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Rosetta
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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 | |
| fa_imm_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 | |
| f_elec_lipidlayer | |
| 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, |
| DimerPairingOP const & | b | ||
| ) |
References core::pose::motif::a(), and protocols::match::upstream::b.
Referenced by core::scoring::SecondaryStructurePotential::sspair().
| std::string const core::scoring::DNA_INT_WTS | ( | "dna_no_gb" | ) |
| std::string const core::scoring::DNA_INT_WTS_GB | ( | "dna" | ) |
| std::string const core::scoring::DOCK_LOW_PATCH | ( | "docking_cen" | ) |
| std::string const core::scoring::DOCK_PATCH | ( | "docking" | ) |
| std::string core::scoring::element_string | ( | std::string const & | atom | ) |
| std::string core::scoring::element_string_dc | ( | std::string const & | atom | ) |
Referenced by core::scoring::DC::get_DC_data_type().
| void core::scoring::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 | ||
| ) |
References core::scoring::MinimizationEdge::active_2benmeths_begin(), core::scoring::MinimizationEdge::active_2benmeths_end(), and core::scoring::MinimizationEdge::res_pair_min_data().
Referenced by core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::SCMinMultifunc::dfunc().
| void core::scoring::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).
References core::scoring::MinimizationNode::active_1benmeths_begin(), core::scoring::MinimizationNode::active_1benmeths_end(), core::scoring::MinimizationNode::active_intrares2benmeths_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().
Referenced by core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative().
| void core::scoring::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.
References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), core::scoring::ScoreFunction::ci_2b_end(), protocols::hybridization::r1, and protocols::hybridization::r2.
| void core::scoring::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.
References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), core::scoring::ScoreFunction::ci_2b_end(), protocols::hybridization::r1, and protocols::hybridization::r2.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| Real core::scoring::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 | ||
| ) |
References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), and core::scoring::MinimizationNode::res_min_data().
Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative(), and core::scoring::ScoreFunction::eval_dof_derivative().
| void core::scoring::eval_res_onebody_energies_for_minnode | ( | MinimizationNode const & | min_node, |
| conformation::Residue const & | rsd, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) |
Deprecated.
References core::scoring::MinimizationNode::active_1benmeths_ext_begin(), core::scoring::MinimizationNode::active_1benmeths_ext_end(), core::scoring::MinimizationNode::active_1benmeths_std_begin(), core::scoring::MinimizationNode::active_1benmeths_std_end(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_end(), core::scoring::MinimizationNode::active_intrares2benmeths_std_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_std_end(), and core::scoring::MinimizationNode::res_min_data().
Referenced by core::scoring::ScoreFunction::asym_eval_onebody_energies(), core::pack::compare_mingraph_and_energy_graph(), core::pack::scmin::CartSCMinMultifunc::operator()(), and core::pack::scmin::SCMinMultifunc::operator()().
| void core::scoring::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.
References core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), and core::scoring::MinimizationEdge::res_pair_min_data().
Referenced by core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies(), core::pack::compare_mingraph_and_energy_graph(), core::pack::scmin::CartSCMinMultifunc::operator()(), and core::pack::scmin::SCMinMultifunc::operator()().
| void core::scoring::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.
References core::scoring::ScoreFunction::cd_2b_begin(), core::scoring::ScoreFunction::cd_2b_end(), core::scoring::ScoreFunction::ci_2b_begin(), core::scoring::ScoreFunction::ci_2b_end(), protocols::hybridization::r1, and protocols::hybridization::r2.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), and protocols::constel::NeighTeller::isneigh().
| void core::scoring::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 | ||
| ) |
| Real core::scoring::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 | ||
| ) |
References core::scoring::MinimizationNode::dof_deriv_1benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_1benmeths_end(), core::scoring::MinimizationNode::dof_deriv_2benmeths_begin(), core::scoring::MinimizationNode::dof_deriv_2benmeths_end(), core::scoring::MinimizationNode::res_min_data(), and core::scoring::MinimizationNode::weight().
| void core::scoring::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 | ||
| ) |
References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationNode::active_1benmeths_ext_begin(), core::scoring::MinimizationNode::active_1benmeths_ext_end(), core::scoring::MinimizationNode::active_1benmeths_std_begin(), core::scoring::MinimizationNode::active_1benmeths_std_end(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_ext_end(), core::scoring::MinimizationNode::active_intrares2benmeths_std_begin(), core::scoring::MinimizationNode::active_intrares2benmeths_std_end(), core::scoring::MinimizationNode::res_min_data(), core::scoring::MinimizationNode::weight(), and core::scoring::EMapVector::zero().
