|
Rosetta
|
Classes | |
| class | APBSWrapper |
| class | PQR |
| class | APBSResult |
| class | APBSConfig |
| class | AtomVDW |
| class | CenHBPotential |
| class | CenRotEnvPairPotential |
| class | ChemicalShiftAnisotropy |
| ChemicalShiftAnisotropys are mainly handled by this class @detail related classed: CSA — a single line in an CSA file - representing a single csa coupling ChemicalShiftAnisotropyEnergy – an energy method which triggers computations handled by this class. More... | |
| class | CSA |
| class | ContextGraph |
| class | ContextGraphFactory |
| class | DenseNeighborIterator |
| class | DenseNeighborConstIterator |
| class | DenseEnergyContainer |
| class | DensityZscoresStatsSetup |
| class | DerivVectorPair |
| A glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms. More... | |
| class | DipolarCoupling |
| DipolarCouplings are mainly handled by this class @detail related classed: DC — a single line in an DC file - representing a single dc coupling DipolarCouplingEnergy – an energy method which triggers computations handled by this class. More... | |
| class | DC |
| class | DockingScoreFunction |
| class | Energies |
| A cached energies object. More... | |
| class | EnergyNode |
| class | EnergyEdge |
| class | EnergyGraph |
| Class to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight. The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation. This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method. More... | |
| class | EMapVector |
| A vector for storing energy data, initially all values are 0. More... | |
| class | CenListInfo |
| Keep track of the cenlist information. More... | |
| class | EnvPairPotential |
| class | GenBornResidueInfo |
| class | GenBornPoseInfo |
| class | GenBornRotamerSetInfo |
| class | GenBornPotential |
| class | BondOrderParser |
| class | SpringParams |
| Parameter set for one torsion angle. More... | |
| class | GenTorsionParams |
| Parameter set for one torsion angle. More... | |
| class | GenericBondedPotential |
| Potential for core/scoring/methods/GenericBondedEnergy method. More... | |
| class | ResidueExclParams |
| class | GenBondedExclInfo |
| struct | TorsionParams |
| class | HydroxylTorsionPotential |
| class | lDDT_Calculator |
| Calculate the lDDT between the reference and the model. https://dx.doi.org/10.1093/bioinformatics/btt473 Uses the same defaults as https://swissmodel.expasy.org/lddt/ Not implemented is any consideration for stereochemical/bond/angle deviation penalties. More... | |
| class | ResidueNeighborIterator |
| class | ResidueNeighborConstIterator |
| class | LREnergyContainer |
| class | Membrane_FAEmbed |
| Membrane Fullatom embedding info. More... | |
| class | Membrane_FAPotential |
| Mmebrane Fullatom Potential - Scoring Class. More... | |
| class | MembraneEmbed |
| Whole Pose Membrane Embedding. More... | |
| class | MembranePotential |
| Rosetta Membrane Low Resolution Scoring Methods. More... | |
| class | MembraneTopology |
| class | ResSingleMinimizationData |
| class | ResPairMinimizationData |
| class | MinimizationNode |
| class | MinimizationEdge |
| class | MinimizationGraph |
| Class to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity. More... | |
| class | MinScoreScoreFunction |
| class | MultipoleElecResidueInfo |
| class | MultipoleElecPoseInfo |
| class | MultipoleElecRotamerSetInfo |
| class | MultipoleParameter |
| class | MultipoleElecPotential |
| class | AtomNeighbor |
| an atom-atom neighborlist object More... | |
| class | NeighborList |
| class | OmegaTether |
| class | OneDDistPotential |
| class | OneToAllNeighborIterator |
| class | OneToAllNeighborConstIterator |
| class | OneToAllEnergyContainer |
| class | P_AA |
| class | P_AA_ABEGO3 |
| class | P_AA_ss |
| class | PairEPotential |
| struct | tableID |
| class | PointWaterPotential |
| class | PoissonBoltzmannPotential |
| class | PolymerBondedNeighborIterator |
| class | PolymerBondedNeighborConstIterator |
| class | PolymerBondedEnergyContainer |
| class | ProQPotential |
| class | Ramachandran |
| class | Ramachandran2B |
| class | RamaPrePro |
| class | data_struct |
| class | ResidualDipolarCoupling |
| ResidualDipolarCouplings are mainly handled by this class @detail related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy – an energy method which triggers computations handled by this class. More... | |
| class | RDC |
| class | ResidualDipolarCoupling_Rohl |
| class | RDC_Rohl |
| class | SmallAtNb |
| class | ResidueNblistData |
| class | ResiduePairNeighborList |
| class | Predicate |
| class | IsProteinCAPredicate |
| class | IsMainAtomPredicate |
| class | IsHeavyAtomPredicate |
| class | IsProteinBackbonePredicate |
| class | IsProteinBackboneIncludingOPredicate |
| class | IsSpecificAtomsPredicate |
| class | ResRangePredicate |
| class | SelectedResPredicate |
| class | ExcludedResPredicate |
| class | PDatom |
| class | PDvertex |
| class | PDinter |
| class | SAnode |
| class | SASAPotential |
| class | ScoreFunction |
| This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated. More... | |
| struct | ScoreFunctionKey |
| A key for looking up previously-loaded scorefunctions (which the ScoreFunctionFactory stores in a map of owning pointers indexed by keys of this type). More... | |
| class | ScoreFunctionFactory |
| A static singleton for making a single score_function. More... | |
| class | ScoreFunctionInfo |
| Info on the scorefunction settings. More... | |
| class | ScoreTypeManager |
| class | ScoringManager |
| class | DimerPairing |
| class | SecondaryStructurePotential |
| secondary structure scoring cut from classic rosetta structure.h/structure.cc More... | |
| class | SecondaryStructureWeights |
| Holds weights and flags for configuring a SecondaryStructureEnergy evaluation. More... | |
| class | SigmoidWeightedCenList |
| Keep track of the cenlist information stores both centroid counts (T = Real) as well as d_centroid_counts (T = Vector) More... | |
| class | SmoothScoreTermCoeffs |
| class | SmoothEnvPairPotential |
| class | SplitUnfoldedTwoBodyPotential |
| class | BB_Pos |
| struct | Strands |
| struct | Helices |
| class | SS_Info |
| struct | Hairpin |
| struct | Hairpins |
| class | SS_Killhairpins_Info |
| class | TenANeighborNode |
| class | TenANeighborEdge |
| class | TenANeighborGraph |
| class | TMscoreStore |
| class | TMscore |
| class | TwelveANeighborNode |
| class | TwelveANeighborEdge |
| class | TwelveANeighborGraph |
| class | UnfoldedStatePotential |
| class | VdWTinkerResidueInfo |
| class | VdWTinkerPoseInfo |
| class | VdWTinkerRotamerSetInfo |
| class | VdWTinkerPotential |
| class | WaterAdductHBondPotential |
Typedefs | |
| typedef utility::pointer::shared_ptr< APBSWrapper > | APBSWrapperOP |
| typedef utility::pointer::shared_ptr< APBSWrapper const > | APBSWrapperCOP |
| typedef utility::pointer::weak_ptr< APBSWrapper > | APBSWrapperAP |
| typedef utility::pointer::weak_ptr< APBSWrapper const > | APBSWrapperCAP |
| typedef utility::pointer::shared_ptr< APBSConfig > | APBSConfigOP |
| typedef utility::pointer::shared_ptr< APBSConfig const > | APBSConfigCOP |
| typedef utility::pointer::weak_ptr< APBSConfig > | APBSConfigAP |
| typedef utility::pointer::weak_ptr< APBSConfig const > | APBSConfigCAP |
| typedef utility::pointer::shared_ptr< APBSResult > | APBSResultOP |
| typedef utility::pointer::shared_ptr< APBSResult const > | APBSResultCOP |
| typedef utility::pointer::weak_ptr< APBSResult > | APBSResultAP |
| typedef utility::pointer::weak_ptr< APBSResult const > | APBSResultCAP |
| typedef utility::pointer::shared_ptr< PQR > | PQROP |
| typedef utility::pointer::shared_ptr< PQR const > | PQRCOP |
| typedef utility::pointer::weak_ptr< PQR > | PQRAP |
| typedef utility::pointer::weak_ptr< PQR const > | PQRCAP |
| typedef utility::pointer::shared_ptr< AtomVDW > | AtomVDWOP |
| typedef utility::pointer::shared_ptr< AtomVDW const > | AtomVDWCOP |
| typedef utility::pointer::shared_ptr< CenHBPotential > | CenHBPotentialOP |
| typedef utility::pointer::shared_ptr< CenHBPotential const > | CenHBPotentialCOP |
| typedef utility::pointer::shared_ptr< CenRotEnvPairPotential > | CenRotEnvPairPotentialOP |
| typedef utility::pointer::shared_ptr< CenRotEnvPairPotential const > | CenRotEnvPairPotentialCOP |
| typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropy > | ChemicalShiftAnisotropyOP |
| typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropy const > | ChemicalShiftAnisotropyCOP |
| typedef utility::pointer::shared_ptr< ContextGraph > | ContextGraphOP |
| typedef utility::pointer::shared_ptr< ContextGraph const > | ContextGraphCOP |
| typedef utility::pointer::shared_ptr< DenseNeighborIterator > | DenseNeighborIteratorOP |
| typedef utility::pointer::shared_ptr< DenseEnergyContainer > | DenseEnergyContainerOP |
| typedef std::map< std::string, std::map< core::Real, core::Real > > | DensZScoreMap |
| private methods /// More... | |
| typedef utility::pointer::shared_ptr< DensityZscoresStatsSetup > | DensityZscoresStatsSetupOP |
| typedef utility::pointer::shared_ptr< DensityZscoresStatsSetup const > | DensityZscoresStatsSetupCOP |
| typedef utility::pointer::shared_ptr< DipolarCoupling > | DipolarCouplingOP |
| typedef utility::pointer::shared_ptr< DipolarCoupling const > | DipolarCouplingCOP |
| typedef utility::pointer::shared_ptr< DockingScoreFunction > | DockingScoreFunctionOP |
| typedef utility::pointer::shared_ptr< DockingScoreFunction const > | DockingScoreFunctionCOP |
| typedef utility::pointer::shared_ptr< Energies > | EnergiesOP |
| typedef utility::pointer::shared_ptr< Energies const > | EnergiesCOP |
| typedef utility::pointer::shared_ptr< EnergyGraph > | EnergyGraphOP |
| typedef EMapVector | EnergyMap |
| typedef utility::pointer::shared_ptr< CenListInfo > | CenListInfoOP |
| typedef utility::pointer::shared_ptr< EnvPairPotential > | EnvPairPotentialOP |
| typedef utility::pointer::shared_ptr< EnvPairPotential const > | EnvPairPotentialCOP |
| typedef utility::pointer::shared_ptr< GenBornResidueInfo > | GenBornResidueInfoOP |
| typedef utility::pointer::shared_ptr< GenBornPoseInfo > | GenBornPoseInfoOP |
| typedef utility::pointer::shared_ptr< GenBornRotamerSetInfo > | GenBornRotamerSetInfoOP |
| typedef utility::pointer::shared_ptr< GenBornPotential > | GenBornPotentialOP |
| typedef utility::pointer::shared_ptr< GenBornPotential const > | GenBornPotentialCOP |
| typedef utility::pointer::shared_ptr< GenericBondedPotential > | GenericBondedPotentialOP |
| typedef utility::pointer::shared_ptr< ResidueExclParams > | ResidueExclParamsOP |
| typedef utility::pointer::shared_ptr< ResidueExclParams const > | ResidueExclParamsCOP |
| typedef utility::pointer::shared_ptr< GenBondedExclInfo > | GenBondedExclInfoOP |
| typedef utility::pointer::shared_ptr< GenBondedExclInfo const > | GenBondedExclInfoCOP |
| typedef utility::pointer::shared_ptr< HydroxylTorsionPotential > | HydroxylTorsionPotentialOP |
| typedef utility::pointer::shared_ptr< HydroxylTorsionPotential const > | HydroxylTorsionPotentialCOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborIterator > | ResidueNeighborIteratorOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborIterator const > | ResidueNeighborIteratorCOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborConstIterator > | ResidueNeighborConstIteratorOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborConstIterator const > | ResidueNeighborConstIteratorCOP |
| typedef utility::pointer::shared_ptr< LREnergyContainer > | LREnergyContainerOP |
| typedef utility::pointer::shared_ptr< LREnergyContainer const > | LREnergyContainerCOP |
| typedef utility::pointer::shared_ptr< Membrane_FAEmbed > | Membrane_FAEmbedOP |
| typedef utility::pointer::shared_ptr< Membrane_FAEmbed const > | Membrane_FAEmbedCOP |
| typedef utility::pointer::shared_ptr< Membrane_FAPotential > | Membrane_FAPotentialOP |
| typedef utility::pointer::shared_ptr< Membrane_FAPotential const > | Membrane_FAPotentialCOP |
| typedef utility::pointer::shared_ptr< MembraneEmbed > | MembraneEmbedOP |
| typedef utility::pointer::shared_ptr< MembraneEmbed const > | MembraneEmbedCOP |
| typedef utility::pointer::shared_ptr< MembranePotential > | MembranePotentialOP |
| typedef utility::pointer::shared_ptr< MembranePotential const > | MembranePotentialCOP |
| typedef utility::pointer::shared_ptr< MembraneTopology > | MembraneTopologyOP |
| typedef utility::pointer::shared_ptr< MembraneTopology const > | MembraneTopologyCOP |
| typedef utility::pointer::shared_ptr< PoissonBoltzmannPotential > | PoissonBoltzmannPotentialOP |
| typedef utility::pointer::shared_ptr< PoissonBoltzmannPotential const > | PoissonBoltzmannPotentialCOP |
| typedef utility::pointer::shared_ptr< ResSingleMinimizationData > | ResSingleMinimizationDataOP |
| typedef utility::pointer::shared_ptr< ResSingleMinimizationData const > | ResSingleMinimizationDataCOP |
| typedef utility::pointer::shared_ptr< ResPairMinimizationData > | ResPairMinimizationDataOP |
| typedef utility::pointer::shared_ptr< ResPairMinimizationData const > | ResPairMinimizationDataCOP |
| typedef utility::pointer::shared_ptr< MinimizationGraph > | MinimizationGraphOP |
| typedef utility::pointer::shared_ptr< MinimizationGraph const > | MinimizationGraphCOP |
| typedef utility::pointer::shared_ptr< MinScoreScoreFunction > | MinScoreScoreFunctionOP |
| typedef utility::pointer::shared_ptr< MinScoreScoreFunction const > | MinScoreScoreFunctionCOP |
| typedef utility::pointer::shared_ptr< MultipoleElecResidueInfo > | MultipoleElecResidueInfoOP |
| typedef utility::pointer::shared_ptr< MultipoleElecResidueInfo const > | MultipoleElecResidueInfoCOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPoseInfo > | MultipoleElecPoseInfoOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPoseInfo const > | MultipoleElecPoseInfoCOP |
| typedef utility::pointer::shared_ptr< MultipoleElecRotamerSetInfo > | MultipoleElecRotamerSetInfoOP |
| typedef utility::pointer::shared_ptr< MultipoleParameter > | MultipoleParameterOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPotential > | MultipoleElecPotentialOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPotential const > | MultipoleElecPotentialCOP |
| typedef utility::pointer::shared_ptr< NeighborList > | NeighborListOP |
| typedef utility::pointer::shared_ptr< NeighborList const > | NeighborListCOP |
| typedef utility::vector1< AtomNeighbor > | AtomNeighbors |
| typedef utility::pointer::shared_ptr< OmegaTether > | OmegaTetherOP |
| typedef utility::pointer::shared_ptr< OmegaTether const > | OmegaTetherCOP |
| typedef utility::pointer::shared_ptr< OneDDistPotential > | OneDDistPotentialOP |
| typedef utility::pointer::shared_ptr< OneDDistPotential const > | OneDDistPotentialCOP |
| typedef utility::pointer::shared_ptr< OneToAllNeighborIterator > | OneToAllNeighborIteratorOP |
| typedef utility::pointer::shared_ptr< OneToAllEnergyContainer > | OneToAllEnergyContainerOP |
| typedef utility::pointer::shared_ptr< P_AA > | P_AAOP |
| typedef utility::pointer::shared_ptr< P_AA const > | P_AACOP |
| typedef utility::pointer::shared_ptr< P_AA_ABEGO3 > | P_AA_ABEGO3_OP |
| typedef utility::pointer::shared_ptr< P_AA_ABEGO3 const > | P_AA_ABEGO3_COP |
| typedef utility::pointer::shared_ptr< P_AA_ss > | P_AA_ssOP |
| typedef utility::pointer::shared_ptr< P_AA_ss const > | P_AA_ssCOP |
| typedef utility::pointer::shared_ptr< PairEPotential > | PairEPotentialOP |
| typedef utility::pointer::shared_ptr< PairEPotential const > | PairEPotentialCOP |
| typedef utility::pointer::shared_ptr< PointWaterPotential > | PointWaterPotentialOP |
| typedef utility::pointer::shared_ptr< PointWaterPotential const > | PointWaterPotentialCOP |
| using | PB = PoissonBoltzmannPotential |
| typedef utility::pointer::weak_ptr< PoissonBoltzmannPotential > | PoissonBoltzmannPotentialAP |
| typedef utility::pointer::weak_ptr< PoissonBoltzmannPotential const > | PoissonBoltzmannPotentialCAP |
| typedef utility::pointer::shared_ptr< PolymerBondedNeighborIterator > | PolymerBondedNeighborIteratorOP |
| typedef utility::pointer::shared_ptr< const PolymerBondedNeighborIterator > | PolymerBondedNeighborIteratorCOP |
| typedef utility::pointer::shared_ptr< PolymerBondedEnergyContainer > | PolymerBondedEnergyContainerOP |
| typedef utility::pointer::shared_ptr< const PolymerBondedEnergyContainer > | PolymerBondedEnergyContainerCOP |
| typedef utility::pointer::shared_ptr< ProQPotential > | ProQPotentialOP |
| using | R = Ramachandran |
| typedef utility::pointer::shared_ptr< Ramachandran > | RamachandranOP |
| typedef utility::pointer::shared_ptr< Ramachandran const > | RamachandranCOP |
| typedef utility::pointer::shared_ptr< Ramachandran2B > | Ramachandran2BOP |
| typedef utility::pointer::shared_ptr< Ramachandran2B const > | Ramachandran2BCOP |
| typedef utility::pointer::shared_ptr< RamaPrePro > | RamaPreProOP |
| typedef utility::pointer::shared_ptr< RamaPrePro const > | RamaPreProCOP |
| typedef core::Real | matrix[3][3] |
| typedef core::Real | rvec[3] |
| typedef core::Real | rvec5[5] |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling > | ResidualDipolarCouplingOP |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling const > | ResidualDipolarCouplingCOP |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling_Rohl > | ResidualDipolarCoupling_RohlOP |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling_Rohl const > | ResidualDipolarCoupling_RohlCOP |
| typedef utility::pointer::shared_ptr< ResidueNblistData > | ResidueNblistDataOP |
| typedef utility::pointer::shared_ptr< ResidueNblistData const > | ResidueNblistDataCOP |
| typedef utility::pointer::shared_ptr< ResiduePairNeighborList > | ResiduePairNeighborListOP |
| typedef utility::pointer::shared_ptr< ResiduePairNeighborList const > | ResiduePairNeighborListCOP |
| typedef std::list< core::Size > | ResidueSelection |
| typedef utility::vector1< core::Size > | ResidueSelectionVector |
| typedef utility::pointer::shared_ptr< Predicate > | PredicateOP |
| typedef utility::pointer::shared_ptr< Predicate const > | PredicateCOP |
| typedef utility::pointer::shared_ptr< PDatom > | PDatomOP |
| typedef utility::pointer::shared_ptr< PDatom const > | PDatomCOP |
| typedef utility::pointer::shared_ptr< PDvertex > | PDvertexOP |
| typedef utility::pointer::shared_ptr< PDvertex const > | PDvertexCOP |
| typedef utility::pointer::shared_ptr< PDinter > | PDinterOP |
| typedef utility::pointer::shared_ptr< PDinter const > | PDinterCOP |
| typedef utility::pointer::shared_ptr< SASAPotential > | SASAPotentialOP |
| typedef utility::pointer::shared_ptr< SASAPotential const > | SASAPotentialCOP |
| typedef numeric::xyzVector< core::Real > | Vector |
| typedef numeric::xyzMatrix< core::Real > | Matrix |
| typedef utility::pointer::shared_ptr< ScoreFunction > | ScoreFunctionOP |
