|
| 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 | 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 | branch_energy_util.cc |
| |
| file | branch_energy_util.hh |
| |
| 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 | 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 | 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 | chainbreak_util.cc |
| | Utility functions for scoring chainbreaks.
|
| |
| file | chainbreak_util.hh |
| | Utility functions for scoring chainbreaks.
|
| |
| 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | FreeDOF_Options.cc |
| |
| file | FreeDOF_Options.fwd.hh |
| |
| file | FreeDOF_Options.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 | 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 | 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 | 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 | 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 | Methods.hh |
| | Energy Method enumeration.
|
| |
| 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 | 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 | 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 | 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 | 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 | NMerSVMEnergy.cc |
| | SVM sequence profile energy method implementation.
|
| |
| file | NMerSVMEnergy.fwd.hh |
| | SVMerence energy method forward declaration.
|
| |
| file | NMerSVMEnergy.hh |
| | SVM energy method declaration.
|
| |
| file | NMerSVMEnergyCreator.hh |
| | Declaration for the class that connects NMerSVMEnergy 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 | 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 |
| | 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 | 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 | 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 | 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_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 | 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 | 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 | 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 | 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 functions for the distance-dependent dielectric potential.
|
| |
| file | VdWTinkerEnergy.cc |
| | VdW treatment using buffered 14-7 approach in Tinker/Amoeba.
|
| |
| file | VdWTinkerEnergy.fwd.hh |
| |
| file | VdWTinkerEnergy.hh |
| | VdW replacement using buffered 14-7 approach in Tinker/Amoeba.
|
| |
| file | VdWTinkerEnergyCreator.hh |
| | Declaration for the class that connects VdWTinkerEnergy 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 | 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 | 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 |
| |
1.8.7