Referenced by core::scoring::ScoreFunction::sym_eval_onebody_energies().
| void core::scoring::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 | ||
| ) |
References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationEdge::active_2benmeths_ext_begin(), core::scoring::MinimizationEdge::active_2benmeths_ext_end(), core::scoring::MinimizationEdge::active_2benmeths_std_begin(), core::scoring::MinimizationEdge::active_2benmeths_std_end(), core::scoring::MinimizationEdge::res_pair_min_data(), core::scoring::MinimizationEdge::weight(), and core::scoring::EMapVector::zero().
Referenced by core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies().
| void core::scoring::evaluaterdc | ( | const core::Real * | par, |
| int | m_dat, | ||
| const void * | data, | ||
| core::Real * | fvec, | ||
| int * | |||
| ) |
References frdc(), frdcDa(), frdcDaR(), frdcR(), NLS, NLSDA, NLSDAR, NLSR, core::scoring::data_struct::r0, core::scoring::data_struct::r1, core::scoring::data_struct::r2, core::scoring::data_struct::rdc, core::scoring::data_struct::rdcconst, core::scoring::data_struct::rdcweight, core::scoring::data_struct::tensorDa, core::scoring::data_struct::tensorR, and core::scoring::data_struct::type_of_computation.
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore_nls().
| std::string const core::scoring::FA_STANDARD_DEFAULT | ( | "FA_STANDARD_DEFAULT" | ) |
global etable_id
| std::string const core::scoring::FA_STANDARD_MULTIPOLE | ( | "FA_STANDARD_MULTIPOLE" | ) |
| std::string const core::scoring::FA_STANDARD_SOFT | ( | "FA_STANDARD_SOFT" | ) |
| void core::scoring::fill_bb_pos | ( | pose::Pose const & | pose, |
| BB_Pos & | bb_pos | ||
| ) |
helper function
References core::scoring::BB_Pos::take_coordinates_from_pose().
Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().
| void core::scoring::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 | ||
| ) |
References core::conformation::Residue::is_virtual_residue(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().
Referenced by CA_gdtmm(), CA_gdttm(), CA_maxsub(), CA_maxsub_by_subset(), CA_or_equiv_rmsd(), CA_rmsd(), and CA_rmsd_symmetric().
| void core::scoring::fill_score_range | ( | std::map< std::string, ScoreType > & | M, |
| std::string const & | prefix, | ||
| int | first, | ||
| int | last | ||
| ) |
Referenced by core::scoring::ScoreTypeManager::setup_score_type_names().
| std::string core::scoring::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.
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 passes either with or without the optional extension.
References core::scoring::ScoreFunction::name().
Referenced by core::scoring::ScoreFunction::add_weights_from_file(), and core::scoring::ScoreFunction::apply_patch_from_file().
| core::Real core::scoring::frdc | ( | core::Real | r0, |
| core::Real | r1, | ||
| core::Real | r2, | ||
| core::Real | rdcconst, | ||
| const core::Real * | par | ||
| ) |
| core::Real core::scoring::frdcDa | ( | core::Real | r0, |
| core::Real | r1, | ||
| core::Real | r2, | ||
| core::Real | rdcconst, | ||
| core::Real const | tensorDa, | ||
| const core::Real * | par | ||
| ) |
| core::Real core::scoring::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 | ||
| ) |
| core::Real core::scoring::frdcR | ( | core::Real | r0, |
| core::Real | r1, | ||
| core::Real | r2, | ||
| core::Real | rdcconst, | ||
| core::Real const | tensorR, | ||
| const core::Real * | par | ||
| ) |
| core::Real core::scoring::gdtha | ( | const core::pose::Pose & | ref, |
| const core::pose::Pose & | mod, | ||
| 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.
References core::conformation::Residue::name1(), ref, core::pose::Pose::residue(), core::simple_metrics::metrics::sum, TR(), and core::pose::Pose::xyz().
Referenced by protocols::mpi_refinement::add_poseinfo_to_ss(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), and protocols::md::MDBase::report_silent().
| core::Real core::scoring::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.
@detail Instead of comparing residue positions on the basis of CAs, gdtsc uses a characteristic atom near the end of each sidechain type for the evaluation of residue-residue distance deviations.
The traditional GDT score is a weighted sum of the fraction of residues superimposed within limits of 1, 2, 4, and 8Å. For gdtsc, the backbone superposition is used to calculate fractions of corresponding model-ref sidechain atom pairs that fit under 10 distance-limit values from 0.5A to 5A. Ambiguity in Asp or Glu terminal oxygen naming is not currently considered.