| typedef utility::pointer::shared_ptr< ScoreFunction const > | ScoreFunctionCOP |
| typedef utility::pointer::shared_ptr< ScoreFunctionInfo > | ScoreFunctionInfoOP |
| typedef utility::pointer::shared_ptr< ScoreFunctionInfo const > | ScoreFunctionInfoCOP |
| typedef utility::vector1< ScoreType > | ScoreTypes |
| using | DimerPairingOP = utility::pointer::shared_ptr< DimerPairing > |
| typedef utility::pointer::shared_ptr< SecondaryStructurePotential > | SecondaryStructurePotentialOP |
| typedef utility::pointer::shared_ptr< SecondaryStructurePotential const > | SecondaryStructurePotentialCOP |
| typedef utility::pointer::shared_ptr< SigmoidWeightedCenList< Real > > | SigmoidWeightedCenListRealOP |
| typedef utility::pointer::shared_ptr< SigmoidWeightedCenList< numeric::xyzVector< Real > > > | SigmoidWeightedCenListVectorOP |
| typedef utility::pointer::shared_ptr< SmoothEnvPairPotential > | SmoothEnvPairPotentialOP |
| typedef utility::pointer::shared_ptr< SmoothEnvPairPotential const > | SmoothEnvPairPotentialCOP |
| typedef utility::pointer::shared_ptr< SplitUnfoldedTwoBodyPotential > | SplitUnfoldedTwoBodyPotentialOP |
| typedef utility::pointer::shared_ptr< SS_Info > | SS_InfoOP |
| typedef utility::pointer::shared_ptr< SS_Info const > | SS_InfoCOP |
| typedef utility::pointer::shared_ptr< SS_Killhairpins_Info > | SS_Killhairpins_InfoOP |
| typedef utility::pointer::shared_ptr< SS_Killhairpins_Info const > | SS_Killhairpins_InfoCOP |
| typedef utility::pointer::shared_ptr< TenANeighborGraph > | TenANeighborGraphOP |
| typedef utility::pointer::shared_ptr< TenANeighborGraph const > | TenANeighborGraphCOP |
| typedef utility::pointer::shared_ptr< TwelveANeighborGraph > | TwelveANeighborGraphOP |
| typedef utility::pointer::shared_ptr< TwelveANeighborGraph const > | TwelveANeighborGraphCOP |
| typedef core::Real | Probability |
| typedef Real | Weight |
| typedef Real | Score |
| typedef float | TableEnergy |
| typedef float | TableProbability |
| typedef ObjexxFCL::CArray< Energy > | CArray_Energy |
| typedef ObjexxFCL::CArrayP< Energy > | CArrayP_Energy |
| typedef ObjexxFCL::CArray< TableEnergy > | CArray_TableEnergy |
| typedef ObjexxFCL::CArrayP< TableEnergy > | CArrayP_TableEnergy |
| typedef ObjexxFCL::FArray1D< Length > | FArray1D_Length |
| typedef ObjexxFCL::FArray2D< Length > | FArray2D_Length |
| typedef ObjexxFCL::FArray3D< Length > | FArray3D_Length |
| typedef ObjexxFCL::FArray4D< Length > | FArray4D_Length |
| typedef ObjexxFCL::FArray5D< Length > | FArray5D_Length |
| typedef ObjexxFCL::FArray1D< Weight > | FArray1D_Weight |
| typedef ObjexxFCL::FArray2D< Weight > | FArray2D_Weight |
| typedef ObjexxFCL::FArray3D< Weight > | FArray3D_Weight |
| typedef ObjexxFCL::FArray4D< Weight > | FArray4D_Weight |
| typedef ObjexxFCL::FArray5D< Weight > | FArray5D_Weight |
| typedef ObjexxFCL::FArray1D< Energy > | FArray1D_Energy |
| typedef ObjexxFCL::FArray2D< Energy > | FArray2D_Energy |
| typedef ObjexxFCL::FArray3D< Energy > | FArray3D_Energy |
| typedef ObjexxFCL::FArray4D< Energy > | FArray4D_Energy |
| typedef ObjexxFCL::FArray5D< Energy > | FArray5D_Energy |
| typedef ObjexxFCL::FArray1D< TableEnergy > | FArray1D_TableEnergy |
| typedef ObjexxFCL::FArray2D< TableEnergy > | FArray2D_TableEnergy |
| typedef ObjexxFCL::FArray3D< TableEnergy > | FArray3D_TableEnergy |
| typedef ObjexxFCL::FArray4D< TableEnergy > | FArray4D_TableEnergy |
| typedef ObjexxFCL::FArray5D< TableEnergy > | FArray5D_TableEnergy |
| typedef ObjexxFCL::FArray2D< CArrayP_TableEnergy > | AtomPairEnergyTable |
| typedef ObjexxFCL::FArray1D< Probability > | FArray1D_Probability |
| typedef ObjexxFCL::FArray2D< Probability > | FArray2D_Probability |
| typedef ObjexxFCL::FArray3D< Probability > | FArray3D_Probability |
| typedef ObjexxFCL::FArray4D< Probability > | FArray4D_Probability |
| typedef ObjexxFCL::FArray5D< Probability > | FArray5D_Probability |
| typedef ObjexxFCL::FArray1D< TableProbability > | FArray1D_TableProbability |
| typedef ObjexxFCL::FArray2D< TableProbability > | FArray2D_TableProbability |
| typedef ObjexxFCL::FArray3D< TableProbability > | FArray3D_TableProbability |
| typedef ObjexxFCL::FArray4D< TableProbability > | FArray4D_TableProbability |
| typedef ObjexxFCL::FArray5D< TableProbability > | FArray5D_TableProbability |
| typedef ObjexxFCL::KeyFArray1D< Real > | KeyFArray1D_Real |
| typedef ObjexxFCL::KeyFArray2D< Real > | KeyFArray2D_Real |
| typedef ObjexxFCL::KeyFArray3D< Real > | KeyFArray3D_Real |
| typedef ObjexxFCL::KeyFArray1D< Weight > | KeyFArray1D_Weight |
| typedef ObjexxFCL::KeyFArray2D< Weight > | KeyFArray2D_Weight |
| typedef ObjexxFCL::KeyFArray3D< Weight > | KeyFArray3D_Weight |
| typedef ObjexxFCL::KeyFArray1D< Energy > | KeyFArray1D_Energy |
| typedef ObjexxFCL::KeyFArray2D< Energy > | KeyFArray2D_Energy |
| typedef ObjexxFCL::KeyFArray3D< Energy > | KeyFArray3D_Energy |
| typedef ObjexxFCL::KeyFArray1D< Probability > | KeyFArray1D_Probability |
| typedef ObjexxFCL::KeyFArray2D< Probability > | KeyFArray2D_Probability |
| typedef ObjexxFCL::KeyFArray3D< Probability > | KeyFArray3D_Probability |
| typedef utility::pointer::shared_ptr< UnfoldedStatePotential > | UnfoldedStatePotentialOP |
| typedef utility::pointer::shared_ptr< VdWTinkerResidueInfo > | VdWTinkerResidueInfoOP |
| typedef utility::pointer::shared_ptr< VdWTinkerResidueInfo const > | VdWTinkerResidueInfoCOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPoseInfo > | VdWTinkerPoseInfoOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPoseInfo const > | VdWTinkerPoseInfoCOP |
| typedef utility::pointer::shared_ptr< VdWTinkerRotamerSetInfo > | VdWTinkerRotamerSetInfoOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPotential > | VdWTinkerPotentialOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPotential const > | VdWTinkerPotentialCOP |
| typedef utility::pointer::shared_ptr< WaterAdductHBondPotential > | WaterAdductHBondPotentialOP |
| typedef utility::pointer::shared_ptr< WaterAdductHBondPotential const > | WaterAdductHBondPotentialCOP |
| typedef utility::pointer::shared_ptr< SetupPoissonBoltzmannPotential > | SetupPoissonBoltzmannPotentialOP |
| typedef utility::pointer::shared_ptr< SetupPoissonBoltzmannPotential const > | SetupPoissonBoltzmannPotentialCOP |
| typedef utility::pointer::weak_ptr< SetupPoissonBoltzmannPotential > | SetupPoissonBoltzmannPotentialAP |
| typedef utility::pointer::weak_ptr< SetupPoissonBoltzmannPotential const > | SetupPoissonBoltzmannPotentialCAP |
Functions | |
| static basic::Tracer | TR ("core.scoring.AtomVDW") |
| void | store_CSA_in_pose (ChemicalShiftAnisotropyOP csa_info, core::pose::Pose &pose) |
| ChemicalShiftAnisotropyCOP | retrieve_CSA_from_pose (core::pose::Pose const &pose) |
| ChemicalShiftAnisotropyOP | retrieve_CSA_from_pose (core::pose::Pose &pose) |
| std::ostream & | operator<< (std::ostream &out, CSA const &csa) |
| std::ostream & | operator<< (std::ostream &out, ChemicalShiftAnisotropy const &csa) |
| static Real const | BOGUS_ENERGY (99999.99) |
| DerivVectorPair | operator* (Real scale, DerivVectorPair const &dvp) |
| DerivVectorPair | operator* (DerivVectorPair const &dvp, Real scale) |
| void | store_DC_in_pose (DipolarCouplingOP dc_info, core::pose::Pose &pose) |
| DipolarCouplingCOP | retrieve_DC_from_pose (core::pose::Pose const &pose) |
| DipolarCouplingOP | retrieve_DC_from_pose (core::pose::Pose &pose) |
| std::ostream & | operator<< (std::ostream &out, DC const &dc) |
| std::ostream & | operator<< (std::ostream &out, DipolarCoupling const &dc) |
| std::string | element_string_dc (std::string const &atom) |
| std::ostream & | operator<< (std::ostream &out, const Energies &e) |
| std::ostream & | operator<< (std::ostream &ost, EMapVector const &emap) |
| output operator (index;value) More... | |
| template<class T , class T_Etable > | |
| void | residue_fast_pair_energy_attached_H (conformation::Residue const &res1, int const atomno1, conformation::Residue const &res2, Size const atomno2, Size const at1hbegin, Size const at1hend, Size const at2hbegin, Size const at2hend, T const &count_pair, T_Etable const &etable_energy, EnergyMap &emap) |
| class T must define More... | |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap, int res1_start, int res1_end, int res2_start, int res2_end) |
| templated atom pair energy calculations More... | |
| template<class T , class T_Etable > | |
| void | inline_intraresidue_atom_pair_energy (conformation::Residue const &res, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| intraresidue atom pair energy evaluations More... | |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_sidechain_whole (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_backbone_backbone (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| template<class T , class T_Etable > | |
| void | inline_residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &res1, conformation::Residue const &res2, T_Etable const &etable_energy, T const &count_pair, EnergyMap &emap) |
| static basic::Tracer | TR ("core.scoring.GenericBondedPotential") |
| uint64_t | get_parameter_hash (Size bondtypr, Size type1, Size type2, Size type3=0, Size type4=0) |
| compress 5 values into one unsigned int; use 12 bits for each More... | |
| core::Size | bin_from_bond (core::chemical::BondName bn, core::chemical::BondRingness br) |
| convert a bond type to a bin index More... | |
| utility::vector1< core::Size > | bondorders_map (std::string bt) |
| helper function to convert string specification of bondorders to indices More... | |
| static basic::Tracer | TR ("core.scoring.HydroxylTorsionPotential") |
| void | interpolate_value_and_deriv (ObjexxFCL::FArray1D< Real > const &potential, Real const &bin_width, Real const &r, Real &value, Real &deriv) |
| static basic::Tracer | TR ("core.scoring.lddt") |
| core::Real | lddt (core::pose::Pose const &ref, core::pose::Pose const &model, bool consider_alt=true) |
| Calculate the lDDT between two structures (1:1 residue correspondence) across all heavy atoms. If consider_alt is false, use the quicker algorithm which doesn't consider automorphic changes (e.g. PHE ring flips) More... | |
| utility::vector1< core::Real > | per_res_lddt (core::pose::Pose const &ref, core::pose::Pose const &model, bool consider_alt=true) |
| Calculate the per-residue lDDT between two structures (1:1 residue correspondence) across all heavy atoms. If consider_alt is false, use the quicker algorithm which doesn't consider automorphic changes (e.g. PHE ring flips) More... | |
| Membrane_FAEmbed const & | Membrane_FAEmbed_from_pose (pose::Pose const &pose) |
| Return a Const Reference to the Embedding Object from the Pose Cache. More... | |
| Membrane_FAEmbed & | nonconst_Membrane_FAEmbed_from_pose (pose::Pose &pose) |
| Return a Non Const Reference to the Embedding Object from the Pose Cache. More... | |
| MembraneEmbed const & | MembraneEmbed_from_pose (pose::Pose const &pose) |
| Add Const Membrane Embedding to the pose cache. More... | |
| MembraneEmbed & | nonconst_MembraneEmbed_from_pose (pose::Pose &pose) |
| Add a non const membrane embedding object to the pose cache. More... | |
| static basic::Tracer | TR ("core.scoring.MembraneTopology") |
| MembraneTopology const & | MembraneTopology_from_pose (pose::Pose const &pose) |
| MembraneTopology & | nonconst_MembraneTopology_from_pose (pose::Pose &pose) |
| void | eval_atom_derivatives_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap const &res_weights, utility::vector1< DerivVectorPair > &atom_derivs) |
| Evaluate the derivatives for all atoms on the input residue for the terms that apply to this residue (which are stored on the input minimization node). More... | |
| void | eval_res_onebody_energies_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| Deprecated. More... | |
| void | eval_atom_derivatives_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, ResSingleMinimizationData const &res1_min_data, ResSingleMinimizationData const &res2_min_data, pose::Pose const &pose, EnergyMap const &respair_weights, utility::vector1< DerivVectorPair > &r1atom_derivs, utility::vector1< DerivVectorPair > &r2atom_derivs) |
| void | eval_weighted_atom_derivatives_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, ResSingleMinimizationData const &res1_min_data, ResSingleMinimizationData const &res2_min_data, pose::Pose const &pose, EnergyMap const &respair_weights, utility::vector1< DerivVectorPair > &r1atom_derivs, utility::vector1< DerivVectorPair > &r2atom_derivs) |
| void | eval_res_pair_energy_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| Deprecated. More... | |
| Real | eval_dof_deriv_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, ScoreFunction const &sfxn, EnergyMap const &weights) |
| void | eval_weighted_res_onebody_energies_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap, EnergyMap &scratch_emap) |
| void | eval_weighted_res_pair_energy_for_minedge (MinimizationEdge const &min_edge, conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap, EnergyMap &scratch_emap) |
| Real | eval_weighted_dof_deriv_for_minnode (MinimizationNode const &min_node, conformation::Residue const &rsd, pose::Pose const &pose, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, ScoreFunction const &sfxn, EnergyMap const &weights) |
| void | create_and_store_atom_tree_minimization_graph_asym (ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose) |
| void | create_and_store_atom_tree_minimization_graph_symm (ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose) |
| void | create_and_store_atom_tree_minimization_graph (ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose) |
| bool | ShouldItCount (conformation::Residue const &rsd, Size const &atm) |
| void | get_damped_scale_factors (MultipoleParameter::MultipoleParameterOP const &mp_param1, MultipoleParameter::MultipoleParameterOP const &mp_param2, core::Real dist, core::Real &scale3, core::Real &scale5, core::Real &scale7) |
| void | get_damped_scale_factors_with_derivs (MultipoleParameter::MultipoleParameterOP const &mp_param1, MultipoleParameter::MultipoleParameterOP const &mp_param2, core::Real dist, core::Real &scale3, core::Real &scale5, core::Real &scale7, core::Real &dscale3_dr, core::Real &dscale5_dr, core::Real &dscale7_dr) |
| bool | same_polarization_group (core::conformation::Residue const &rsd1, MultipoleElecResidueInfo const &mp1, core::Size atm1, core::conformation::Residue const &rsd2, core::Size atm2) |
| static basic::Tracer | tr ("core.scoring.NeighborList") |
| void | get_minval_binwidth (numeric::MathNTensor< core::Real, 1 > const &T, utility::json_spirit::mObject const &json, utility::fixedsizearray1< numeric::Real, 1 > &minval, utility::fixedsizearray1< numeric::Real, 1 > &binwidth) |
| ABEGO_index | abego_to_index (char abego) |
| int | abego3aa_to_index (const char abego1, const char abego2, const char abego3, const core::chemical::AA aa_index) |
| int | abego3aa_to_index (const char abego1, const char abego2, const char abego3, const char aa) |
| static basic::Tracer | TR ("core.scoring.PolymerBondedEnergyContainer") |
| static basic::Tracer | TR_it ("core.scoring.PolymerBondedNeighborIterator") |
| std::ostream & | operator<< (std::ostream &os, PolymerBondedEnergyContainer const &t) |
| Operator to allow object to be summarized. More... | |
| static basic::Tracer | TR ("core.scoring.ProQPotential") |
| bool | polymeric_termini_incomplete (conformation::Residue res) |
| static basic::Tracer | T ("core.scoring.Ramachandran2B") |
| static basic::Tracer | TR ("core.scoring.RamaPrePro") |
| Real | sqr (Real x) |
| void | store_RDC_in_pose (ResidualDipolarCouplingOP rdc_info, core::pose::Pose &pose) |
| ResidualDipolarCouplingCOP | retrieve_RDC_from_pose (core::pose::Pose const &pose) |
| ResidualDipolarCouplingOP | retrieve_RDC_from_pose (core::pose::Pose &pose) |
| std::ostream & | operator<< (std::ostream &out, RDC const &rdc) |
| std::ostream & | operator<< (std::ostream &out, ResidualDipolarCoupling const &rdc) |
| std::string | element_string (std::string const &atom) |
| int | m_inv_gen (ResidualDipolarCoupling::Tensor5 const &m, int n, ResidualDipolarCoupling::Tensor5 &minv) |
| void | jacobi (ResidualDipolarCoupling::Tensor5 &a, ResidualDipolarCoupling::rvec5 &d, ResidualDipolarCoupling::Tensor5 &v, int &nrot) |
| void | jacobi3 (ResidualDipolarCoupling::Tensor &a, ResidualDipolarCoupling::rvec &d, ResidualDipolarCoupling::Tensor &v, int &nrot) |
| Real | iprod (const rvec a, const rvec b) |
| void | mvmul (matrix a, const rvec src, rvec dest) |
| int | compare_by_abs (const void *a, const void *b) |
| core::Real | frdc (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, const core::Real *par) |
| core::Real | frdcDa (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, core::Real const tensorDa, const core::Real *par) |
| core::Real | frdcR (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, core::Real const tensorR, const core::Real *par) |
| core::Real | frdcDaR (core::Real r0, core::Real r1, core::Real r2, core::Real rdcconst, core::Real const tensorDa, core::Real const tensorR, const core::Real *par) |
| void | evaluaterdc (const core::Real *par, int m_dat, const void *data, core::Real *fvec, int *) |
| template<class T > | |
| void | ROTATE (T &a, int i, int j, int k, int l, Real s, Real tau) |
| void | store_RDC_ROHL_in_pose (ResidualDipolarCoupling_RohlOP rdc_info, core::pose::Pose &pose) |
| ResidualDipolarCoupling_RohlCOP | retrieve_RDC_ROHL_from_pose (core::pose::Pose const &pose) |
| ResidualDipolarCoupling_RohlOP | retrieve_RDC_ROHL_from_pose (core::pose::Pose &pose) |
| static basic::Tracer | TR ("core.scoring.rms_util") |
| core::Real | gdtsc (const core::pose::Pose &ref, const core::pose::Pose &model, const std::map< core::Size, core::Size > &residues) |
| Returns a single, Global Distance Test-like value that measures the extent to which the functional ends of a model's sidechains agree with their counterparts in a given reference structure. More... | |
| core::Real | gdtha (const core::pose::Pose &ref, const core::pose::Pose &model, const std::map< core::Size, core::Size > &residues) |
| Returns the average fraction of residues superimposable under a series of distance thresholds– 0.5, 1.0, 2.0, and 4.0 Angstroms. More... | |
| void | invert_exclude_residues (Size nres, utility::vector1< int > const &exclude_list, ResidueSelection &residue_selection) |
| ResidueSelection | invert_exclude_residues (core::Size nres, utility::vector1< int > const &exclude_list) |
| Real | native_CA_rmsd (const core::pose::Pose &native_pose, const core::pose::Pose &pose) |
| Real | native_CA_gdtmm (const core::pose::Pose &native_pose, const core::pose::Pose &pose) |
| core::Real | automorphic_rmsd (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, bool superimpose) |
