy.fwd.hh
 
file  P_AA_pp_Energy.hh
 Probability of observing an amino acid, given its phi/psi energy method forward declaration.
 
file  P_AA_pp_EnergyCreator.hh
 Declaration for the class that connects P_AA_pp_Energy with the ScoringManager.
 
file  P_AA_ss_Energy.cc
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method implementation.
 
file  P_AA_ss_Energy.fwd.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration.
 
file  P_AA_ss_Energy.hh
 Probability of observing an amino acid (NOT conditional on phi/psi), energy method declaration.
 
file  P_AA_ss_EnergyCreator.hh
 Declaration for the class that connects P_AA_ss_Energy with the ScoringManager.
 
file  PackStatEnergy.cc
 Radius of gyration energy function definition. Returns -1 * RG for a given Pose.
 
file  PackStatEnergy.hh
 
file  PackStatEnergyCreator.hh
 Declaration for the class that connects PackStatEnergy with the ScoringManager.
 
file  PairEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  PairEnergy.fwd.hh
 Statistically derived rotamer pair potential class forward declaration.
 
file  PairEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  PairEnergyCreator.hh
 Declaration for the class that connects PairEnergy with the ScoringManager.
 
file  PeptideBondEnergy.cc
 
file  PeptideBondEnergy.fwd.hh
 
file  PeptideBondEnergy.hh
 scoring method that defines ideal bond lengths between carbonyl carbon of residue N and nitrogen of residue N+1.
 
file  PeptideBondEnergyCreator.hh
 Declaration for the class that connects PeptideBondEnergy with the ScoringManager.
 
file  pHEnergy.cc
 Energy due to ionization state of the residue at a particular pH (see pHEnergy.hh for a detailed description)
 
file  pHEnergy.fwd.hh
 pH energy forward declaration
 
file  pHEnergy.hh
 
file  pHEnergyCreator.hh
 Declaration for the class that connects pHEnergy with the ScoringManager.
 
file  PointWaterEnergy.cc
 
file  PointWaterEnergy.fwd.hh
 
file  PointWaterEnergy.hh
 Statistical point water energy function.
 
file  PointWaterEnergyCreator.hh
 
file  PoissonBoltzmannEnergy.cc
 Ramachandran energy method class implementation.
 
file  PoissonBoltzmannEnergy.fwd.hh
 Ramachandran energy method class forward declaration.
 
file  PoissonBoltzmannEnergy.hh
 Membrane Environment Cbeta Energy.
 
file  PoissonBoltzmannEnergyCreator.hh
 
file  ProClosureEnergy.cc
 Proline ring closure energy method class implementation.
 
file  ProClosureEnergy.fwd.hh
 Proline ring closure energy method class forward declaration.
 
file  ProClosureEnergy.hh
 Proline ring closure energy method class declaration.
 
file  ProClosureEnergyCreator.hh
 Declaration for the class that connects ProClosureEnergy with the ScoringManager.
 
file  ProQ_Energy.cc
 ProQ energy function definition.
 
file  ProQ_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  ProQ_EnergyCreator.hh
 Declaration for the class that connects ProQ_Energy with the ScoringManager.
 
file  PyEnergy.hh
 Various Energy classes for subclassing in PyRosetta.
 
file  RamachandranEnergy.cc
 Ramachandran energy method class implementation.
 
file  RamachandranEnergy.fwd.hh
 Ramachandran energy method class forward declaration.
 
file  RamachandranEnergy.hh
 Ramachandran energy method class declaration.
 
file  RamachandranEnergy2B.cc
 
file  RamachandranEnergy2B.fwd.hh
 
file  RamachandranEnergy2B.hh
 Ramachandran energy method class declaration.
 
file  RamachandranEnergy2BCreator.hh
 Declaration for the class that connects RamachandranEnergy2B with the ScoringManager.
 
file  RamachandranEnergyCreator.hh
 Declaration for the class that connects RamachandranEnergy with the ScoringManager.
 
file  RamaPreProEnergy.cc
 A variation on the Ramachandran scorefunction that has separate probability tables for residues that precede prolines.
 