Reference: Keedy, DA. The other 90% of the protein. Proteins. 2009; 77 Suppl 9:29-49.
References core::pose::Pose::is_fullatom(), core::conformation::Residue::name1(), ref, core::pose::Pose::residue(), core::simple_metrics::metrics::sum, TR(), and core::pose::Pose::xyz().
Referenced by protocols::comparative_modeling::Align_RmsdEvaluator::apply().
| ObjexxFCL::FArray2D_int const & core::scoring::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)
References angles(), and input_sasa_dats().
| std::map< id::AtomID, utility::vector1< Real > > core::scoring::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.
Pose will be rescored with the scorefunction (hence it being non-const) Not all energies are atomistic
References get_pairwise_atom_energies(), and get_single_atom_energies().
|
inline |
References REF_2015.
|
inline |
References protocols::mean_field::min().
Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().
|
inline |
References protocols::mean_field::min().
Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs().
| ObjexxFCL::FArray2D_ubyte const & core::scoring::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)
References input_sasa_dats(), and masks().
|
inline |
References T().
Referenced by core::scoring::OneDDistPotential::initialize_from_json().
| int core::scoring::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)
References num_bytes.
| void core::scoring::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)
ronj This function is used to get two indexes (phi and theta) which are used to get the index of a dot on the ronj surface of the 'a' sphere. When calculating how much surface area sphere b covers on a, we can get the degree ronj of overlap from the function above, but it's not necessarily the case that the vector that connects the center ronj of atom 'a' and atom 'b' goes through one of the predetermined dot locations on the surface of 'a'. In fact, ronj it's very unlikely that the vector goes through a predetermined dot. Instead, what is done is the actual point ronj of intersection (the outermost point of a on the line from the center of 'a' to center of 'b') is converted ronj to spherical polar coordinates. Then, the values are used to find the location of the closest predetermined ronj point on the surface of 'a' using a lookup table. So what this function needs to do is convert the ronj cartesian coordinate of the actual point of intersection into polar coordinates. ronj ronj To get the spherical, polar coordinates of a cartesian point x,y,z, use these equations: ronj r = sqrt( x^2 + y^2 + z^2 ) ronj theta = arccos( z / r ) ronj phi = arctan( y / x )
ronj Then, once we have the true phi and theta, we need to translate this into an index (or offset) for the correct ronj value in the database file. There are 64 phi angle bin and 64 theta bins in the database file sampling/SASA-angles.dat. ronj We need to convert the phi and theta into indexes for this file by multiplying them by num_phi / 2*pi. ronj Note: I think phi and theta have been reversed in the function below. The code below uses the following: ronj phi = arccos( z ) ronj theta = arctan( y / x )
ronj After a couple of weeks trying to write tests for this function, I have been unsuccessful in figuring out why ronj it's doing what it does. Despite using the wrong equations, it seems to work. Comparing the total residue ronj SASA values calculated by calc_per_atom_sasa() below results in a correlation of 0.98 against what the program ronj NACCESS finds for the same residues. This test was done on a small 110aa protein. I also looked at the per-atom ronj total SASA and the correlation for all atoms (mini v. NACCESS) was approximately 0.94. I'm using exactly the same ronj van der Waals radii for both programs so I feel like the correlations should be 1.0. Explanations for the ronj differences can be 1) this method is doing something wrong in calculating the closest surface point, 2) this ronj method is correct but the masks that are in the database are not aligned to the surface points correctly, 3) the ronj differences are solely due to the different way that the two program calculate surface area.
References num_phi, and num_theta.
Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().
| void core::scoring::get_overlap | ( | Real const | radius_a, |
| Real const | radius_b, | ||
| Real const | distance_ijxyz, | ||
| int & | degree_of_overlap | ||
| ) |
getting overlap from a to b (or i to j, as the atoms are referred to in calc_per_atom_sasa below). this returns the degree of overlap between two atoms adapted from erics code in area.c GetD2 and returns value from 1 to 100. This calculation is based on the law of cosines. See LeGrand and Merz, Journal of Computational Chemistry 14(3):349-52 (1993). Note that equation (4) is wrong, the denominator should be 2*ri*riq instead of 2*ri*rq (j)
The function gets passed in the sasa radius of atom i (plus the probe radius), the sasa radius of atom j (plus the probe radius), the distance between the atom centers, and a reference to the degree of overlap (represented as an int). The degree of overlap that's returned can be thought of as how much of atom a is covered by atom b. A value of 100 means that atom a is completely covered up by atom b. A value of 1 means that not much of the surface of 'a' is covered up by 'b'. The law of cosines relates the cosine of one angle of a triangle to the lengths of its sides. More specifically, c^2 = a^2 + b^2 - 2*a*b*cos theta, where theta is the angle between sides a and b. For the function we want to compute the angle of the cone of intersection between spheres 'a' and 'b'. Let the radius of atom a be ri, and the radius of atom b be rq, and the distance between atom centers be riq. Let the angle between ri and riq be theta_iq. The cosine of theta_iq will be equivalent to ( ri^2 + riq^2 - rq^2 ) / 2 * ri * riq
Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().