| RMSD between residues, accounting for automorphisms (symmetries). For example if you have something like a tyrosine, you won't get a higher rmsd just because you flipped the ring 180 degrees (Rocco). Does NOT include H atoms – they add lots of extra symmetries. More... | |
| core::Real | residue_rmsd_super (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< core::Size > const &atom_map, bool skip_hydro) |
| Calculate the RMSD between two residues, using the provided atom map. The atom map is indexed by rsd1 index, and give the corresponding rsd2 index. Use a value of 0 to omit the rsd pairing. Superimposes the residues (remove rigid-body rotational/translational component of the rmsd.) More... | |
| core::Real | residue_rmsd_nosuper (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< core::Size > const &atom_map, bool skip_hydro) |
| Calculate the RMSD between two residues, using the provided atom map. The atom map is indexed by rsd1 index, and give the corresponding rsd2 index. Use a value of 0 to omit the rsd pairing. Does not superimpose the residues. More... | |
| bool | is_protein_CA (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_protein_CA_or_equiv (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_protein_CA_or_CB (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_protein_backbone (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_protein_backbone_including_O (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_protein_sidechain_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_ligand_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_ligand_heavyatom_residues (core::conformation::Residue const &residue1, core::conformation::Residue const &, core::Size atomno) |
| bool | is_polymer_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_carbohydrate_ring_atom (core::pose::Pose const &pose1, core::pose::Pose const &, core::uint const resno, core::uint const atomno) |
| Return true is the pose residue and atom specified is a non-virtual, heavy ring atom of a carbohydrate. More... | |
| bool | is_non_peptide_heavy_atom (core::pose::Pose const &pose1, core::pose::Pose const &, core::uint const resno, core::uint const atomno) |
| Return true if the pose residues and atoms specified are non-peptide heavy atoms. More... | |
| bool | is_heavyatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_scatom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_nbr_atom (core::pose::Pose const &pose1, core::pose::Pose const &, core::Size resno, core::Size atomno) |
| bool | is_any_atom (core::pose::Pose const &, core::pose::Pose const &, core::Size, core::Size) |
| Returns true always. More... | |
| core::DistanceSquared | non_peptide_heavy_atom_RMSD (core::pose::Pose const &pose1, core::pose::Pose const &pose2) |
| Return the RMSD of the non-peptide heavy atoms of two poses. More... | |
| core::Real | CA_or_equiv_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start=1, Size end=0) |
| Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose. More... | |
| core::Real | CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start=1, Size end=0) |
| Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose. More... | |
| void | retrieve_coordinates (const core::pose::Pose &pose, const utility::vector1< core::Size > &residues, FArray2D< core::Real > *coords) |
| core::Real | CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, const std::map< core::Size, core::Size > &residues) |
| Compute the CA RMSD between two poses. More... | |
| core::Real | CA_gdtmm (const core::pose::Pose &pose1, const core::pose::Pose &pose2, const std::map< core::Size, core::Size > &residues) |
| Compute the CA RMSD between two poses. More... | |
| core::Real | CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Size start, Size end, utility::vector1< Size > const &exclude) |
| core::Real | bb_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2) |
| Compute rmsd for only backbone residues (excluding carboxyl oxygen) More... | |
| core::Real | bb_rmsd_including_O (const core::pose::Pose &pose1, const core::pose::Pose &pose2) |
| Compute rmsd for only backbone residues (including carboxyl oxygen) More... | |
| core::Real | CA_or_equiv_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > const &residue_selection) |
| core::Real | CA_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection) |
| core::Real | all_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2) |
| core::Real | all_atom_rmsd_incl_hydrogens (const core::pose::Pose &pose1, const core::pose::Pose &pose2) |
| core::Real | all_scatom_rmsd_nosuper (const core::pose::Pose &pose1, const core::pose::Pose &pose2) |
| core::Real | all_atom_rmsd_nosuper (const core::pose::Pose &pose1, const core::pose::Pose &pose2) |
| core::Real | all_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection) |
| core::Real | all_atom_rmsd_nosuper (const core::pose::Pose &pose1, const core::pose::Pose &pose2, utility::vector1< core::Size > const &pose1_residues, utility::vector1< core::Size > const &pose2_residues) |
| core::Real | nbr_atom_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2) |
| int | CA_maxsub (const core::pose::Pose &pose1, const core::pose::Pose &pose2, Real rms=4.0) |
| Calculates a C-alpha maxsub-based superposition between pose1 and pose2, returns the number of residues superimposed past a certain threshold. See maxsub.hh and maxsub.cc for more information. More... | |
| int | CA_maxsub (const core::pose::Pose &pose1, const core::pose::Pose &pose2, std::list< Size > residue_selection, Real rms) |
| int | xyz_maxsub (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, int natoms) |
| int | CA_maxsub_by_subset (const core::pose::Pose &pose1, const core::pose::Pose &pose2, utility::vector1< bool >) |
| core::Real | CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< Size > const &residue_selection, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4) |
| core::Real | CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4) |
| Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the five components of the gdtmm score. More... | |
| core::Real | xyz_gdtmm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a) |
| core::Real | xyz_gdtmm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4) |
| core::Real | CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2) |
| Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. More... | |
| core::Real | CA_gdtmm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< Size > const &residue_selection) |
| Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. More... | |
| void | CA_gdttm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Real &gdttm_score, core::Real &gdtha_score, std::list< Size > const &residue_selection) |
| Calculate gdttm score based on the C-alpha positions in pose1 and pose2. More... | |
| void | CA_gdttm (const core::pose::Pose &pose1, const core::pose::Pose &pose2, core::Real &gdttm_score, core::Real &gdtha_score, const std::map< core::Size, core::Size > &residues) |
| void | CA_gdttm (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Real &gdttm_score, core::Real &gdtha_score) |
| void | xyz_gdttm (FArray2D< core::Real > p1a, FArray2D< core::Real > p2a, core::Real &gdttm_score, core::Real &gdtha_score) |
| Real | superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real const &rms_calc_offset_val=1.0e-7, bool const realign=false, bool const throw_on_failure=true) |
| Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map. More... | |
| core::Real | superimpose_polymer_heavyatoms (core::pose::Pose &mod_pose, core::pose::Pose const &ref_pose, bool const mainchain_only, core::Real const &rms_calc_offset_val, bool const realign, bool const throw_on_failure) |
| Superimpose polymer heavyatoms of mod_pose onto ref_pose, and return the computed RMSD. If mainchain_only is true, this restricts itself to mainchain heavyatoms; otherwise it does all polymer heavyatoms. More... | |
| Real | superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, std::map< id::AtomID, id::AtomID > const &atom_map, core::Real const &rms_calc_offset_val=1.0e-7, bool const realign=false, bool const throw_on_failure=true) |
| Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by map< AtomID, AtomID > More... | |
| Real | superimpose_pose (pose::Pose &mod_pose, pose::MiniPose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real const &rms_calc_offset_val=1.0e-7, bool const realign=false, bool const throw_on_failure=true) |
| Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map. More... | |
| Real | calpha_superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose) |
| Superimpose two poses by their calpha coordinates. Ignores residues that do not have atoms named "CA.". More... | |
| core::Real | CA_rmsd_symmetric (const core::pose::Pose &native_pose, const core::pose::Pose &pose) |
| void | create_shuffle_map_recursive_rms (std::vector< int > sequence, int const N, std::vector< std::vector< int > > &map) |
| Real | rms_at_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map) |
| Real | rms_at_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, utility::vector1< Size > const &calc_rms_res) |
| Real | rms_at_all_corresponding_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map) |
| Real | rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map) |
| Real | rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, utility::vector1< Size > const &calc_rms_res) |
| std::map< core::Size, core::Real > | per_res_rms_at_corresponding_atoms_no_super (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, utility::vector1< bool > const &mask) |
| Calculate RMSD for each residue in mask, return a map of res to value. More... | |
| Real | rms_at_corresponding_heavy_atoms (pose::Pose const &mod_pose, pose::Pose const &ref_pose) |
| void | setup_matching_heavy_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map) |
| core::Real | residue_sc_rmsd_no_super (core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2, bool const fxnal_group_only=false) |
| utility function to calculate per-residue sidechain rmsd without superposition More... | |
| void | setup_matching_CA_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map) |
| void | setup_matching_protein_backbone_heavy_atoms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map) |
| void | setup_matching_atoms_with_given_names (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< std::string > const &atom_names_to_find, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map) |
| void | compute_jump_rmsd (const core::pose::Pose &reference, const core::pose::Pose &model, boost::unordered_map< core::Size, core::Real > &rmsds) |
| Computes the RMSD of the jump residues between <model> and <native>, storing the results in a map keyed by jump_id. More... | |
| std::map< rmsd_atoms, utility::vector1< std::string > > | setup_rmsd_atom_names () |
| std::map< std::string, rmsd_atoms > | get_rmsd_type_name_map () |
| Setup a name mapping for rmsd_atoms. More... | |
| utility::vector1< std::string > | get_rmsd_type_names () |
| Setup a name mapping for rmsd_atoms. More... | |
| int | xyz_maxsub (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a, int natoms) |
| core::Real | xyz_gdtmm (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a, core::Real &m_1_1, core::Real &m_2_2, core::Real &m_3_3, core::Real &m_4_3, core::Real &m_7_4) |
| Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a. More... | |
| core::Real | xyz_gdtmm (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a) |
| Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a. More... | |
| void | xyz_gdttm (ObjexxFCL::FArray2D< core::Real > p1a, ObjexxFCL::FArray2D< core::Real > p2a, core::Real &gdttm_score, core::Real &gdtha_score) |
| template<class T > | |
| core::Real | rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< core::Size > const &pose1_residues, utility::vector1< core::Size > const &pose2_residues, T *predicate) |
| Select atoms for RMS via a predicate function/functor. More... | |
| template<class T > | |
| core::Real | rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< core::Size > const &subset_residues, T *predicate) |
| template<class T > | |
| core::Real | rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate) |
| Select atoms for RMS via a predicate function/functor. More... | |
| template<class T > | |
| core::Real | rmsd_with_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate) |
| Select a subset atoms for RMS via a predicate function/functor. More... | |
| template<class T > | |
| core::Real | rmsd_with_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, core::id::SequenceMapping const &seqmap, T *predicate) |
| like function above, but uses sequence mapping, i.e. sections of poses of different lengths can be compared at the moment sorta assumes that residues at corresponding positions have the same identity, mainly becaue the predicates are structured that way... More... | |
| template<class T > | |
| core::Real | rmsd_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< core::Size > const &pose1_residues, utility::vector1< core::Size > const &pose2_residues, T *predicate) |
| Select atoms for RMS via a predicate function/functor at given residues. More... | |
| template<class T > | |
| core::Real | rmsd_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate) |
| Select atoms for RMS via a predicate function/functor. More... | |
| template<class T > | |
| core::Real | rmsd_no_super (core::conformation::ResidueCOPs const &residues1, core::conformation::ResidueCOPs const &residues2, T *predicate) |
| template<class T > | |
| core::Real | rmsd_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate) |
| Select atoms for RMS via a predicate function/functor. More... | |
| template<class T > | |
| core::Real | rmsd_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, core::id::SequenceMapping const &seqmap, T *predicate) |
| like function above, but uses sequence mapping, i.e. sections of poses of different lengths can be compared at the moment sorta assumes that residues at corresponding positions have the same identity, mainly becaue the predicates are structured that way... More... | |
| template<class T > | |
| core::Real | biggest_residue_deviation_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate) |
| function to return the biggest deviation between an atom in a pair of poses, More... | |
| template<class T > | |
| core::Real | biggest_residue_deviation_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate) |
| function to return the biggest deviation between an atom in a pair of poses, More... | |
| template<class T > | |
| void | fill_rmsd_coordinates (int &natoms, ObjexxFCL::FArray2D< core::Real > &p1a, ObjexxFCL::FArray2D< core::Real > &p2a, core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate) |
| template<class T > | |
| core::Real | sym_rmsd_with_super_subset (core::pose::Pose const &native_pose, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate) |
| Select a subset atoms for Symmetric RMS via a predicate function/functor. Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);. More... | |
| ObjexxFCL::FArray2D_int | angles (num_phi, num_theta) |
| ObjexxFCL::FArray2D_ubyte | masks (num_bytes, num_overlaps *num_orientations) |
| void | input_sasa_dats () |
| Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above. More... | |
| void | get_overlap (Real const radius_a, Real const radius_b, Real const distance_ijxyz, int °ree_of_overlap) |
| void | get_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_index, int &theta_index, Real distance_ijxyz) |
| Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j) More... | |
| Real | calc_total_sasa (pose::Pose const &pose, Real const probe_radius) |
| returns total sasa More... | |
| Real | calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H=false) |
| Return total SASA. More... | |
| Real | calc_per_atom_sasa_sc (pose::Pose const &pose, utility::vector1< Real > &rsd_sasa, bool normalize) |
| Real | normalizing_area (char const res) |
| Get the area of the sidechain. More... | |
| Real | normalizing_area_total (char const res) |
| Given a one-letter code for a canonical amino acid, return its total surface area. More... | |
| Real | normalizing_area_total_hydrophobic_atoms_only (char const res) |
| Given a one-letter code for a canonical amino acid, return its total surface area, computed only using hydrophobic atoms. More... | |
| Real | normalizing_area_total_polar_atoms_only (char const res) |
| Given a one-letter code for a canonical amino acid, return its total surface area, computed only using polar atoms. More... | |
| Real | calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H, id::AtomID_Map< bool > &atom_subset, bool const use_naccess_sasa_radii=false, bool const expand_polar_radii=false, Real const polar_expansion_radius=1.0, bool const include_probe_radius_in_atom_radii=true, bool const use_lj_radii=false) |
| returns total sasa More... | |
| void | calc_atom_masks (core::conformation::Residue const &irsd, core::conformation::Residue const &jrsd, Real const probe_radius, Real const cutoff_distance, utility::vector1< Real > const &radii, id::AtomID_Map< bool > const &atom_subset, core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > &atom_masks) |
| int | get_num_bytes () |
| Returns the number of bytes the overlap arrays use for tracking SASA. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More... | |
| ObjexxFCL::FArray2D_int const & | get_angles () |
| Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More... | |
| ObjexxFCL::FArray2D_ubyte const & | get_masks () |
| Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More... | |
| Real | calc_per_res_hydrophobic_sasa (pose::Pose const &pose, utility::vector1< Real > &rsd_sasa, utility::vector1< Real > &rsd_hydrophobic_sasa, Real const probe_radius, bool use_naccess_sasa_radii) |
| Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj) More... | |
| bool | SASAShouldItCount (conformation::Residue const &rsd, Size const &atm) |
| void | show_detail (std::ostream &out, EnergyMap &energies, EnergyMap weights) |
| template<class T > | |
| void | vector1_remove (utility::vector1< T > &v, T const &t) |
| private – handles setting the derived data More... | |
| std::string | find_weights_file (std::string const &name, std::string const &extension) |
| Utility function to locate a weights or patch file, either with a fully qualified path, in the local directory, or in the database. Names may be passed either with or without the optional extension. More... | |
| ScoreFunctionOP | deep_copy (ScoreFunction const &source) |
| std::ostream & | operator<< (std::ostream &out, ScoreFunction const &sf) |
| std::string const | REF_2015 ("ref2015") |
| std::string const | TALARIS_2014 ("talaris2014") |