file  RamaPreProEnergy.fwd.hh
 
file  RamaPreProEnergy.hh
 A variation on the Ramachandran scorefunction that has separate probability tables for residues that precede prolines.
 
file  RamaPreProEnergyCreator.hh
 Declaration for the class that connects RamaPreProEnergy with the ScoringManager.
 
file  ReferenceEnergy.cc
 
file  ReferenceEnergy.fwd.hh
 Reference energy method forward declaration.
 
file  ReferenceEnergy.hh
 Reference energy method implementation.
 
file  ReferenceEnergyCreator.hh
 Declaration for the class that connects ReferenceEnergy with the ScoringManager.
 
file  ReferenceEnergyNoncanonical.cc
 Reference energy method implementation.
 
file  ReferenceEnergyNoncanonical.fwd.hh
 Reference energy method forward declaration.
 
file  ReferenceEnergyNoncanonical.hh
 Reference energy method declaration.
 
file  ReferenceEnergyNoncanonicalCreator.hh
 Declaration for the class that connects ReferenceEnergyNoncanonical with the ScoringManager.
 
file  ResidualDipolarCouplingEnergy.cc
 RDC energy - comparing experimental RDC values to calculated values.
 
file  ResidualDipolarCouplingEnergy.fwd.hh
 
file  ResidualDipolarCouplingEnergy.hh
 RDC energy - comparing experimental RDC values to calculated values.
 
file  ResidualDipolarCouplingEnergy_Rohl.cc
 RDC energy - comparing experimental RDC values to calculated values.
 
file  ResidualDipolarCouplingEnergy_Rohl.hh
 
file  ResidualDipolarCouplingEnergy_RohlCreator.hh
 Declaration for the class that connects ResidualDipolarCouplingEnergy_Rohl with the ScoringManager.
 
file  ResidualDipolarCouplingEnergyCreator.hh
 Declaration for the class that connects ResidualDipolarCouplingEnergy with the ScoringManager.
 
file  RG_Energy_Fast.cc
 Radius of gyration energy function definition.
 
file  RG_Energy_Fast.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RG_Energy_FastCreator.hh
 Declaration for the class that connects RG_Energy_Fast with the ScoringManager.
 
file  RG_Energy_RNA.cc
 
file  RG_Energy_RNA.hh
 
file  RG_Energy_RNACreator.hh
 Declaration for the class that connects RG_Energy_RNA with the ScoringManager.
 
file  RG_LocalEnergy.cc
 Radius of gyration for local region.
 
file  RG_LocalEnergy.hh
 only calculates RG the length of the repeat. Uses code from RG_Energy_fast
 
file  RG_LocalEnergyCreator.hh
 
file  RingClosureEnergy.cc
 Noncanonical ring closure energy method class implementation.
 
file  RingClosureEnergy.fwd.hh
 Noncanonical ring closure energy method class forward declaration.
 
file  RingClosureEnergy.hh
 Noncanonical ring closure energy method class headers.
 
file  RingClosureEnergyCreator.hh
 Declaration for the class that connects RingClosureEnergy with the ScoringManager.
 
file  RMS_Energy.cc
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  RMS_Energy.hh
 RMS Energy function. Used to optimize the RMSD between two structures.
 
file  RMS_EnergyCreator.hh
 Declaration for the class that connects RMS_Energy with the ScoringManager.
 
file  RNA_BulgeEnergy.cc
 
file  RNA_BulgeEnergy.fwd.hh
 
file  RNA_BulgeEnergy.hh
 
file  RNA_BulgeEnergyCreator.hh
 Declaration for the class that connects RNA_BulgeEnergy with the ScoringManager.
 
file  RNA_ChemicalMappingEnergy.cc
 
file  RNA_ChemicalMappingEnergy.fwd.hh
 
file  RNA_ChemicalMappingEnergy.hh
 
file  RNA_ChemicalMappingEnergyCreator.hh
 
file  RNA_ChemicalShiftEnergy.cc
 Energy score based on the agreement between experimentally determined and theoretically calculated NMR chemical_shift.
 