| std::string const | TALARIS_2013 ("talaris2013") |
| std::string const | TALARIS_2013_CART ("talaris2013_cart") |
| std::string const | PRE_TALARIS_2013_STANDARD_WTS ("pre_talaris_2013_standard") |
| std::string const | CENTROID_WTS ("cen_std") |
| std::string const | SOFT_REP_WTS ("soft_rep") |
| std::string const | SOFT_REP_DESIGN_WTS ("soft_rep_design") |
| std::string const | DNA_INT_WTS ("dna_no_gb") |
| std::string const | DNA_INT_WTS_GB ("dna") |
| std::string const | MM_STD_WTS ("mm_std") |
| std::string const | RNA_LORES_WTS ("rna/denovo/rna_lores") |
| std::string const | RNA_HIRES_WTS ("rna/denovo/rna_hires") |
| std::string const | RNA_LORES_PLUS_HIRES_WTS ("rna/denovo/rna_lores_plus_hires") |
| std::string const | MEMB_HIGHRES_WTS ("membrane_highres") |
| std::string const | SCORE12_PATCH ("score12") |
| std::string const | SCORE13 ("score13") |
| std::string const | DOCK_PATCH ("docking") |
| std::string const | DOCK_LOW_PATCH ("docking_cen") |
| std::string const | SCORE4_SMOOTH_CART ("score4_smooth_cart") |
| std::string const | BETA_GENPOT ("beta_genpot") |
| std::string const | BETA_NOV16 ("beta_nov16") |
| std::string const | BETA_NOV15 ("beta_nov15") |
| std::string const | BETA_JULY15 ("beta_july15") |
| core::scoring::ScoreFunctionOP | get_score_function (bool const is_fullatom=true) |
| A helper function which returns a scoring function held in an owning pointer according to the user's command line parameters -score:weights and -score:patch By default it returns weights=talaris2013 for fullatom, and weights=cen_std and patch="" for centroid. More... | |
| core::scoring::ScoreFunctionOP | get_score_function (core::pose::Pose const &pose, bool const is_fullatom=true) |
| Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. More... | |
| core::scoring::ScoreFunctionOP | get_score_function (core::pose::Pose const &pose, utility::options::OptionCollection const &options, bool const is_fullatom=true) |
| Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. Local Options collection. More... | |
| core::scoring::ScoreFunctionOP | get_score_function (utility::options::OptionCollection const &options, bool const is_fullatom=true) |
| A helper function which creates a scoring function held in an owning pointer reading from the input OptionCollection. More... | |
| void | list_read_options_in_get_score_function (utility::options::OptionKeyList &opts) |
| A documentation function which reports the set of options read by get_score_function. More... | |
| core::scoring::ScoreFunctionOP | get_score_function_legacy (std::string const &pre_talaris_2013_weight_set, std::string const &pre_talaris_2013_patch_file="") |
| A helper function that either returns a ScoreFunctionOP created by get_score_function() or the one specified by the protocol which is activated by the -restore_pre_talaris_2013_behavior flag. The purpose of this function is to preserve legacy behavior for the sake of reproducibility and so that a record of the old behavior is still preserved in the code to ease the process of reverting the change to get_score_function if that were the wrong behavior. More... | |
| core::scoring::ScoreFunctionOP | get_score_function_legacy (utility::options::OptionCollection const &options, std::string const &pre_talaris_2013_weight_set, std::string const &pre_talaris_2013_patch_file) |
| void | list_read_options_in_get_score_function_legacy (utility::options::OptionKeyList &opts) |
| A documentation function which reports the set of options read by get_score_function_legacy. More... | |
| std::string | get_score_functionName (bool const is_fullatom=true) |
| use the logic of get_score_function to get the name. The name format is <weights_tag>[_<patch_tag> ... ] More... | |
| std::string | basename_for_score_function (std::string const &sfxn_name) |
| returns family name for a specific score function. For example, ref2015_cart returns ref2015 and beta_nov16_cst returns beta_nov16 Returns an empty string if no match is found More... | |
| void | apply_set_weights (ScoreFunctionOP scorefxn, utility::vector1< std::string > const &settings) |
| std::string | get_current_default_score_function_name () |
| bool | operator== (ScoreFunctionInfo const &a, ScoreFunctionInfo const &b) |
| ScoreType | score_type_from_name (std::string const &name) |
| give a ScoreType string name and return its enum type More... | |
| std::istream & | operator>> (std::istream &is, ScoreType &score_type) |
| input operator for ScoreType enum type More... | |
| std::ostream & | operator<< (std::ostream &os, ScoreType const &score_type) |
| output operator for ScoreType enum type More... | |
| std::ostream & | operator<< (std::ostream &os, ScoreTypes const &score_types) |
| output operator for ScoreTypes list type More... | |
| std::string | name_from_score_type (ScoreType score_type) |
| Returns the name of the ScoreType <score_type> More... | |
| void | fill_score_range (std::map< std::string, ScoreType > &M, std::string const &prefix, int first, int last) |
| std::string const | FA_STANDARD_DEFAULT ("FA_STANDARD_DEFAULT") |
| global etable_id More... | |
| std::string const | FA_STANDARD_SOFT ("FA_STANDARD_SOFT") |
| std::string const | FA_STANDARD_MULTIPOLE ("FA_STANDARD_MULTIPOLE") |
| std::string const | UNFOLDED_SCORE12 ("UNFOLDED_SCORE12") |
| std::string const | UNFOLDED_MM_STD ("UNFOLDED_MM_STD") |
| std::string const | UNFOLDED_RNA ("UNFOLDED_RNA") |
| std::string const | UNFOLDED_SPLIT_TALARIS2013 ("UNFOLDED_SPLIT_TALARIS2013") |
| std::string const | UNFOLDED_SPLIT_MM_STD ("UNFOLDED_SPLIT_MM_STD") |
| std::string const | UNFOLDED_SPLIT_USER_DEFINED ("UNFOLDED_SPLIT_USER_DEFINED") |
| std::string const | SPLIT_UNFOLDED_ELE ("SPLIT_UNFOLDED_ELE") |
| std::string const | SPLIT_UNFOLDED_PDB ("SPLIT_UNFOLDED_PDB") |
| std::string const | SPLIT_UNFOLDED_ROSETTA ("SPLIT_UNFOLDED_ROSETTA") |
| std::string const | SPLIT_UNFOLDED_MM ("SPLIT_UNFOLDED_MM") |
| std::string const | SPLIT_UNFOLDED_UNIQUE ("SPLIT_UNFOLDED_UNIQUE") |
| std::string const | SPLIT_UNFOLDED_MEAN ("SPLIT_UNFOLDED_MEAN") |
| std::string const | SPLIT_UNFOLDED_MEDIAN ("SPLIT_UNFOLDED_MEDIAN") |
| std::string const | SPLIT_UNFOLDED_MODE ("SPLIT_UNFOLDED_MODE") |
| std::string const | SPLIT_UNFOLDED_BOLTZ ("SPLIT_UNFOLDED_BOLTZ") |
| std::string const | SPLIT_UNFOLDED_USER_DEFINED ("SPLIT_UNFOLDED_USER_DEFINED") |
| SS_Info const & | retrieve_const_ss_info_from_pose (pose::Pose const &pose) |
| helper function More... | |
| SS_Info & | retrieve_nonconst_ss_info_from_pose (pose::Pose &pose) |
| helper function More... | |
| void | fill_bb_pos (pose::Pose const &pose, BB_Pos &bb_pos) |
| helper function More... | |
| bool | dimer_pairing_pointer_sorter (DimerPairingOP const &a, DimerPairingOP const &b) |
| std::ostream & | operator<< (std::ostream &out, Strands const &s) |
| std::ostream & | operator<< (std::ostream &out, Helices const &s) |
| static basic::Tracer | trKillHairpinsIO ("core.score.SS_Killhairpins_Info") |
| std::ostream & | operator<< (std::ostream &out, Hairpin const &s) |
| std::ostream & | operator<< (std::ostream &out, Hairpins const &) |
| static basic::Tracer | TR ("core.scoring.TMscore") |
| void | eval_scsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1sc_centroid, Vector const &r2sc_centroid, Real const &r1sc_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function. More... | |
| void | eval_bbsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2sc_centroid, Real const &r1bb_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| With two bounding spheres for a backbone and a sidechain, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_sidechain_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More... | |
| void | eval_bbbb_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2bb_centroid, Real const &r1bb_radius, Real const &r2bb_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) |
| With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More... | |
| Vector | compute_bb_centroid (conformation::Residue const &r1) |
| Compute the average coordinate of the backbone heavy atoms (aka center of mass). More... | |
| Real | compute_bb_radius (conformation::Residue const &r1, Vector const &r1bb_centroid) |
| Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point. More... | |
| Vector | compute_sc_centroid (conformation::Residue const &r1) |
| Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone. More... | |
| Real | compute_sc_radius (conformation::Residue const &r1, Vector const &r1sc_centroid) |
| Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point. More... | |
| bool | check_score_function_sanity (utility::options::OptionCollection const &options, std::string const &scorefxn_key, bool throw_exception=false) |
| Check if a score function is requested with incompatible option flags Will return true if scorefunction is "sane" and false if not. If throw_exception is true, will raise an exception instead of returning false. More... | |
| std::map< id::AtomID, utility::vector1< Real > > | get_single_atom_energies (core::pose::Pose &pose, ScoreFunction const &scorefxn, ScoreTypes const &types, select::residue_selector::ResidueSubsetOP subset=nullptr) |
| Get the (pseudo-one-body) energies for a set of atoms. Only atoms with non-zero energies will be present in the returned map. The output vector will be ordered by the types in the passed ScoreTypes If subset is passed, only atoms in residues from the subset will be considered. More... | |
| std::map< std::pair< id::AtomID, id::AtomID >, utility::vector1< Real > > | get_pairwise_atom_energies (core::pose::Pose &pose, ScoreFunction const &scorefxn, ScoreTypes const &types, select::residue_selector::ResidueSubsetOP subset1=nullptr, select::residue_selector::ResidueSubsetOP subset2=nullptr) |
| Get the pairwise energies for a set of atoms. Only atom pairs with non-zero energies will be present in the returned map. The output vector will be ordered by the types in the passed ScoreTypes If both subsets are passed, only pairwise interactions between atoms in residues across the two sets will be considered If just subset1 is passed, only pairwise interactions which involve at least one atom in a residue in the set will be considered If neither is passed, all pairwise interactions will be considered. More... | |
| std::map< id::AtomID, utility::vector1< Real > > | get_atomistic_energies (core::pose::Pose &pose, ScoreFunction const &scorefxn, ScoreTypes const &types, select::residue_selector::ResidueSubsetOP subset=nullptr) |
| Get the per-atom contributions to the energy. This differs from get_single_atom_energies() in that it also considers the atoms' contributions to pairwise energies. The output vector will be ordered by the types in the passed ScoreTypes If subset is passed, only atoms in residues from the subset will be considered. More... | |
| bool | VdWShouldItCount (conformation::Residue const &rsd, Size const &atm) |
| core::scoring::ScoreFunctionOP | parse_score_function (utility::tag::TagCOP tag, std::string const &option_name, basic::datacache::DataMap const &data, std::string const &dflt_key="commandline") |
| Look up the score function defined in the <SCOREFXNS> through the given option. Defaults to 'commandline'. More... | |
| core::scoring::ScoreFunctionOP | parse_score_function (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const &dflt_key="commandline") |
| Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Defaults to 'commandline'. More... | |
| std::string | get_score_function_name (utility::tag::TagCOP tag, std::string const &option_name) |
| Look up the name of assigned score function to the given option. Use this to prevent hard coding default score functions into protocols. More... | |
| std::string | get_score_function_name (utility::tag::TagCOP tag) |
| Look up the name of assigned score function to the 'scorefxn=' option. Use this to prevent hard coding default score functions into protocols. More... | |
| void | attributes_for_get_score_function_name (utility::tag::AttributeList &attributes) |
| Get attributes ( i.e. options ) for movers to build xml schemas. More... | |
| void | attributes_for_get_score_function_name (utility::tag::AttributeList &attributes, std::string const &option_name) |
| Appends the attributes read by get_score_function_name w/ name argument. More... | |
| void | attributes_for_get_score_function_name_w_description (utility::tag::AttributeList &attributes, std::string const &description) |
| Appends the attributes read by get_score_function_name. More... | |
| void | attributes_for_get_score_function_name_w_description (utility::tag::AttributeList &attributes, std::string const &option_name, std::string const &description) |
| Appends the attributes read by get_score_function_name w/ name argument. More... | |
| void | attributes_for_parse_score_function (utility::tag::AttributeList &attributes) |
| Appends the attributes read by parse_score_function. More... | |
| void | attributes_for_parse_score_function (utility::tag::AttributeList &attributes, std::string const &sfxn_option_name) |
| Appends the attributes read by parse_score_function w/ name argument. More... | |
| void | attributes_for_parse_score_function_w_description (utility::tag::AttributeList &attributes, std::string const &description) |
| Appends the attributes read by parse_score_function with description. More... | |
| void | attributes_for_parse_score_function_w_description (utility::tag::AttributeList &attributes, std::string const &sfxn_option_name, std::string const &description) |
| Appends the attributes read by parse_score_function w/ name argument and description. More... | |
| void | attributes_for_parse_score_function_w_description_when_required (utility::tag::AttributeList &attributes, std::string const &sfxn_option_name, std::string const &description="") |
| Appends the attributes read by parse_score_function w/ name argument and description. More... | |
Variables | |
| short const | bit_count [] |
| int const | num_bytes = 21 |
| int const | num_phi = 64 |
| int const | num_theta = 64 |
| int const | num_overlaps = 100 |
| int const | num_orientations = 162 |
| int const | maskbits = 162 |
| std::string const | REF_2015 |
| std::string const | TALARIS_2014 |
| std::string const | TALARIS_2013 |
| std::string const | TALARIS_2013_CART |
| std::string const | PRE_TALARIS_2013_STANDARD_WTS |
| std::string const | SCORE13 |
| std::string const | CENTROID_WTS |
| std::string const | SOFT_REP_WTS |
| std::string const | SOFT_REP_DESIGN_WTS |
| std::string const | DNA_INT_WTS |
| std::string const | DNA_INT_WTS_GB |
| std::string const | MM_STD_WTS |
| std::string const | RNA_LORES_WTS |
| std::string const | RNA_HIRES_WTS |
| std::string const | RNA_LORES_PLUS_HIRES_WTS |
| std::string const | MEMB_HIGHRES_WTS |
| std::string const | SCORE12_PATCH |
| std::string const | DOCK_PATCH |
| std::string const | DOCK_LOW_PATCH |
| std::string const | SCORE4_SMOOTH_CART |
| std::string const | BETA_GENPOT |
| std::string const | BETA_NOV16 |
| std::string const | BETA_NOV15 |
| std::string const | BETA_JULY15 |
| std::string const | FA_STANDARD_DEFAULT |
| std::string const | FA_STANDARD_SOFT |
| std::string const | FA_STANDARD_MULTIPOLE |
| std::string const | UNFOLDED_SCORE12 |
| std::string const | UNFOLDED_MM_STD |
| std::string const | UNFOLDED_RNA |
| std::string const | UNFOLDED_SPLIT_TALARIS2013 |
| std::string const | UNFOLDED_SPLIT_MM_STD |
| std::string const | UNFOLDED_SPLIT_USER_DEFINED |
| std::string const | SPLIT_UNFOLDED_ELE |
| std::string const | SPLIT_UNFOLDED_PDB |
| std::string const | SPLIT_UNFOLDED_ROSETTA |
| std::string const | SPLIT_UNFOLDED_MM |
| std::string const | SPLIT_UNFOLDED_UNIQUE |
| std::string const | SPLIT_UNFOLDED_MEAN |
| std::string const | SPLIT_UNFOLDED_MEDIAN |
| std::string const | SPLIT_UNFOLDED_MODE |
| std::string const | SPLIT_UNFOLDED_BOLTZ |
| std::string const | SPLIT_UNFOLDED_USER_DEFINED |
| typedef utility::pointer::weak_ptr< APBSConfig > core::scoring::APBSConfigAP |
| typedef utility::pointer::weak_ptr< APBSConfig const > core::scoring::APBSConfigCAP |
| typedef utility::pointer::shared_ptr< APBSConfig const > core::scoring::APBSConfigCOP |
| typedef utility::pointer::shared_ptr< APBSConfig > core::scoring::APBSConfigOP |
| typedef utility::pointer::weak_ptr< APBSResult > core::scoring::APBSResultAP |
| typedef utility::pointer::weak_ptr< APBSResult const > core::scoring::APBSResultCAP |
| typedef utility::pointer::shared_ptr< APBSResult const > core::scoring::APBSResultCOP |
| typedef utility::pointer::shared_ptr< APBSResult > core::scoring::APBSResultOP |
| typedef utility::pointer::weak_ptr< APBSWrapper > core::scoring::APBSWrapperAP |
| typedef utility::pointer::weak_ptr< APBSWrapper const > core::scoring::APBSWrapperCAP |
| typedef utility::pointer::shared_ptr< APBSWrapper const > core::scoring::APBSWrapperCOP |
| typedef utility::pointer::shared_ptr< APBSWrapper > core::scoring::APBSWrapperOP |
| typedef utility::vector1< AtomNeighbor > core::scoring::AtomNeighbors |
| typedef ObjexxFCL::FArray2D< CArrayP_TableEnergy > core::scoring::AtomPairEnergyTable |
| typedef utility::pointer::shared_ptr< AtomVDW const > core::scoring::AtomVDWCOP |
| typedef utility::pointer::shared_ptr< AtomVDW > core::scoring::AtomVDWOP |
| typedef ObjexxFCL::CArray< Energy > core::scoring::CArray_Energy |
| typedef ObjexxFCL::CArray< TableEnergy > core::scoring::CArray_TableEnergy |
| typedef ObjexxFCL::CArrayP< Energy > core::scoring::CArrayP_Energy |
| typedef ObjexxFCL::CArrayP< TableEnergy > core::scoring::CArrayP_TableEnergy |
| typedef utility::pointer::shared_ptr< CenHBPotential const > core::scoring::CenHBPotentialCOP |
| typedef utility::pointer::shared_ptr< CenHBPotential > core::scoring::CenHBPotentialOP |
| typedef utility::pointer::shared_ptr< CenListInfo > core::scoring::CenListInfoOP |
| typedef utility::pointer::shared_ptr< CenRotEnvPairPotential const > core::scoring::CenRotEnvPairPotentialCOP |
| typedef utility::pointer::shared_ptr< CenRotEnvPairPotential > core::scoring::CenRotEnvPairPotentialOP |
| typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropy const > core::scoring::ChemicalShiftAnisotropyCOP |
| typedef utility::pointer::shared_ptr< ChemicalShiftAnisotropy > core::scoring::ChemicalShiftAnisotropyOP |
| typedef utility::pointer::shared_ptr< ContextGraph const > core::scoring::ContextGraphCOP |
| typedef utility::pointer::shared_ptr< ContextGraph > core::scoring::ContextGraphOP |
| typedef utility::pointer::shared_ptr< DenseEnergyContainer > core::scoring::DenseEnergyContainerOP |
| typedef utility::pointer::shared_ptr< DenseNeighborIterator > core::scoring::DenseNeighborIteratorOP |
| typedef utility::pointer::shared_ptr< DensityZscoresStatsSetup const > core::scoring::DensityZscoresStatsSetupCOP |
| typedef utility::pointer::shared_ptr< DensityZscoresStatsSetup > core::scoring::DensityZscoresStatsSetupOP |
| typedef std::map< std::string, std::map < core::Real, core::Real > > core::scoring::DensZScoreMap |
private methods ///
| using core::scoring::DimerPairingOP = typedef utility::pointer::shared_ptr<DimerPairing> |
| typedef utility::pointer::shared_ptr< DipolarCoupling const > core::scoring::DipolarCouplingCOP |
| typedef utility::pointer::shared_ptr< DipolarCoupling > core::scoring::DipolarCouplingOP |
| typedef utility::pointer::shared_ptr< DockingScoreFunction const > core::scoring::DockingScoreFunctionCOP |
| typedef utility::pointer::shared_ptr< DockingScoreFunction > core::scoring::DockingScoreFunctionOP |
| typedef utility::pointer::shared_ptr< Energies const > core::scoring::EnergiesCOP |
| typedef utility::pointer::shared_ptr< Energies > core::scoring::EnergiesOP |
| typedef utility::pointer::shared_ptr< EnergyGraph > core::scoring::EnergyGraphOP |
| typedef EMapVector core::scoring::EnergyMap |
| typedef utility::pointer::shared_ptr< EnvPairPotential const > core::scoring::EnvPairPotentialCOP |
| typedef utility::pointer::shared_ptr< EnvPairPotential > core::scoring::EnvPairPotentialOP |
| typedef ObjexxFCL::FArray1D< Energy > core::scoring::FArray1D_Energy |
| typedef ObjexxFCL::FArray1D< Length > core::scoring::FArray1D_Length |
| typedef ObjexxFCL::FArray1D< Probability > core::scoring::FArray1D_Probability |
| typedef ObjexxFCL::FArray1D< TableEnergy > core::scoring::FArray1D_TableEnergy |
| typedef ObjexxFCL::FArray1D< TableProbability > core::scoring::FArray1D_TableProbability |
| typedef ObjexxFCL::FArray1D< Weight > core::scoring::FArray1D_Weight |
| typedef ObjexxFCL::FArray2D< Energy > core::scoring::FArray2D_Energy |
| typedef ObjexxFCL::FArray2D< Length > core::scoring::FArray2D_Length |
| typedef ObjexxFCL::FArray2D< Probability > core::scoring::FArray2D_Probability |
| typedef ObjexxFCL::FArray2D< TableEnergy > core::scoring::FArray2D_TableEnergy |
| typedef ObjexxFCL::FArray2D< TableProbability > core::scoring::FArray2D_TableProbability |
| typedef ObjexxFCL::FArray2D< Weight > core::scoring::FArray2D_Weight |
| typedef ObjexxFCL::FArray3D< Energy > core::scoring::FArray3D_Energy |
| typedef ObjexxFCL::FArray3D< Length > core::scoring::FArray3D_Length |
| typedef ObjexxFCL::FArray3D< Probability > core::scoring::FArray3D_Probability |
| typedef ObjexxFCL::FArray3D< TableEnergy > core::scoring::FArray3D_TableEnergy |
| typedef ObjexxFCL::FArray3D< TableProbability > core::scoring::FArray3D_TableProbability |
| typedef ObjexxFCL::FArray3D< Weight > core::scoring::FArray3D_Weight |
| typedef ObjexxFCL::FArray4D< Energy > core::scoring::FArray4D_Energy |
| typedef ObjexxFCL::FArray4D< Length > core::scoring::FArray4D_Length |
| typedef ObjexxFCL::FArray4D< Probability > core::scoring::FArray4D_Probability |
| typedef ObjexxFCL::FArray4D< TableEnergy > core::scoring::FArray4D_TableEnergy |
| typedef ObjexxFCL::FArray4D< TableProbability > core::scoring::FArray4D_TableProbability |
| typedef ObjexxFCL::FArray4D< Weight > core::scoring::FArray4D_Weight |
| typedef ObjexxFCL::FArray5D< Energy > core::scoring::FArray5D_Energy |
| typedef ObjexxFCL::FArray5D< Length > core::scoring::FArray5D_Length |
| typedef ObjexxFCL::FArray5D< Probability > core::scoring::FArray5D_Probability |
| typedef ObjexxFCL::FArray5D< TableEnergy > core::scoring::FArray5D_TableEnergy |
| typedef ObjexxFCL::FArray5D< TableProbability > core::scoring::FArray5D_TableProbability |
| typedef ObjexxFCL::FArray5D< Weight > core::scoring::FArray5D_Weight |
| typedef utility::pointer::shared_ptr< GenBondedExclInfo const > core::scoring::GenBondedExclInfoCOP |
| typedef utility::pointer::shared_ptr< GenBondedExclInfo > core::scoring::GenBondedExclInfoOP |
| typedef utility::pointer::shared_ptr< GenBornPoseInfo > core::scoring::GenBornPoseInfoOP |
| typedef utility::pointer::shared_ptr< GenBornPotential const > core::scoring::GenBornPotentialCOP |
| typedef utility::pointer::shared_ptr< GenBornPotential > core::scoring::GenBornPotentialOP |
| typedef utility::pointer::shared_ptr< GenBornResidueInfo > core::scoring::GenBornResidueInfoOP |
| typedef utility::pointer::shared_ptr< GenBornRotamerSetInfo > core::scoring::GenBornRotamerSetInfoOP |
| typedef utility::pointer::shared_ptr< GenericBondedPotential > core::scoring::GenericBondedPotentialOP |
| typedef utility::pointer::shared_ptr< HydroxylTorsionPotential const > core::scoring::HydroxylTorsionPotentialCOP |
| typedef utility::pointer::shared_ptr< HydroxylTorsionPotential > core::scoring::HydroxylTorsionPotentialOP |
| typedef ObjexxFCL::KeyFArray1D< Energy > core::scoring::KeyFArray1D_Energy |
| typedef ObjexxFCL::KeyFArray1D< Probability > core::scoring::KeyFArray1D_Probability |
| typedef ObjexxFCL::KeyFArray1D< Real > core::scoring::KeyFArray1D_Real |
| typedef ObjexxFCL::KeyFArray1D< Weight > core::scoring::KeyFArray1D_Weight |
| typedef ObjexxFCL::KeyFArray2D< Energy > core::scoring::KeyFArray2D_Energy |
| typedef ObjexxFCL::KeyFArray2D< Probability > core::scoring::KeyFArray2D_Probability |
| typedef ObjexxFCL::KeyFArray2D< Real > core::scoring::KeyFArray2D_Real |
| typedef ObjexxFCL::KeyFArray2D< Weight > core::scoring::KeyFArray2D_Weight |
| typedef ObjexxFCL::KeyFArray3D< Energy > core::scoring::KeyFArray3D_Energy |
| typedef ObjexxFCL::KeyFArray3D< Probability > core::scoring::KeyFArray3D_Probability |
| typedef ObjexxFCL::KeyFArray3D< Real > core::scoring::KeyFArray3D_Real |
| typedef ObjexxFCL::KeyFArray3D< Weight > core::scoring::KeyFArray3D_Weight |
| typedef utility::pointer::shared_ptr< LREnergyContainer const > core::scoring::LREnergyContainerCOP |
| typedef utility::pointer::shared_ptr< LREnergyContainer > core::scoring::LREnergyContainerOP |
| typedef core::Real core::scoring::matrix[3][3] |
| typedef numeric::xyzMatrix< core::Real > core::scoring::Matrix |
| typedef utility::pointer::shared_ptr< Membrane_FAEmbed const > core::scoring::Membrane_FAEmbedCOP |
| typedef utility::pointer::shared_ptr< Membrane_FAEmbed > core::scoring::Membrane_FAEmbedOP |
| typedef utility::pointer::shared_ptr< Membrane_FAPotential const > core::scoring::Membrane_FAPotentialCOP |
| typedef utility::pointer::shared_ptr< Membrane_FAPotential > core::scoring::Membrane_FAPotentialOP |
| typedef utility::pointer::shared_ptr< MembraneEmbed const > core::scoring::MembraneEmbedCOP |
| typedef utility::pointer::shared_ptr< MembraneEmbed > core::scoring::MembraneEmbedOP |
| typedef utility::pointer::shared_ptr< MembranePotential const > core::scoring::MembranePotentialCOP |
| typedef utility::pointer::shared_ptr< MembranePotential > core::scoring::MembranePotentialOP |
| typedef utility::pointer::shared_ptr< MembraneTopology const > core::scoring::MembraneTopologyCOP |
| typedef utility::pointer::shared_ptr< MembraneTopology > core::scoring::MembraneTopologyOP |
| typedef utility::pointer::shared_ptr< MinimizationGraph const > core::scoring::MinimizationGraphCOP |
| typedef utility::pointer::shared_ptr< MinimizationGraph > core::scoring::MinimizationGraphOP |
| typedef utility::pointer::shared_ptr< MinScoreScoreFunction const > core::scoring::MinScoreScoreFunctionCOP |
| typedef utility::pointer::shared_ptr< MinScoreScoreFunction > core::scoring::MinScoreScoreFunctionOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPoseInfo const > core::scoring::MultipoleElecPoseInfoCOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPoseInfo > core::scoring::MultipoleElecPoseInfoOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPotential const > core::scoring::MultipoleElecPotentialCOP |
| typedef utility::pointer::shared_ptr< MultipoleElecPotential > core::scoring::MultipoleElecPotentialOP |
| typedef utility::pointer::shared_ptr< const MultipoleElecResidueInfo > core::scoring::MultipoleElecResidueInfoCOP |
| typedef utility::pointer::shared_ptr< MultipoleElecResidueInfo > core::scoring::MultipoleElecResidueInfoOP |
| typedef utility::pointer::shared_ptr< MultipoleElecRotamerSetInfo > core::scoring::MultipoleElecRotamerSetInfoOP |
| typedef utility::pointer::shared_ptr< MultipoleParameter > core::scoring::MultipoleParameterOP |
| typedef utility::pointer::shared_ptr< NeighborList const > core::scoring::NeighborListCOP |
| typedef utility::pointer::shared_ptr< NeighborList > core::scoring::NeighborListOP |
| typedef utility::pointer::shared_ptr< OmegaTether const > core::scoring::OmegaTetherCOP |
| typedef utility::pointer::shared_ptr< OmegaTether > core::scoring::OmegaTetherOP |
| typedef utility::pointer::shared_ptr< OneDDistPotential const > core::scoring::OneDDistPotentialCOP |
| typedef utility::pointer::shared_ptr< OneDDistPotential > core::scoring::OneDDistPotentialOP |
| typedef utility::pointer::shared_ptr< OneToAllEnergyContainer > core::scoring::OneToAllEnergyContainerOP |
| typedef utility::pointer::shared_ptr< OneToAllNeighborIterator > core::scoring::OneToAllNeighborIteratorOP |
| typedef utility::pointer::shared_ptr< P_AA_ABEGO3 const > core::scoring::P_AA_ABEGO3_COP |
| typedef utility::pointer::shared_ptr< P_AA_ABEGO3 > core::scoring::P_AA_ABEGO3_OP |
| typedef utility::pointer::shared_ptr< P_AA_ss const > core::scoring::P_AA_ssCOP |
| typedef utility::pointer::shared_ptr< P_AA_ss > core::scoring::P_AA_ssOP |
| typedef utility::pointer::shared_ptr< P_AA const > core::scoring::P_AACOP |
| typedef utility::pointer::shared_ptr< P_AA > core::scoring::P_AAOP |
| typedef utility::pointer::shared_ptr< PairEPotential const > core::scoring::PairEPotentialCOP |
| typedef utility::pointer::shared_ptr< PairEPotential > core::scoring::PairEPotentialOP |
| using core::scoring::PB = typedef PoissonBoltzmannPotential |
| typedef utility::pointer::shared_ptr< PDatom const > core::scoring::PDatomCOP |
| typedef utility::pointer::shared_ptr< PDatom > core::scoring::PDatomOP |
| typedef utility::pointer::shared_ptr< PDinter const > core::scoring::PDinterCOP |
| typedef utility::pointer::shared_ptr< PDinter > core::scoring::PDinterOP |
| typedef utility::pointer::shared_ptr< PDvertex const > core::scoring::PDvertexCOP |
| typedef utility::pointer::shared_ptr< PDvertex > core::scoring::PDvertexOP |
| typedef utility::pointer::shared_ptr< PointWaterPotential const > core::scoring::PointWaterPotentialCOP |
| typedef utility::pointer::shared_ptr< PointWaterPotential > core::scoring::PointWaterPotentialOP |
| typedef utility::pointer::weak_ptr< PoissonBoltzmannPotential > core::scoring::PoissonBoltzmannPotentialAP |
| typedef utility::pointer::weak_ptr< PoissonBoltzmannPotential const > core::scoring::PoissonBoltzmannPotentialCAP |
| typedef utility::pointer::shared_ptr< PoissonBoltzmannPotential const > core::scoring::PoissonBoltzmannPotentialCOP |
| typedef utility::pointer::shared_ptr< PoissonBoltzmannPotential > core::scoring::PoissonBoltzmannPotentialOP |
| typedef utility::pointer::shared_ptr< const PolymerBondedEnergyContainer > core::scoring::PolymerBondedEnergyContainerCOP |
| typedef utility::pointer::shared_ptr< PolymerBondedEnergyContainer > core::scoring::PolymerBondedEnergyContainerOP |
| typedef utility::pointer::shared_ptr< const PolymerBondedNeighborIterator > core::scoring::PolymerBondedNeighborIteratorCOP |
| typedef utility::pointer::shared_ptr< PolymerBondedNeighborIterator > core::scoring::PolymerBondedNeighborIteratorOP |
| typedef utility::pointer::weak_ptr< PQR > core::scoring::PQRAP |
| typedef utility::pointer::weak_ptr< PQR const > core::scoring::PQRCAP |
| typedef utility::pointer::shared_ptr< PQR const > core::scoring::PQRCOP |
| typedef utility::pointer::shared_ptr< PQR > core::scoring::PQROP |
| typedef utility::pointer::shared_ptr< Predicate const > core::scoring::PredicateCOP |
| typedef utility::pointer::shared_ptr< Predicate > core::scoring::PredicateOP |
| typedef core::Real core::scoring::Probability |
| typedef utility::pointer::shared_ptr< ProQPotential > core::scoring::ProQPotentialOP |
| using core::scoring::R = typedef Ramachandran |
| typedef utility::pointer::shared_ptr< Ramachandran2B const > core::scoring::Ramachandran2BCOP |
| typedef utility::pointer::shared_ptr< Ramachandran2B > core::scoring::Ramachandran2BOP |
| typedef utility::pointer::shared_ptr<Ramachandran const > core::scoring::RamachandranCOP |
| typedef utility::pointer::shared_ptr<Ramachandran > core::scoring::RamachandranOP |
| typedef utility::pointer::shared_ptr< RamaPrePro const > core::scoring::RamaPreProCOP |
| typedef utility::pointer::shared_ptr< RamaPrePro > core::scoring::RamaPreProOP |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling_Rohl const > core::scoring::ResidualDipolarCoupling_RohlCOP |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling_Rohl > core::scoring::ResidualDipolarCoupling_RohlOP |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling const > core::scoring::ResidualDipolarCouplingCOP |
| typedef utility::pointer::shared_ptr< ResidualDipolarCoupling > core::scoring::ResidualDipolarCouplingOP |
| typedef utility::pointer::shared_ptr< ResidueExclParams const > core::scoring::ResidueExclParamsCOP |
| typedef utility::pointer::shared_ptr< ResidueExclParams > core::scoring::ResidueExclParamsOP |
| typedef utility::pointer::shared_ptr< ResidueNblistData const > core::scoring::ResidueNblistDataCOP |
| typedef utility::pointer::shared_ptr< ResidueNblistData > core::scoring::ResidueNblistDataOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborConstIterator const > core::scoring::ResidueNeighborConstIteratorCOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborConstIterator > core::scoring::ResidueNeighborConstIteratorOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborIterator const > core::scoring::ResidueNeighborIteratorCOP |
| typedef utility::pointer::shared_ptr< ResidueNeighborIterator > core::scoring::ResidueNeighborIteratorOP |
| typedef utility::pointer::shared_ptr< ResiduePairNeighborList const > core::scoring::ResiduePairNeighborListCOP |
| typedef utility::pointer::shared_ptr< ResiduePairNeighborList > core::scoring::ResiduePairNeighborListOP |
| typedef std::list< core::Size > core::scoring::ResidueSelection |
| typedef utility::vector1< core::Size > core::scoring::ResidueSelectionVector |
| typedef utility::pointer::shared_ptr< ResPairMinimizationData const > core::scoring::ResPairMinimizationDataCOP |
| typedef utility::pointer::shared_ptr< ResPairMinimizationData > core::scoring::ResPairMinimizationDataOP |
| typedef utility::pointer::shared_ptr< ResSingleMinimizationData const > core::scoring::ResSingleMinimizationDataCOP |
| typedef utility::pointer::shared_ptr< ResSingleMinimizationData > core::scoring::ResSingleMinimizationDataOP |
| typedef core::Real core::scoring::rvec[3] |
| typedef core::Real core::scoring::rvec5[5] |
| typedef utility::pointer::shared_ptr< SASAPotential const > core::scoring::SASAPotentialCOP |
| typedef utility::pointer::shared_ptr< SASAPotential > core::scoring::SASAPotentialOP |
| typedef Real core::scoring::Score |
| typedef utility::pointer::shared_ptr< ScoreFunction const > core::scoring::ScoreFunctionCOP |
| typedef utility::pointer::shared_ptr< ScoreFunctionInfo const > core::scoring::ScoreFunctionInfoCOP |
| typedef utility::pointer::shared_ptr< ScoreFunctionInfo > core::scoring::ScoreFunctionInfoOP |
| typedef utility::pointer::shared_ptr< ScoreFunction > core::scoring::ScoreFunctionOP |
| typedef utility::vector1< ScoreType > core::scoring::ScoreTypes |
| typedef utility::pointer::shared_ptr< SecondaryStructurePotential const > core::scoring::SecondaryStructurePotentialCOP |
| typedef utility::pointer::shared_ptr< SecondaryStructurePotential > core::scoring::SecondaryStructurePotentialOP |
| typedef utility::pointer::weak_ptr< SetupPoissonBoltzmannPotential > core::scoring::SetupPoissonBoltzmannPotentialAP |
| typedef utility::pointer::weak_ptr< SetupPoissonBoltzmannPotential const > core::scoring::SetupPoissonBoltzmannPotentialCAP |
| typedef utility::pointer::shared_ptr< SetupPoissonBoltzmannPotential const > core::scoring::SetupPoissonBoltzmannPotentialCOP |
| typedef utility::pointer::shared_ptr< SetupPoissonBoltzmannPotential > core::scoring::SetupPoissonBoltzmannPotentialOP |
| typedef utility::pointer::shared_ptr< SigmoidWeightedCenList<Real> > core::scoring::SigmoidWeightedCenListRealOP |
| typedef utility::pointer::shared_ptr< SigmoidWeightedCenList<numeric::xyzVector<Real> > > core::scoring::SigmoidWeightedCenListVectorOP |
| typedef utility::pointer::shared_ptr< SmoothEnvPairPotential const > core::scoring::SmoothEnvPairPotentialCOP |
| typedef utility::pointer::shared_ptr< SmoothEnvPairPotential > core::scoring::SmoothEnvPairPotentialOP |
| typedef utility::pointer::shared_ptr< SplitUnfoldedTwoBodyPotential > core::scoring::SplitUnfoldedTwoBodyPotentialOP |
| typedef utility::pointer::shared_ptr< SS_Info const > core::scoring::SS_InfoCOP |
| typedef utility::pointer::shared_ptr< SS_Info > core::scoring::SS_InfoOP |
| typedef utility::pointer::shared_ptr< SS_Killhairpins_Info const > core::scoring::SS_Killhairpins_InfoCOP |
| typedef utility::pointer::shared_ptr< SS_Killhairpins_Info > core::scoring::SS_Killhairpins_InfoOP |
| typedef float core::scoring::TableEnergy |
| typedef float core::scoring::TableProbability |
| typedef utility::pointer::shared_ptr< TenANeighborGraph const > core::scoring::TenANeighborGraphCOP |
| typedef utility::pointer::shared_ptr< TenANeighborGraph > core::scoring::TenANeighborGraphOP |
| typedef utility::pointer::shared_ptr< TwelveANeighborGraph const > core::scoring::TwelveANeighborGraphCOP |
| typedef utility::pointer::shared_ptr< TwelveANeighborGraph > core::scoring::TwelveANeighborGraphOP |
| typedef utility::pointer::shared_ptr< UnfoldedStatePotential > core::scoring::UnfoldedStatePotentialOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPoseInfo const > core::scoring::VdWTinkerPoseInfoCOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPoseInfo > core::scoring::VdWTinkerPoseInfoOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPotential const > core::scoring::VdWTinkerPotentialCOP |
| typedef utility::pointer::shared_ptr< VdWTinkerPotential > core::scoring::VdWTinkerPotentialOP |
| typedef utility::pointer::shared_ptr< const VdWTinkerResidueInfo > core::scoring::VdWTinkerResidueInfoCOP |
| typedef utility::pointer::shared_ptr< VdWTinkerResidueInfo > core::scoring::VdWTinkerResidueInfoOP |
| typedef utility::pointer::shared_ptr< VdWTinkerRotamerSetInfo > core::scoring::VdWTinkerRotamerSetInfoOP |
| typedef numeric::xyzVector< core::Real > core::scoring::Vector |
| typedef utility::pointer::shared_ptr< WaterAdductHBondPotential const > core::scoring::WaterAdductHBondPotentialCOP |
| typedef utility::pointer::shared_ptr< WaterAdductHBondPotential > core::scoring::WaterAdductHBondPotentialOP |
| typedef Real core::scoring::Weight |
Type for looking up cached energies.