file  RNA_ChemicalShiftEnergy.hh
 Energy score based on the agreement between experimentally determined and theoretically calculated NMR chemical_shift.
 
file  RNA_ChemicalShiftEnergyCreator.hh
 
file  RNA_DataBackboneEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  RNA_DataBackboneEnergy.fwd.hh
 
file  RNA_DataBackboneEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  RNA_DataBackboneEnergyCreator.hh
 
file  RNA_FA_ElecEnergy.cc
 Electrostatics energy method for RNA class implementation.
 
file  RNA_FA_ElecEnergy.fwd.hh
 Electrostatics for RNA class forward declaration.
 
file  RNA_FA_ElecEnergy.hh
 
file  RNA_FA_ElecEnergyCreator.hh
 Declaration for the class that connects RNA_FA_ElecEnergy with the ScoringManager.
 
file  RNA_FullAtomStackingEnergy.cc
 
file  RNA_FullAtomStackingEnergy.fwd.hh
 
file  RNA_FullAtomStackingEnergy.hh
 
file  RNA_FullAtomStackingEnergyCreator.hh
 Declaration for the class that connects RNA_FullAtomStackingEnergy with the ScoringManager.
 
file  RNA_FullAtomVDW_BasePhosphate.cc
 
file  RNA_FullAtomVDW_BasePhosphate.fwd.hh
 
file  RNA_FullAtomVDW_BasePhosphate.hh
 FullAtom VDW energy between the base and phosphate group in the same (intra) nucleotide.
 
file  RNA_FullAtomVDW_BasePhosphateCreator.fwd.hh
 
file  RNA_FullAtomVDW_BasePhosphateCreator.hh
 
file  RNA_JR_SuiteEnergy.cc
 
file  RNA_JR_SuiteEnergy.fwd.hh
 
file  RNA_JR_SuiteEnergy.hh
 
file  RNA_JR_SuiteEnergyCreator.hh
 
file  RNA_LJ_BaseEnergy.cc
 
file  RNA_LJ_BaseEnergy.fwd.hh
 
file  RNA_LJ_BaseEnergy.hh
 
file  RNA_LJ_BaseEnergyCreator.hh
 Declaration for the class that connects RNA_LJ_BaseEnergy with the ScoringManager.
 
file  RNA_MgPointEnergy.cc
 Statistically derived Mg(2+) binding potential for RNA.
 
file  RNA_MgPointEnergy.hh
 Statistically derived Mg(2+) binding potential for RNA.
 
file  RNA_MgPointEnergyCreator.hh
 Declaration for the class that connects RNA_MgPointEnergy with the ScoringManager.
 
file  RNA_PairwiseLowResolutionEnergy.cc
 
file  RNA_PairwiseLowResolutionEnergy.fwd.hh
 
file  RNA_PairwiseLowResolutionEnergy.hh
 
file  RNA_PairwiseLowResolutionEnergyCreator.hh
 Declaration for the class that connects RNA_PairwiseLowResolutionEnergy with the ScoringManager.
 
file  RNA_PartitionEnergy.cc
 
file  RNA_PartitionEnergy.hh
 
file  RNA_PartitionEnergyCreator.hh
 Declaration for the class that connects RNA_PartitionEnergy with the ScoringManager.
 
file  RNA_StubCoordinateEnergy.cc
 
file  RNA_StubCoordinateEnergy.fwd.hh
 
file  RNA_StubCoordinateEnergy.hh
 
file  RNA_StubCoordinateEnergyCreator.hh
 Declaration for the class that connects RNA_StubCoordinateEnergy with the ScoringManager.
 
file  RNA_SugarCloseEnergy.cc
 
file  RNA_SugarCloseEnergy.fwd.hh
 
file  RNA_SugarCloseEnergy.hh
 
file  RNA_SugarCloseEnergyCreator.hh
 Declaration for the class that connects RNA_SugarCloseEnergy with the ScoringManager.
 