| Enumerator | |
|---|---|
| fa_atr | |
| fa_rep | |
| fa_sol | |
| fa_intra_atr | |
| fa_intra_rep | |
| fa_intra_sol | |
| fa_intra_atr_xover4 | |
| fa_intra_rep_xover4 | |
| fa_intra_sol_xover4 | |
| fa_intra_atr_nonprotein | |
| fa_intra_rep_nonprotein | |
| fa_intra_sol_nonprotein | |
| fa_intra_RNA_base_phos_atr | |
| fa_intra_RNA_base_phos_rep | |
| fa_intra_RNA_base_phos_sol | |
| fa_atr_dummy | |
| fa_rep_dummy | |
| fa_sol_dummy | |
| fa_vdw_tinker | |
| lk_hack | |
| lk_ball | |
| lk_ball_wtd | |
| lk_ball_iso | |
| lk_ball_bridge | |
| lk_ball_bridge_uncpl | |
| lk_dome | |
| lk_dome_iso | |
| lk_dome_bridge | |
| lk_dome_bridge_uncpl | |
| lk_ball_bridge2 | |
| lk_ball_bridge_uncpl2 | |
| lk_dome_pack | |
| coarse_fa_atr | |
| coarse_fa_rep | |
| coarse_fa_sol | |
| coarse_beadlj | |
| mm_lj_intra_rep | |
| mm_lj_intra_atr | |
| mm_lj_inter_rep | |
| mm_lj_inter_atr | |
| mm_twist | |
| mm_bend | |
| mm_stretch | |
| lk_costheta | |
| lk_polar | |
| lk_nonpolar | |
| lk_polar_intra_RNA | |
| lk_nonpolar_intra_RNA | |
| fa_elec | |
| fa_elec_bb_bb | |
| fa_elec_bb_sc | |
| fa_elec_sc_sc | |
| fa_intra_elec | |
| h2o_hbond | |
| dna_dr | |
| dna_bp | |
| dna_bs | |
| dna_ref | |
| peptide_bond | |
| pcs | |
| pcsTs1 | |
| pcsTs2 | |
| pcsTs3 | |
| pcsTs4 | |
| pcs2 | |
| fastsaxs | |
| saxs_score | |
| saxs_cen_score | |
| saxs_fa_score | |
| pddf_score | |
| fiberdiffraction | |
| fiberdiffractiondens | |
| epr_deer_score | |
| fa_mbenv | |
| fa_mbsolv | |
| fa_elec_rna_phos_phos | |
| fa_elec_rna_phos_sugr | |
| fa_elec_rna_phos_base | |
| fa_elec_rna_sugr_sugr | |
| fa_elec_rna_sugr_base | |
| fa_elec_rna_base_base | |
| fa_elec_rna_phos_phos_fast | |
| fa_elec_rna_phos_sugr_fast | |
| fa_elec_rna_phos_base_fast | |
| fa_elec_rna_sugr_sugr_fast | |
| fa_elec_rna_sugr_base_fast | |
| fa_elec_rna_base_base_fast | |
| fa_elec_aro_aro | |
| fa_elec_aro_all | |
| hack_aro | |
| rna_fa_atr_base | |
| rna_fa_rep_base | |
| rna_data_backbone | |
| ch_bond | |
| ch_bond_bb_bb | |
| ch_bond_sc_sc | |
| ch_bond_bb_sc | |
| pro_close | |
| rama2b | |
| vdw | |
| cenpack | |
| cenpack_smooth | |
| cen_hb | |
| hybrid_vdw | |
| gauss | |
| rna_vdw | |
| rnp_vdw | |
| rna_base_backbone | |
| rna_backbone_backbone | |
| rna_repulsive | |
| rna_base_pair_pairwise | |
| rna_base_axis_pairwise | |
| rna_base_stagger_pairwise | |
| rna_base_stack_pairwise | |
| rna_base_stack_axis_pairwise | |
| rna_data_base | |
| rna_base_pair | |
| rna_base_axis | |
| rna_base_stagger | |
| rna_base_stack | |
| rna_base_stack_axis | |
| rnp_base_pair | |
| rnp_stack | |
| rnp_stack_xy | |
| rnp_pair | |
| rnp_pair_dist | |
| rnp_aa_to_rna_backbone | |
| rna_mg_point | |
| rna_mg_point_indirect | |
| mg | |
| mg_lig | |
| mg_sol | |
| mg_ref | |
| hoh_ref | |
| rna_torsion | |
| rna_torsion_sc | |
| rna_suite | |
| rna_jr_suite | |
| suiteness_bonus | |
| tna_suite | |
| rna_sugar_close | |
| fa_stack | |
| fa_stack_lower | |
| fa_stack_upper | |
| fa_stack_aro | |
| fa_stack_ext | |
| fa_stack_sol | |
| fa_stack_lr | |
| fa_stack_rna_protein | |
| fa_stack_rna_protein_aro | |
| ss_contact_worst | |
| stack_elec | |
| stack_elec_base_base | |
| stack_elec_base_bb | |
| alignment | |
| dna_bb_torsion | |
| dna_sugar_close | |
| dna_base_distance | |
| geom_sol_fast | |
| geom_sol_fast_intra_RNA | |
| fa_cust_pair_dist | |
| custom_atom_pair | |
| orbitals_hpol_bb | |
| pci_cation_pi | |
| pci_pi_pi | |
| pci_salt_bridge | |
| pci_hbond | |
| arg_cation_pi | |
| python | |
| n_ci_2b_score_types | |
| fa_pair | |
| fa_pair_aro_aro | |
| fa_pair_aro_pol | |
| fa_pair_pol_pol | |
| hbond_sr_bb | |
| hbond_lr_bb | |
| hbond_bb_sc | |
| hbond_sr_bb_sc | |
| hbond_lr_bb_sc | |
| hbond_sc | |
| hbond_intra | |
| hbond_wat | |
| wat_entropy | |
| hbond | |
| npd_hbond_sr_bb | |
| npd_hbond_lr_bb | |
| npd_hbond_bb_sc | |
| npd_hbond_sr_bb_sc | |
| npd_hbond_lr_bb_sc | |
| npd_hbond_sc | |
| npd_hbond_intra | |
| npd_hbond | |
| fa_grpelec | |
| interface_dd_pair | |
| geom_sol | |
| geom_sol_intra_RNA | |
| occ_sol_fitted | |
| occ_sol_fitted_onebody | |
| occ_sol_exact | |
| cen_rot_pair | |
| cen_rot_pair_ang | |
| cen_rot_pair_dih | |
| pair | |
| cen_pair_smooth | |
| Mpair | |
| MPPair | |
| FaMPSolv | |
| suck | |
| rna_rg | |
| rna_motif | |
| facts_elec | |
| facts_solv | |
| facts_sasa | |
| motif_dock | |
| pointwater | |
| goap | |
| goap_dist | |
| goap_angle | |
| approximate_buried_unsat_penalty | |
| interchain_pair | |
| interchain_vdw | |
| n_shortranged_2b_score_types | |
| gb_elec | |
| multipole_elec | |
| fa_sasa | |
| dslf_ss_dst | |
| dslf_cs_ang | |
| dslf_ss_dih | |
| dslf_ca_dih | |
| dslf_cbs_ds | |
| dslf_fa13 | |
| dslfc_cen_dst | |
| dslfc_cb_dst | |
| dslfc_ang | |
| dslfc_cb_dih | |
| dslfc_bb_dih | |
| dslfc_rot | |
| dslfc_trans | |
| dslfc_RT | |
| atom_pair_constraint | |
| base_pair_constraint | |
| coarse_chainbreak_constraint | |
| constant_constraint | |
| coordinate_constraint | |
| angle_constraint | |
| dihedral_constraint | |
| big_bin_constraint | |
| dunbrack_constraint | |
| site_constraint | |
| metalhash_constraint | |
| metalbinding_constraint | |
| rna_stub_coord_hack | |
| bond_geometry | |
| rna_bond_geometry | |
| Hpol_bond_geometry | |
| rama | |
| omega | |
| fa_dun | |
| fa_dun_dev | |
| fa_dun_rot | |
| fa_dun_semi | |
| cen_rot_dun | |
| dna_chi | |
| p_aa_pp | |
| p_aa_ss | |
| yhh_planarity | |
| hxl_tors | |
| h2o_intra | |
| ref | |
| ref_nc | |
| seqdep_ref | |
| nmer_ref | |
| nmer_pssm | |
| nmer_svm | |
| envsmooth | |
| e_pH | |
| rna_bulge | |
| dna_dihedral_bb | |
| dna_dihedral_chi | |
| dna_dihedral_sugar | |
| sugar_bb | |
| free_suite | |
| free_2HOprime | |
| free_side_chain | |
| free_base | |
| free_res | |
| free_dof | |
| intermol | |
| other_pose | |
| special_rot | |
| PB_elec | |
| cen_env_smooth | |
| cbeta_smooth | |
| cen_rot_env | |
| cen_rot_cbeta | |
| env | |
| cbeta | |
| DFIRE | |
| Menv | |
| Mcbeta | |
| Menv_non_helix | |
| Menv_termini | |
| Menv_tm_proj | |
| Mlipo | |
| rg | |
| rg_local | |
| co | |
| hs_pair | |
| ss_pair | |
| rsigma | |
| sheet | |
| burial_v2 | |
| burial | |
| abego | |
| covalent_labeling | |
| covalent_labeling_fa | |
| hrf_ms_labeling | |
| hrf_dynamics | |
| ccs_imms | |
| depc_ms | |
| rnp_env | |
| loop_close | |
| missing_res | |
| MPEnv | |
| MPCbeta | |
| MPLipo | |
| MPTermini | |
| MPNonHelix | |
| MPTMProj | |
| FaMPEnv | |
| FaMPEnvSmooth | |
| fa_water_to_bilayer | |
| FaMPAsymEzCB | |
| FaMPAsymEzCG | |
| MPResidueLipophilicity | |
| span_ins | |
| mp_span_ang | |
| MPHelicality | |
| natbias_ss | |
| natbias_hs | |
| natbias_hh | |
| natbias_stwist | |
| aa_cmp | |
| dock_ens_conf | |
| csa | |
| dc | |
| rdc | |
| rdc_segments | |
| rdc_rohl | |
| nmr_pcs | |
| nmr_rdc | |
| nmr_pre | |
| cen_pair_motifs | |
| cen_pair_motif_degree | |
| holes | |
| holes_decoy | |
| holes_resl | |
| holes_min | |
| holes_min_mean | |
| rna_chem_shift | |
| rna_chem_map | |
| rna_chem_map_lores | |
| rna_partition | |
| dab_sasa | |
| dab_sev | |
| sa | |
| d2h_sa | |
| ProQM | |
| ProQ | |
| interchain_env | |
| interchain_contact | |
| chainbreak | |
| linear_chainbreak | |
| overlap_chainbreak | |
| distance_chainbreak | |
| dof_constraint | |
| branch_conn | |
| linear_branch_conn | |
| rama_prepro | |
| paa_abego3 | |
| cart_bonded | |
| cart_bonded_angle | |
| cart_bonded_length | |
| cart_bonded_ring | |
| cart_bonded_torsion | |
| cart_bonded_proper | |
| cart_bonded_improper | |
| gen_bonded | |
| gen_bonded_bond | |
| gen_bonded_angle | |
| gen_bonded_torsion | |
| gen_bonded_improper | |
| neigh_vect | |
| neigh_count | |
| neigh_vect_raw | |
| symE_bonus | |
| sym_lig | |
| mhc_epitope | |
| pack_stat | |
| rms | |
| res_type_constraint | |
| res_type_linking_constraint | |
| pocket_constraint | |
| backbone_stub_constraint | |
| backbone_stub_linear_constraint | |
| surface | |
| p_aa | |
| unfolded | |
| split_unfolded_two_body | |
| fa_atr_ref | |
| fa_rep_ref | |
| fa_sol_ref | |
| fa_elec_ref | |
| hbond_ref | |
| dslf_fa13_ref | |
| fa_intra_atr_ref | |
| fa_intra_rep_ref | |
| fa_intra_sol_ref | |
| pro_close_ref | |
| fa_dun_ref | |
| fa_dun_dev_ref | |
| fa_dun_rot_ref | |
| fa_dun_semi_ref | |
| rama_ref | |
| p_aa_pp_ref | |
| omega_ref | |
| mm_lj_intra_rep_ref | |
| mm_lj_intra_atr_ref | |
| mm_twist_ref | |
| elec_dens_fast | |
| elec_dens_window | |
| elec_dens_whole_structure_ca | |
| elec_dens_whole_structure_allatom | |
| elec_dens_atomwise | |
| grid_vdw | |
| xtal_ml | |
| xtal_rwork | |
| xtal_rfree | |
| hpatch | |
| Menv_smooth | |
| wat_desolv | |
| ring_close | |
| aa_repeat | |
| aa_composition | |
| aspartimide_penalty | |
| hbnet | |
| buried_unsatisfied_penalty | |
| netcharge | |
| voids_penalty | |
| sap_constraint | |
| dna_env | |
| dna_pair | |
| dump_trajectory | |
| sidechain_neighbors | |
| target_clash | |
| membrane_span_constraint | |
| membrane_span_term_z_constraint | |
| aromatic_restraint | |
| rna_coarse_dist | |
| total_score | |
| dummy_score_type | |
| n_score_types | This element marks the end of the active score types. Elements in the enumeration up to this point will have space allocated for them in the EnergyMap object. Elements past this point are considered inactive and will not have space allocated for them. If you wish to use an inactive score type, you must move that score type into its appropriate position in the ScoreType enumeration (described above) and then recompile. Inactive score types must still have their names included in the ScoreTypeManager's string-to-score-type map. |
| end_of_score_type_enumeration | This element marks the very end of the score type enumeration. Elements between the n_score_types element and this element are considered inactive. They may not be used by any EnergyMethod or they will result in an out-of-bounds write and unexpected behavior. To use an inactive score type, the score type must be moved to an earlier position in this enumeration, and the program must be recompiled. Keep this guy last. |
|
inline |
|
inline |
|
inline |
References abego, ABEGO_index_A, ABEGO_index_B, ABEGO_index_E, ABEGO_index_G, ABEGO_index_INVALID, and ABEGO_index_O.