file  RNA_SuiteEnergy.cc
 
file  RNA_SuiteEnergy.fwd.hh
 
file  RNA_SuiteEnergy.hh
 
file  RNA_SuiteEnergyCreator.hh
 Declaration for the class that connects RNA_ChemicalMappingEnergy with the ScoringManager.
 
file  RNA_TorsionEnergy.cc
 
file  RNA_TorsionEnergy.fwd.hh
 
file  RNA_TorsionEnergy.hh
 
file  RNA_TorsionEnergyCreator.hh
 Declaration for the class that connects RNA_TorsionEnergy with the ScoringManager.
 
file  RNA_VDW_Energy.cc
 
file  RNA_VDW_Energy.fwd.hh
 
file  RNA_VDW_Energy.hh
 
file  RNA_VDW_EnergyCreator.hh
 Declaration for the class that connects RNA_VDW_Energy with the ScoringManager.
 
file  RNP_LowResEnergy.cc
 
file  RNP_LowResEnergy.fwd.hh
 
file  RNP_LowResEnergy.hh
 
file  RNP_LowResEnergyCreator.hh
 Energy method creator for the low resolution RNA/protein potential.
 
file  RNP_LowResPairDistEnergy.cc
 
file  RNP_LowResPairDistEnergy.fwd.hh
 
file  RNP_LowResPairDistEnergy.hh
 
file  RNP_LowResPairDistEnergyCreator.hh
 Energy method creator for the low resolution RNA/protein potential.
 
file  RNP_LowResStackEnergy.cc
 
file  RNP_LowResStackEnergy.fwd.hh
 
file  RNP_LowResStackEnergy.hh
 
file  RNP_LowResStackEnergyCreator.hh
 Energy method creator for the low resolution RNA/protein potential.
 
file  SA_Energy.cc
 sa energy function definition.
 
file  SA_Energy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  SA_EnergyCreator.hh
 
file  SASAEnergy.cc
 Power Diagram-derived solvent-accessible surface area energy.
 
file  SASAEnergy.fwd.hh
 Power Diagram-derived solvent-accessible surface area energy.
 
file  SASAEnergy.hh
 Power Diagram-derived solvent-accessible surface area energy.
 
file  SASAEnergyCreator.hh
 Declaration for the class that connects SASAEnergy with the ScoringManager.
 
file  SAXSEnergy.cc
 FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010)
 
file  SAXSEnergy.hh
 
file  SAXSEnergyCEN.hh
 
file  SAXSEnergyCreator.hh
 Declaration for the class that connects SAXSEnergyCreator with the ScoringManager.
 
file  SAXSEnergyCreatorCEN.cc
 
file  SAXSEnergyCreatorCEN.hh
 Declaration for the class that connects SAXSEnergyCreatorCEN with the ScoringManager.
 
file  SAXSEnergyCreatorFA.cc
 
file  SAXSEnergyCreatorFA.hh
 Declaration for the class that connects SAXSEnergyCreatorFA with the ScoringManager.
 
file  SAXSEnergyFA.hh
 
file  SecondaryStructureEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  SecondaryStructureEnergy.fwd.hh
 
file  SecondaryStructureEnergy.hh
 Statistically derived rotamer pair potential class declaration.
 
file  SecondaryStructureEnergyCreator.hh
 Declaration for the class that connects SecondaryStructureEnergy with the ScoringManager.
 
file  SequenceDependentRefEnergy.cc
 
file  SequenceDependentRefEnergy.fwd.hh
 Reference energy method forward declaration.
 
file  SequenceDependentRefEnergy.hh
 Reference energy method implementation.
 
file  SequenceDependentRefEnergyCreator.hh
 Declaration for the class that connects SequenceDependentRefEnergy with the ScoringManager.
 
file  SmoothCenPairEnergy.cc
 Smooth, differentiable, version of cenpair.
 
file  SmoothCenPairEnergy.hh
 
file  SmoothCenPairEnergyCreator.hh
 
file  SmoothEnvEnergy.cc
 Smooth, differentiable, version of centroid env.
 
file  SmoothEnvEnergy.hh
 
file  SmoothEnvEnergyCreator.hh
 
file  SplitUnfoldedTwoBodyEnergy.cc
 Split unfolded energy two body energy method.
 