Referenced by abego3aa_to_index().
| core::Real core::scoring::all_atom_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
References is_heavyatom(), rms, and rmsd_with_super().
Referenced by protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::idealize::basic_idealize(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::check_for_closeness_without_working_parameters(), protocols::rna::denovo::movers::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::pose_reporters::RMSDReporter::report_property().
| core::Real core::scoring::all_atom_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| std::list< Size > | residue_selection | ||
| ) |
References is_heavyatom(), rms, and rmsd_with_super().
| core::Real core::scoring::all_atom_rmsd_incl_hydrogens | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
References is_any_atom(), rms, and rmsd_with_super().
| core::Real core::scoring::all_atom_rmsd_nosuper | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
References is_heavyatom(), rms, and rmsd_no_super().
Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::ligand_docking::ga_ligand_dock::constraint_relax(), protocols::cluster::GatherPosesMover::get_distance_measure(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().
| core::Real core::scoring::all_atom_rmsd_nosuper | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| utility::vector1< core::Size > const & | pose1_residues, | ||
| utility::vector1< core::Size > const & | pose2_residues | ||
| ) |
References is_heavyatom(), rms, and rmsd_no_super().
| core::Real core::scoring::all_scatom_rmsd_nosuper | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
References is_scatom(), rms, and rmsd_no_super().
Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::nmr::pcs::PCSTensor::diagonalize_tensor(), core::scoring::nmr::rdc::RDCTensor::diagonalize_tensor(), get_angles(), core::scoring::packstat::old::input_sasa_dats(), input_sasa_dats(), core::scoring::nmr::order_tensor_parameters(), core::scoring::packstat::prune_1pass(), core::scoring::packstat::prune_hidden_cavity_balls(), and core::scoring::nmr::rotation_matrix_from_euler_angles().
| void core::scoring::apply_set_weights | ( | ScoreFunctionOP | scorefxn, |
| utility::vector1< std::string > const & | settings | ||
| ) |
References score_type_from_name(), protocols::hybridization::t, and TR().
Referenced by core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_scorefxn(), protocols::rna::denovo::RNA_DeNovoProtocol::initialize_scorefxn(), and protocols::glycan_docking::GlycanDockProtocol::setup_scorefxn().
| void core::scoring::attributes_for_get_score_function_name | ( | utility::tag::AttributeList & | attributes | ) |
Get attributes ( i.e. options ) for movers to build xml schemas.
Appends the attributes read by get_score_function_name.
References attributes_for_get_score_function_name_w_description().
Referenced by core::simple_metrics::composite_metrics::CompositeEnergyMetric::provide_xml_schema(), core::simple_metrics::metrics::InteractionEnergyMetric::provide_xml_schema(), core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::provide_xml_schema(), protocols::buns::BuriedUnsatHbondFilter2::provide_xml_schema(), protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_xml_schema(), protocols::carbohydrates::CreateGlycanSequonMover::provide_xml_schema(), protocols::carbohydrates::GlycanSampler::provide_xml_schema(), protocols::carbohydrates::GlycanTreeModeler::provide_xml_schema(), and protocols::simple_filters::BuriedUnsatHbondFilter::provide_xml_schema().
| void core::scoring::attributes_for_get_score_function_name | ( | utility::tag::AttributeList & | attributes, |
| std::string const & | option_name | ||
| ) |
Appends the attributes read by get_score_function_name w/ name argument.
References attributes_for_get_score_function_name_w_description().
| void core::scoring::attributes_for_get_score_function_name_w_description | ( | utility::tag::AttributeList & | attributes, |
| std::string const & | description | ||
| ) |
Appends the attributes read by get_score_function_name.
Referenced by attributes_for_get_score_function_name().
| void core::scoring::attributes_for_get_score_function_name_w_description | ( | utility::tag::AttributeList & | attributes, |
| std::string const & | option_name, | ||
| std::string const & | description | ||
| ) |
Appends the attributes read by get_score_function_name w/ name argument.
| void core::scoring::attributes_for_parse_score_function | ( | utility::tag::AttributeList & | attributes | ) |
Appends the attributes read by parse_score_function.
References attributes_for_parse_score_function_w_description().
Referenced by protocols::calc_taskop_filters::RelativePoseFilter::attributes(), protocols::antibody::design::attributes_for_get_ab_design_global_scorefxn(), protocols::hbnet::HBNet::attributes_for_hbnet(), protocols::loop_modeling::utilities::attributes_for_set_scorefxn_from_tag(), protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(), protocols::relax::FastRelax::complex_type_generator_for_fast_relax(), protocols::minimization_packing::MinMover::complex_type_generator_for_min_mover(), protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(), protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover(), protocols::simple_ddg::ddG::define_ddG_schema(), protocols::simple_moves::ExplicitWaterMover::define_explicit_water_mover_schema(), protocols::denovo_design::movers::FoldArchitectMover::define_folder_group(), protocols::loop_modeling::LoopBuilder::get_score_function_attributes(), protocols::calc_taskop_movers::DesignRepackMover::get_xsd_complex_type(), protocols::abinitio::abscript::AbscriptLoopCloserCM::provide_xml_schema(), protocols::analysis::InterfaceAnalyzerMover::provide_xml_schema(), protocols::antibody::AntibodyCDRGrafter::provide_xml_schema(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::provide_xml_schema(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::provide_xml_schema(), protocols::calc_taskop_movers::ConsensusDesignMover::provide_xml_schema(), protocols::calc_taskop_movers::ForceDisulfidesMover::provide_xml_schema(), protocols::canonical_sampling::MetropolisHastingsMover::provide_xml_schema(), protocols::cryst::ReportGradientsMover::provide_xml_schema(), protocols::cryst::SetCrystWeightMover::provide_xml_schema(), protocols::cryst::CrystRMS::provide_xml_schema(), protocols::cryst::DockLatticeMover::provide_xml_schema(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::provide_xml_schema(), protocols::denovo_design::DisulfidizeMover::provide_xml_schema(), protocols::dna::DesignProteinBackboneAroundDNA::provide_xml_schema(), protocols::dna::DnaInterfaceMultiStateDesign::provide_xml_schema(), protocols::dna::DnaInterfacePacker::provide_xml_schema(), protocols::enzdes::BackboneSampler::provide_xml_schema(), protocols::enzdes::LigInterfaceEnergyFilter::provide_xml_schema(), protocols::enzdes::EnzScoreFilter::provide_xml_schema(), protocols::enzdes::RepackWithoutLigandFilter::provide_xml_schema(), protocols::enzdes::EnzRepackMinimize::provide_xml_schema(), protocols::enzdes::PackRotamersMoverPartGreedy::provide_xml_schema(), protocols::evolution::AlignmentAAFinder::provide_xml_schema(), protocols::evolution::AlignmentGapInserter::provide_xml_schema(), protocols::evolution::NucleotideMutation::provide_xml_schema(), protocols::farnesyl::SampleFarnesylMover::provide_xml_schema(), protocols::features::InterfaceDdGMover::provide_xml_schema(), protocols::features::RotamerRecoveryFeatures::provide_xml_schema(), protocols::fldsgn::BluePrintBDR::provide_xml_schema(), protocols::flxbb::FlxbbDesign::provide_xml_schema(), protocols::hbnet::UnsatSelector::provide_xml_schema(), protocols::helical_bundle::BundleGridSampler::provide_xml_schema(), protocols::helical_bundle::BundleReporterFilter::provide_xml_schema(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::provide_xml_schema(), protocols::matdes::SchemePlaceMotifsMover::provide_xml_schema(), protocols::mean_field::GenMeanFieldMover::provide_xml_schema(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::provide_xml_schema(), protocols::membrane_benchmark::PeptideOrientationMover::provide_xml_schema(), protocols::minimization_packing::BoltzmannRotamerMover::provide_xml_schema(), protocols::minimization_packing::PertMinMover::provide_xml_schema(), protocols::minimization_packing::RotamerTrialsMinMover::provide_xml_schema(), protocols::minimization_packing::TaskAwareMinMover::provide_xml_schema(), protocols::ncbb::ResidueReplacementRebuildMover::provide_xml_schema(), protocols::ncbb::SecStructMinimizeMover::provide_xml_schema(), protocols::parser::MonteCarloLoader::provide_xml_schema(), protocols::peptide_deriver::PeptideDeriverFilter::provide_xml_schema(), protocols::pose_creation::SliceToMiniProteinMover::provide_xml_schema(), protocols::pose_sewing::movers::BlockwiseAnalysisMover::provide_xml_schema(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::provide_xml_schema(), protocols::protein_interface_design::filters::BindingStrainFilter::provide_xml_schema(), protocols::protein_interface_design::filters::FilterScanFilter::provide_xml_schema(), protocols::protein_interface_design::filters::FNatFilter::provide_xml_schema(), protocols::protein_interface_design::filters::HbondsToResidueFilter::provide_xml_schema(), protocols::protein_interface_design::filters::IRmsdFilter::provide_xml_schema(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::provide_xml_schema(), protocols::protein_interface_design::movers::BackrubDDMover::provide_xml_schema(), protocols::protein_interface_design::movers::DisulfideMover::provide_xml_schema(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::provide_xml_schema(), protocols::protein_interface_design::movers::HotspotHasherMover::provide_xml_schema(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::provide_xml_schema(), protocols::protein_interface_design::movers::LoopRemodel::provide_xml_schema(), protocols::protein_interface_design::movers::MapHotspot::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceOnLoop::provide_xml_schema(), protocols::protein_interface_design::movers::PrepackMover::provide_xml_schema(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::provide_xml_schema(), protocols::protein_interface_design::movers::RandomMutation::provide_xml_schema(), protocols::protein_interface_design::movers::SecretionOptimizationMover::provide_xml_schema(), protocols::protein_interface_design::movers::TryRotamers::provide_xml_schema(), protocols::quantum_annealing::InteractionGraphSummaryMetric::provide_xml_schema(), protocols::recon_design::FindConsensusSequence::provide_xml_schema(), protocols::relax::AcceptToBestMover::provide_xml_schema(), protocols::relax::loop::LoopRelaxMover::provide_xml_schema(), protocols::residue_selectors::HBondSelector::provide_xml_schema(), protocols::rna::movers::ERRASER2Protocol::provide_xml_schema(), protocols::rotamer_recovery::RotamerRecoveryMover::provide_xml_schema(), protocols::score_filters::ScoreTypeFilter::provide_xml_schema(), protocols::seeded_abinitio::CloseFold::provide_xml_schema(), protocols::seeded_abinitio::SeedSetupMover::provide_xml_schema(), protocols::seeded_abinitio::SegmentHybridizer::provide_xml_schema(), protocols::seeded_abinitio::SwapSegment::provide_xml_schema(), protocols::simple_ddg::AlaScan::provide_xml_schema(), protocols::simple_ddg::DdgFilter::provide_xml_schema(), protocols::simple_ddg::DdGScan::provide_xml_schema(), protocols::simple_ddg::SSElementBisectddGFilter::provide_xml_schema(), protocols::simple_filters::DeltaFilter::provide_xml_schema(), protocols::simple_filters::EnergyPerResidueFilter::provide_xml_schema(), protocols::simple_filters::ResidueIEFilter::provide_xml_schema(), protocols::simple_filters::ResidueSetChainEnergyFilter::provide_xml_schema(), protocols::simple_filters::SimpleHbondsToAtomFilter::provide_xml_schema(), protocols::simple_filters::SSElementLengthFilter::provide_xml_schema(), protocols::simple_filters::TaskAwareScoreTypeFilter::provide_xml_schema(), protocols::simple_moves::AddChainMover::provide_xml_schema(), protocols::simple_moves::DisulfideInsertionMover::provide_xml_schema(), protocols::simple_moves::DumpPdb::provide_xml_schema(), protocols::simple_moves::ReportEffectivePKA::provide_xml_schema(), protocols::simple_moves::SwitchChainOrderMover::provide_xml_schema(), protocols::splice::Splice::provide_xml_schema(), protocols::splice::SpliceIn::provide_xml_schema(), protocols::splice::SpliceInAntibody::provide_xml_schema(), protocols::splice::SpliceInTail::provide_xml_schema(), protocols::splice::SpliceOut::provide_xml_schema(), protocols::splice::SpliceOutAntibody::provide_xml_schema(), protocols::splice::SpliceOutTail::provide_xml_schema(), protocols::splice::TailSegmentMover::provide_xml_schema(), protocols::stepwise::monte_carlo::mover::AddMover::provide_xml_schema(), protocols::stepwise::monte_carlo::mover::FromScratchMover::provide_xml_schema(), protocols::switches::GraftSwitchMover::provide_xml_schema(), protocols::symmetric_docking::SymDockProtocol::provide_xml_schema(), protocols::task_operations::SelectByDeltaScoreOperation::provide_xml_schema(), core::pack::task::residue_selector::ClashBasedShellSelector::provide_xml_schema_attributes(), protocols::design_opt::GreedyOptMutationMover::root_node_for_greedy_opt(), protocols::denovo_design::movers::BridgeChainsMover::setup_attlist_for_derived_classes(), and protocols::rosetta_scripts::RosettaScriptsSchemaValidator::write_ROSETTASCRIPTS_complex_type().
| void core::scoring::attributes_for_parse_score_function | ( | utility::tag::AttributeList & | attributes, |
| std::string const & | sfxn_option_name | ||
| ) |
Appends the attributes read by parse_score_function w/ name argument.
References attributes_for_parse_score_function_w_description().
| void core::scoring::attributes_for_parse_score_function_w_description | ( | utility::tag::AttributeList & | attributes, |
| std::string const & | description | ||
| ) |
Appends the attributes read by parse_score_function with description.
Referenced by attributes_for_parse_score_function(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_shared_xml_schema_elements(), protocols::denovo_design::DisulfidizeMover::provide_xml_schema(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::provide_xml_schema(), protocols::fold_from_loops::NubInitioMover::provide_xml_schema(), protocols::minimization_packing::MinPackMover::provide_xml_schema(), and protocols::simple_filters::InterfaceHbondsFilter::provide_xml_schema().
| void core::scoring::attributes_for_parse_score_function_w_description | ( | utility::tag::AttributeList & | attributes, |
| std::string const & | sfxn_option_name, | ||
| std::string const & | description | ||
| ) |
Appends the attributes read by parse_score_function w/ name argument and description.
| void core::scoring::attributes_for_parse_score_function_w_description_when_required | ( | utility::tag::AttributeList & | attributes, |
| std::string const & | sfxn_option_name, | ||
| std::string const & | description = "" |
||
| ) |
Appends the attributes read by parse_score_function w/ name argument and description.
This version appends the attributes as required attributes.
Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::provide_xml_schema(), protocols::cyclic_peptide::CrosslinkerMover::provide_xml_schema(), and protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::provide_xml_schema().
| core::Real core::scoring::automorphic_rmsd | ( | core::conformation::Residue const & | rsd1, |
| core::conformation::Residue const & | rsd2, | ||
| bool | superimpose | ||
| ) |
RMSD between residues, accounting for automorphisms (symmetries). For example if you have something like a tyrosine, you won't get a higher rmsd just because you flipped the ring 180 degrees (Rocco). Does NOT include H atoms – they add lots of extra symmetries.
Just iterates over all automorphisms for this residue type and chooses the minimum RMS.
References core::chemical::ResidueTypeBase::name(), core::chemical::AutomorphismIterator::next(), core::conformation::Residue::nheavyatoms(), residue_rmsd_nosuper(), residue_rmsd_super(), core::conformation::Residue::seqpos(), protocols::toolbox::superimpose(), TR(), and core::conformation::Residue::type().
Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_ddg::ddG::calculate(), protocols::ligand_docking::check_RMSD(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::ligand_docking::get_automorphic_RMSDs(), protocols::motifs::MotifSearch::incorporate_motifs(), core::scoring::nmr::NMRDummySpinlabelEnsemble::init_from_database_file(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking().
| std::string core::scoring::basename_for_score_function | ( | std::string const & | sfxn_name | ) |
returns family name for a specific score function. For example, ref2015_cart returns ref2015 and beta_nov16_cst returns beta_nov16 Returns an empty string if no match is found
References BETA_GENPOT, BETA_JULY15, BETA_NOV15, BETA_NOV16, CENTROID_WTS, DNA_INT_WTS, DNA_INT_WTS_GB, DOCK_LOW_PATCH, DOCK_PATCH, MEMB_HIGHRES_WTS, MM_STD_WTS, PRE_TALARIS_2013_STANDARD_WTS, REF_2015, RNA_HIRES_WTS, RNA_LORES_PLUS_HIRES_WTS, RNA_LORES_WTS, SCORE12_PATCH, SCORE13, SCORE4_SMOOTH_CART, SOFT_REP_DESIGN_WTS, SOFT_REP_WTS, TALARIS_2013, TALARIS_2014, and TR().
Referenced by protocols::relax::FastRelax::get_possible_relax_script_names().
| core::Real core::scoring::bb_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
Compute rmsd for only backbone residues (excluding carboxyl oxygen)
References is_protein_backbone(), rms, and rmsd_with_super().
Referenced by protocols::membrane::MPQuickRelaxMover::apply(), and protocols::relax::RangeRelaxMover::apply().
| core::Real core::scoring::bb_rmsd_including_O | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
Compute rmsd for only backbone residues (including carboxyl oxygen)
Protein-specific.
References is_protein_backbone_including_O(), rms, and rmsd_with_super().
Referenced by protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), and protocols::grafting::perturb_backbone_for_test().
| std::string const core::scoring::BETA_GENPOT | ( | "beta_genpot" | ) |
| std::string const core::scoring::BETA_JULY15 | ( | "beta_july15" | ) |
| std::string const core::scoring::BETA_NOV15 | ( | "beta_nov15" | ) |
| std::string const core::scoring::BETA_NOV16 | ( | "beta_nov16" | ) |
| core::Real core::scoring::biggest_residue_deviation_no_super | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| T * | predicate | ||
| ) |
function to return the biggest deviation between an atom in a pair of poses,
References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().
Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf().
| core::Real core::scoring::biggest_residue_deviation_no_super_subset | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| ObjexxFCL::FArray1D_bool const & | subset, | ||
| T * | predicate | ||
| ) |
function to return the biggest deviation between an atom in a pair of poses,
as specified by the predicate and the subset
References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().
| core::Size core::scoring::bin_from_bond | ( | core::chemical::BondName | bn, |
| core::chemical::BondRingness | br | ||
| ) |
convert a bond type to a bin index
References core::chemical::BondNotInRing, and core::chemical::UnknownRingness.
Referenced by core::scoring::BondOrderParser::factor(), core::scoring::BondOrderParser::invfactor(), protocols::ligand_docking::ga_ligand_dock::TorsionSampler::lookup_tors_distr_params(), and core::scoring::GenericBondedPotential::lookup_tors_params().
|
static |
| utility::vector1< core::Size > core::scoring::bondorders_map | ( | std::string | bt | ) |
helper function to convert string specification of bondorders to indices
References core::scoring::BondOrderParser::parse().
Referenced by core::scoring::GenericBondedPotential::modify_tors_params(), protocols::ligand_docking::ga_ligand_dock::TorsionSampler::read_database(), and core::scoring::GenericBondedPotential::read_database().
| core::Real core::scoring::CA_gdtmm | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| const std::map< core::Size, core::Size > & | residues | ||
| ) |
Compute the CA RMSD between two poses.
Computes the gdtmm between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.
References retrieve_coordinates(), and xyz_gdtmm().
Referenced by protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_filters::StructuralSimilarityEvaluator::apply(), protocols::simple_moves::ScoreMover::apply(), CA_gdtmm(), protocols::cluster::GatherPosesMover::get_distance_measure(), native_CA_gdtmm(), and protocols::jobdist::not_universal_main().
| core::Real core::scoring::CA_gdtmm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2 | ||
| ) |
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.
References CA_gdtmm().
| core::Real core::scoring::CA_gdtmm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| core::Real & | m_1_1, | ||
| core::Real & | m_2_2, | ||
| core::Real & | m_3_3, | ||
| core::Real & | m_4_3, | ||
| core::Real & | m_7_4 | ||
| ) |
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the five components of the gdtmm score.
References fill_rmsd_coordinates(), is_protein_CA(), core::pose::Pose::size(), and xyz_gdtmm().
| core::Real core::scoring::CA_gdtmm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| std::list< Size > const & | residue_selection | ||
| ) |
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.
References CA_gdtmm().
| core::Real core::scoring::CA_gdtmm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| std::list< Size > const & | residue_selection, | ||
| core::Real & | m_1_1, | ||
| core::Real & | m_2_2, | ||
| core::Real & | m_3_3, | ||
| core::Real & | m_4_3, | ||
| core::Real & | m_7_4 | ||
| ) |
References fill_rmsd_coordinates(), core::pose::Pose::size(), TR(), and xyz_gdtmm().
| void core::scoring::CA_gdttm | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| core::Real & | gdttm_score, | ||
| core::Real & | gdtha_score, | ||
| const std::map< core::Size, core::Size > & | residues | ||
| ) |
| void core::scoring::CA_gdttm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| core::Real & | gdttm_score, | ||
| core::Real & | gdtha_score, | ||
| std::list< Size > const & | residue_selection | ||
| ) |
Calculate gdttm score based on the C-alpha positions in pose1 and pose2.
References core::scoring::TMscore::apply(), fill_rmsd_coordinates(), core::scoring::TMscore::get_GDTHA(), core::scoring::TMscore::get_GDTTS(), core::pose::Pose::size(), and TR().
Referenced by protocols::mpi_refinement::add_poseinfo_to_ss(), and protocols::md::CartesianMD::report_MD().
| void core::scoring::CA_gdttm | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| core::Real & | gdttm_score, | ||
| core::Real & | gdtha_score | ||
| ) |
| int core::scoring::CA_maxsub | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| Real | rms | ||
| ) |
Calculates a C-alpha maxsub-based superposition between pose1 and pose2, returns the number of residues superimposed past a certain threshold. See maxsub.hh and maxsub.cc for more information.
References fill_rmsd_coordinates(), is_protein_CA(), rms, and core::pose::Pose::size().
Referenced by protocols::simple_filters::SelectMaxsubEvaluator::apply(), protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_moves::ScoreMover::apply(), and protocols::jobdist::not_universal_main().
| int core::scoring::CA_maxsub | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| std::list< Size > | residue_selection, | ||
| Real | rms | ||
| ) |
References fill_rmsd_coordinates(), rms, and TR().
| int core::scoring::CA_maxsub_by_subset | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| utility::vector1< bool > | |||
| ) |
References fill_rmsd_coordinates(), is_protein_CA(), and core::pose::Pose::size().
| core::Real core::scoring::CA_or_equiv_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| Size | start, | ||
| Size | end | ||
| ) |
Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose.
References core::sequence::end, fill_rmsd_coordinates(), protocols::mean_field::min(), rms, core::pose::Pose::size(), protocols::loops::start, and TR().
Referenced by CA_or_equiv_rmsd(), CA_rmsd(), core::energy_methods::RMS_Energy::finalize_total_energy(), and native_CA_rmsd().
| core::Real core::scoring::CA_or_equiv_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| std::list< Size > const & | residue_selection | ||
| ) |
References CA_or_equiv_rmsd(), fill_rmsd_coordinates(), and TR().
| core::Real core::scoring::CA_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| const std::map< core::Size, core::Size > & | residues | ||
| ) |
Compute the CA RMSD between two poses.
Computes the root mean squared deviation between zero or more CA residues in pose1 and pose2, whose correspondence is specified in the map parameter.
References retrieve_coordinates().
| core::Real core::scoring::CA_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| Size | start, | ||
| Size | end, | ||
| utility::vector1< Size > const & | exclude | ||
| ) |
References core::sequence::end, fill_rmsd_coordinates(), rms, and protocols::loops::start.
| core::Real core::scoring::CA_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| Size | start, | ||
| Size | end | ||
| ) |
Compute rmsd for residues between start and end. If start and end aren't specified, use the entire pose.
References CA_or_equiv_rmsd(), core::sequence::end, fill_rmsd_coordinates(), protocols::mean_field::min(), rms, core::pose::Pose::size(), protocols::loops::start, and TR().
Referenced by protocols::simple_filters::RmsdEvaluator::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::normalmode::NormalModeRelaxMover::apply_on_pose(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::pose_creation::MergePDBMover::check_duplicate(), compute_jump_rmsd(), protocols::simple_moves::RepeatPropagationMover::determine_overlap(), protocols::pose_creation::MergePDBMover::determine_overlap(), protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_pose(), core::energy_methods::RMS_Energy::finalize_total_energy(), protocols::relax::fix_worst_bad_ramas(), protocols::loophash::LoopHashLibrary::get_all(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::jobdist::main_plain_pdb_mover(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), native_CA_rmsd(), protocols::loops::native_loop_core_CA_rmsd(), protocols::jobdist::not_universal_main(), protocols::abinitio::hConvergenceCheck::operator()(), protocols::hybridization::hConvergenceCheck::operator()(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::pose_metric_calculators::FragQualCalculator::recompute(), protocols::glycopeptide_docking::record_pose_metrics(), protocols::relax::RepeatProteinRelax::relax_pose(), protocols::md::CartesianMD::report_MD(), protocols::pose_reporters::RMSDReporter::report_property(), core::fragment::FragmentRmsd::rmsd(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::simple_moves::ShakeStructureMover::set_temp_based_on_ens_diversity(), protocols::mpi_refinement::StructAvrgMover::shave_poses(), protocols::optimize_weights::IterativeOptEDriver::single_structure_data_for_pose(), protocols::jobdist::universal_main(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().
| core::Real core::scoring::CA_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2, | ||
| std::list< Size > | residue_selection | ||
| ) |
References CA_or_equiv_rmsd(), fill_rmsd_coordinates(), and TR().
| core::Real core::scoring::CA_rmsd_symmetric | ( | const core::pose::Pose & | native_pose, |
| const core::pose::Pose & | pose | ||
| ) |
References core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), fill_rmsd_coordinates(), is_protein_CA(), core::pose::symmetry::is_symmetric(), core::chemical::element::N, rms, and TR().
Referenced by protocols::simple_filters::SymmetricRmsdEvaluator::apply(), protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::cluster::GatherPosesMover::get_distance_measure(), and protocols::relax::FastRelax::inner_loop_accept_to_best_command().
| void core::scoring::calc_atom_masks | ( | core::conformation::Residue const & | irsd, |
| core::conformation::Residue const & | jrsd, | ||
| Real const | probe_radius, | ||
| Real const | cutoff_distance, | ||
| utility::vector1< Real > const & | radii, | ||
| id::AtomID_Map< bool > const & | atom_subset, | ||
| core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > & | atom_masks | ||
| ) |
References angles(), core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), get_orientation(), get_overlap(), core::chemical::AtomType::is_h2o(), masks(), core::conformation::Residue::natoms(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), num_bytes, core::conformation::Residue::seqpos(), and core::conformation::Atom::xyz().
Referenced by calc_per_atom_sasa().
| Real core::scoring::calc_per_atom_sasa | ( | pose::Pose const & | pose, |
| id::AtomID_Map< Real > & | atom_sasa, | ||
| utility::vector1< Real > & | rsd_sasa, | ||
| Real const | probe_radius, | ||
| bool const | use_big_polar_H, | ||
| id::AtomID_Map< bool > & | atom_subset, | ||
| bool const | use_naccess_sasa_radii, | ||
| bool const | expand_polar_radii, | ||
| Real const | polar_expansion_radius, | ||
| bool const | include_probe_radius_in_atom_radii, | ||
| bool const | use_lj_radii | ||
| ) |
returns total sasa
References core::conformation::Residue::atom_type_set(), bit_count, calc_atom_masks(), core::id::AtomID_Map< T >::clear(), core::chemical::AtomType::element(), core::chemical::AtomTypeSet::extra_parameter_index(), core::chemical::element::F, core::chemical::element::I, core::pose::initialize_atomid_map(), input_sasa_dats(), core::chemical::AtomType::is_polar_hydrogen(), maskbits, protocols::mean_field::max(), core::chemical::AtomTypeSet::n_atomtypes(), core::chemical::AtomType::name(), num_bytes, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().
Referenced by calc_per_atom_sasa(), calc_per_atom_sasa_sc(), and calc_total_sasa().
| Real core::scoring::calc_per_atom_sasa | ( | pose::Pose const & | pose, |
| id::AtomID_Map< Real > & | atom_sasa, | ||
| utility::vector1< Real > & | rsd_sasa, | ||
| Real const | probe_radius, | ||
| bool const | use_big_polar_H | ||
| ) |
Return total SASA.
References calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), and core::pose::initialize_atomid_map().
Referenced by protocols::task_operations::SelectBySASAOperation::apply(), protocols::fldsgn::topology::calc_delta_sasa(), calc_per_res_hydrophobic_sasa(), protocols::forge::methods::calc_rsd_sasa(), core::select::util::SelectResiduesByLayer::calc_rsd_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::sasa_scores::compute_residue_sasas_for_sasa_scores(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::motif::get_sasa(), protocols::constel::FilterBySASA::init(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), core::pose::metrics::simple_calculators::SasaCalculatorLegacy::recompute(), protocols::features::HBondFeatures::report_features(), protocols::features::ResidueBurialFeatures::report_features(), and core::pack::guidance_scoreterms::sap::sap_atom_sasa().
| Real core::scoring::calc_per_atom_sasa_sc | ( | pose::Pose const & | pose, |
| utility::vector1< Real > & | rsd_sasa, | ||
| bool | normalize | ||
| ) |
References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), core::pose::initialize_atomid_map(), core::id::AtomID_Map< T >::n_atom(), core::conformation::Residue::name1(), normalizing_area(), core::pose::Pose::residue(), and core::id::AtomID_Map< T >::size().
Referenced by protocols::task_operations::CrystalContactsOperation::apply(), core::energy_methods::ProQ_Energy::calculate_feature_vector(), and core::energy_methods::ProQ_Energy::calculate_feature_vector_proq2().
| Real core::scoring::calc_per_res_hydrophobic_sasa | ( | pose::Pose const & | pose, |
| utility::vector1< Real > & | rsd_sasa, | ||
| utility::vector1< Real > & | rsd_hydrophobic_sasa, | ||
| Real const | probe_radius, | ||
| bool | use_naccess_sasa_radii | ||
| ) |
Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj)
References core::conformation::Residue::atom_type(), calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), core::chemical::AtomType::element(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::chemical::ResidueType::natoms(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::resize(), core::pose::Pose::size(), and TR().
| Real core::scoring::calc_total_sasa | ( | pose::Pose const & | pose, |
| Real const | probe_radius | ||
| ) |
returns total sasa
References calc_per_atom_sasa().
Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), and core::energy_methods::SA_Energy::finalize_total_energy().
| Real core::scoring::calpha_superimpose_pose | ( | pose::Pose & | mod_pose, |
| pose::Pose const & | ref_pose | ||
| ) |
Superimpose two poses by their calpha coordinates. Ignores residues that do not have atoms named "CA.".
both poses must have the same length.
References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), core::pose::Pose::size(), and superimpose_pose().
Referenced by protocols::mpi_refinement::StructAvrgMover::add_deviations(), protocols::simple_moves::CombinePoseMover::apply(), protocols::mpi_refinement::CA_Sscore(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::star::Extender::extend_unaligned(), protocols::mpi_refinement::superimpose_all(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().
| std::string const core::scoring::CENTROID_WTS | ( | "cen_std" | ) |
| bool core::scoring::check_score_function_sanity | ( | utility::options::OptionCollection const & | options, |
| std::string const & | scorefxn_key, | ||
| bool | throw_exception | ||
| ) |
Check if a score function is requested with incompatible option flags Will return true if scorefunction is "sane" and false if not. If throw_exception is true, will raise an exception instead of returning false.
References TR().
Referenced by protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), and parse_score_function().
|
inline |
References core::pose::motif::a(), and protocols::match::upstream::b.
Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().
| Vector core::scoring::compute_bb_centroid | ( | conformation::Residue const & | res | ) |
Compute the average coordinate of the backbone heavy atoms (aka center of mass).
returns the origin if there are no backbone atoms
References core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by compute_sc_centroid(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().
| Real core::scoring::compute_bb_radius | ( | conformation::Residue const & | res, |
| Vector const & | bb_centroid | ||
| ) |
Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point.
References core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().
| void core::scoring::compute_jump_rmsd | ( | const core::pose::Pose & | reference, |
| const core::pose::Pose & | model, | ||
| boost::unordered_map< core::Size, core::Real > & | rmsds | ||
| ) |
Computes the RMSD of the jump residues between <model> and <native>, storing the results in a map keyed by jump_id.
Computes the RMSD of the jump residues (jump point +/- 1 residue) of <model> and <reference>. Jump residues are identified by scanning <reference>'s FoldTree. Results are stored in the output parameter <rmsds>, keyed by the index of the jump point. For example,
Jump 100 => 10 rmsds[10] = rmsd(residues 9-11 in reference, residues 9-11 in model)
References CA_rmsd(), core::pose::Pose::fold_tree(), and core::pose::Pose::size().
Referenced by protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd().
| Vector core::scoring::compute_sc_centroid | ( | conformation::Residue const & | res | ) |
Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone.
References compute_bb_centroid(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by protocols::constel::NeighTeller::isneigh(), core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().
| Real core::scoring::compute_sc_radius | ( | conformation::Residue const & | res, |
| Vector const & | centroid | ||
| ) |
Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point.
References core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by protocols::constel::NeighTeller::isneigh(), core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), core::pack::interaction_graph::OnTheFlyNode::set_rotamers(), and core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().
| void core::scoring::create_and_store_atom_tree_minimization_graph | ( | ScoreFunction const & | sfxn, |
| kinematics::MinimizerMapBase const & | min_map, | ||
| pose::Pose & | pose | ||
| ) |
| void core::scoring::create_and_store_atom_tree_minimization_graph_asym | ( | ScoreFunction const & | sfxn, |
| kinematics::MinimizerMapBase const & | min_map, | ||
| pose::Pose & | pose | ||
| ) |
References core::scoring::ScoreFunction::all_methods(), core::kinematics::MinimizerMapBase::domain_map(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::scoring::Energies::set_minimization_graph(), core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge(), and core::pose::Pose::size().
Referenced by create_and_store_atom_tree_minimization_graph().
| void core::scoring::create_and_store_atom_tree_minimization_graph_symm | ( | ScoreFunction const & | sfxn, |
| kinematics::MinimizerMapBase const & | min_map, | ||
| pose::Pose & | pose | ||
| ) |
References core::scoring::ScoreFunction::all_methods(), core::conformation::symmetry::SymmetryInfo::bb_follows(), core::pose::Pose::conformation(), core::conformation::symmetry::SymmetryInfo::deriv_multiply(), core::kinematics::MinimizerMapBase::domain_map(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::conformation::symmetry::SymmetryInfo::fa_is_independent(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo(), core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::conformation::symmetry::SymmetryInfo::score_multiply(), core::conformation::symmetry::SymmetryInfo::score_multiply_factor(), core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge(), and core::pose::Pose::size().
Referenced by create_and_store_atom_tree_minimization_graph().
| void core::scoring::create_shuffle_map_recursive_rms | ( | std::vector< int > | sequence, |
| int const | N, | ||
| std::vector< std::vector< int > > & | map | ||
| ) |
This is a recursive algorithm to generate all combinations of n digits where a number can only occur once in the sequence. The size scales as N! so don't use this for large values of N!!!
References core::chemical::element::N.
Referenced by CA_rmsd_symmetric(), and sym_rmsd_with_super_subset().
|
inline |
References core::scoring::ScoreFunction::clone().
| bool core::scoring::dimer_pairing_pointer_sorter | ( | DimerPairingOP const & | a, |