file  SplitUnfoldedTwoBodyEnergy.fwd.hh
 Forward header for energy method for the two body portion of the split unfolded energy.
 
file  SplitUnfoldedTwoBodyEnergy.hh
 Header for the split unfolded energy two body component energy method.
 
file  SplitUnfoldedTwoBodyEnergyCreator.cc
 
file  SplitUnfoldedTwoBodyEnergyCreator.hh
 Energy creator for the split unfolded two body energy method.
 
file  SSElementMotifContactEnergy.cc
 
file  SSElementMotifContactEnergy.h
 
file  SSElementMotifContactEnergy.hh
 Will's motif score to determine how well packed the protein core is.
 
file  SSElementMotifContactEnergyCreator.hh
 
file  StackElecEnergy.cc
 
file  StackElecEnergy.fwd.hh
 
file  StackElecEnergy.hh
 
file  StackElecEnergyCreator.hh
 Declaration for the class that connects StackElecEnergy with the ScoringManager.
 
file  SuckerEnergy.cc
 Statistically derived rotamer pair potential class implementation.
 
file  SuckerEnergy.fwd.hh
 Statistically derived rotamer pair potential class forward declaration.
 
file  SuckerEnergy.hh
 energy attracting atoms to sucker atoms
 
file  SuckerEnergyCreator.hh
 Declaration for the class that connects SuckerEnergy with the ScoringManager.
 
file  SugarBackboneEnergy.cc
 
file  SugarBackboneEnergy.fwd.hh
 Forward declarations for SugarBackboneEnergy.
 
file  SugarBackboneEnergy.hh
 Method definitions for SugarBackboneEnergy and SugarBackboneEnergyCreator.
 
file  SugarBackboneEnergyCreator.hh
 
file  SurfEnergy.cc
 Packing Score.
 
file  SurfEnergy.hh
 Packing Score.
 
file  SurfEnergyCreator.hh
 Declaration for the class that connects SurfEnergy with the ScoringManager.
 
file  SurfVolEnergy.cc
 Packing Score.
 
file  SurfVolEnergy.hh
 
file  SurfVolEnergyCreator.hh
 Declaration for the class that connects SurfVolEnergy 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  TNA_SuiteEnergy.cc
 
file  TNA_SuiteEnergy.fwd.hh
 
file  TNA_SuiteEnergy.hh
 
file  TNA_SuiteEnergyCreator.hh
 Declaration for the class that connects TNA_SuiteEnergy with the ScoringManager.
 
file  UnfoldedStateEnergy.cc
 Unfolded state energy method implementation; energies based on eneriges of residues in fragments.
 
file  UnfoldedStateEnergy.fwd.hh
 Unfolded state energy method, forward declaration.
 
file  UnfoldedStateEnergy.hh
 Unfolded state energy declaration header file.
 
file  UnfoldedStateEnergyCreator.hh
 Declaration for the class that connects UnfoldedStateEnergy with the ScoringManager.
 
file  VdWTinkerEnergy.cc
 VdW treatment using buffered 14-7 approach in Tinker/Amoeba.
 
file  VdWTinkerEnergy.fwd.hh
 
file  VdWTinkerEnergy.hh
 
file  VdWTinkerEnergyCreator.hh
 Declaration for the class that connects VdWTinkerEnergy with the ScoringManager.
 
file  WaterAdductHBondEnergy.cc
 
file  WaterAdductHBondEnergy.fwd.hh
 
file  WaterAdductHBondEnergy.hh
 
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  WaterSpecificEnergy.cc
 
file  WaterSpecificEnergy.fwd.hh
 
file  WaterSpecificEnergy.hh
 Energetic considerations for explicit water molecules,.
 
file  WaterSpecificEnergyCreator.hh
 Declaration for the class that connects WaterSpecificEnergy with the ScoringManager.
 
file  XtalMLEnergy.cc
 
file  XtalMLEnergy.hh
 
file  XtalMLEnergyCreator.hh
 ML target.
 
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