| std::map< std::pair< id::AtomID, id::AtomID >, utility::vector1< Real > > core::scoring::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.
Pose will be rescored with the scorefunction (hence it being non-const) Not all energies are atomistic
References protocols::cluster::calibur::aa, core::scoring::ScoreFunction::all_energies_begin(), core::scoring::ScoreFunction::all_energies_end(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::EMapVector::sum(), core::id::to_string(), and core::scoring::ScoreFunction::weights().
Referenced by get_atomistic_energies().
| uint64_t core::scoring::get_parameter_hash | ( | Size | bondtypr, |
| Size | type1, | ||
| Size | type2, | ||
| Size | type3, | ||
| Size | type4 | ||
| ) |
compress 5 values into one unsigned int; use 12 bits for each
Referenced by core::scoring::ResidueExclParams::find_by_atmpairno(), core::scoring::GenBondedExclInfo::get_residue_pair_data(), core::scoring::GenericBondedPotential::lookup_angle_params(), core::scoring::GenericBondedPotential::lookup_bond_params(), core::scoring::GenericBondedPotential::lookup_improper_params(), protocols::ligand_docking::ga_ligand_dock::TorsionSampler::lookup_tors_distr_params(), core::scoring::GenericBondedPotential::lookup_tors_params(), core::scoring::GenericBondedPotential::modify_tors_params(), protocols::ligand_docking::ga_ligand_dock::TorsionSampler::read_database(), core::scoring::GenericBondedPotential::read_database(), and core::scoring::ResidueExclParams::store_by_atmpairno().
| std::map< std::string, rmsd_atoms > core::scoring::get_rmsd_type_name_map | ( | ) |
Setup a name mapping for rmsd_atoms.
References rmsd_all, rmsd_all_heavy, rmsd_protein_bb_ca, rmsd_protein_bb_heavy, rmsd_protein_bb_heavy_including_O, rmsd_sc, and rmsd_sc_heavy.
Referenced by get_rmsd_type_names(), core::simple_metrics::metrics::RMSDMetric::setup_name_mapping(), and core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::setup_name_mapping().
| utility::vector1< std::string > core::scoring::get_rmsd_type_names | ( | ) |
Setup a name mapping for rmsd_atoms.
References get_rmsd_type_name_map().
Referenced by core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(), and core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema().
| core::scoring::ScoreFunctionOP core::scoring::get_score_function | ( | bool const | is_fullatom | ) |
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.
Referenced by protocols::topology_broker::TopologyBroker::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::dna::DnaInterfaceMinMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::antibody::AntibodyCDRGrafter::apply(), protocols::calc_taskop_movers::ConsensusDesignMover::apply(), protocols::carbohydrates::GlycanTreeMinMover::apply(), protocols::comparative_modeling::LoopRelaxThreadingMover::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::hbnet::HBNet::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::membrane::benchmark::SampleTiltAngles::apply(), protocols::minimization_packing::DisulfideOptimizationMover::apply(), protocols::minimization_packing::MinMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::rna::denovo::movers::RNA_Relaxer::apply(), protocols::rna::denovo::movers::RNP_HighResMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::antibody_legacy::AntibodyModeler::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), core::pack::task::residue_selector::ClashBasedShellSelector::apply(), protocols::residue_selectors::HBondSelector::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::antibody::snugdock::SnugDockProtocol::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::design_opt::Supercharge::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::switches::GraftSwitchMover::apply(), protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_energy_selector(), protocols::rbsegment_relax::AutoRBMover::AutoRBMover(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::calculate(), protocols::canonical_sampling::canonical_sampling_main(), protocols::buns::BuriedUnsatHbondFilter2::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::protein_interface_design::filters::HbondsToAtomFilter::compute(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::ResiduesInInterfaceFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), protocols::ligand_docking::ga_ligand_dock::constraint_relax(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::count_hbonds(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_fullatom_scorefunction(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::electron_density::create_minimize_pose_into_density_options(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), protocols::stepwise::legacy::modeler::rna::create_scorefxn(), protocols::ddG_main(), protocols::fold_from_loops::NubInitioMover::default_filter_scorefxn(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_fullatom_scorefxn(), protocols::fold_from_loops::NubInitioMover::default_fullatom_scorefxn(), protocols::fold_from_loops::filters::ConstraintFulfilmentFilter::default_scorefxn(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::default_scorefxn(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::design_opt::Supercharge::design_supercharge(), protocols::design_opt::Supercharge::design_supercharge_AvNAPSA(), protocols::loop_modeling::refiners::MinimizationRefiner::do_apply(), protocols::electron_density::DockFragmentsIntoDensityMover::do_refinement(), protocols::docking::DockingHighRes::DockingHighRes(), protocols::docking::DockingHighResFilter::DockingHighResFilter(), protocols::cryst::DockLatticeMover::DockLatticeMover(), protocols::electron_density::dockPoseIntoMap(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::antibody::GraftOneCDRLoop::finalize_setup(), protocols::backrub::BackrubProtocol::finalize_setup(), protocols::protein_interface_design::movers::finalize_stub_set(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::floppy_tail::FloppyTailMover::FloppyTailMover(), protocols::flxbb::FlxbbDesign_main(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::GALigandDock(), protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::relax::generate_relax_from_cmd(), protocols::metal_interface::ZincHeterodimerMover::generate_scorefunctions(), protocols::abinitio::AbrelaxApplication::generate_scorefxn(), protocols::features::strand_assembly::SandwichFeatures::generate_scorefxn(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::generous_hbond(), protocols::antibody::design::get_ab_design_global_scorefxn(), protocols::antibody::design::get_ab_design_min_scorefxn(), protocols::features::get_current_model_score(), protocols::rpc::JSON_RPC::get_fa_score(), protocols::loops::get_fa_scorefxn(), protocols::antibody::get_LoopHighRes_ScoreFxn(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::get_metric_names(), protocols::relax::RelaxScriptManager::get_nearest_sfxn_if_in_database(), protocols::relax::RelaxScriptManager::get_relax_script(), protocols::rna::denovo::get_rna_hires_scorefxn(), protocols::denovo_design::movers::get_score_function(), get_score_function(), get_score_function_legacy(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::features::helixAssembly::HelixBundleFeatures::HelixBundleFeatures(), protocols::hydrate::Hydrate::Hydrate(), protocols::antibody::CDRsMinPackMin::init(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::MRMover::init(), protocols::surface_docking::SurfaceDockingProtocol::init(), protocols::docking::DockingProtocol::init(), core::init::init_nonideal_correction(), protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(), protocols::coupled_moves::CoupledMovesProtocol::initialize_from_options(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options(), protocols::calc_taskop_movers::CreateSequenceMotifMover::initialize_objects(), protocols::ligand_docking::LigandBaseProtocol::initialize_scorefxns(), core::simple_metrics::metrics::InteractionEnergyMetric::InteractionEnergyMetric(), protocols::features::InterfaceFeatures::InterfaceFeatures(), protocols::simple_filters::InterfaceHbondsFilter::InterfaceHbondsFilter(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::relax::LocalRelax::LocalRelax(), protocols::loop_grower::LoopGrower::LoopGrower(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::LoopMover_Refine_Backrub(), protocols::make_rot_lib::MakeRotLibMover::MakeRotLibMover(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::minimization_packing::PertMinMover::min(), protocols::forge::remodel::RemodelLigandHandler::minimize(), protocols::simple_moves::PeptideStapleMover::minimize_(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::ncbb::NcbbDockDesignProtocol::NcbbDockDesignProtocol(), protocols::jobdist::not_universal_main(), protocols::ncbb::oop::OopDockDesignProtocol::OopDockDesignProtocol(), core::pack::optimize_H_and_notify(), protocols::dna::PDBOutput::output_pdb(), protocols::frag_picker::FragmentCandidate::output_silent(), core::pack::pack_missing_sidechains(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::nmr::ParaNMRScoreMover::ParaNMRScoreMover(), protocols::minimization_packing::RotamerTrialsMinMover::parse_my_tag(), protocols::buns::BuriedUnsatHbondFilter2::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::features::HBondFeatures::parse_my_tag(), protocols::minimization_packing::DisulfideOptimizationMover::parse_my_tag(), protocols::pose_reporters::EnergyReporter::parse_my_tag(), protocols::rna::movers::ERRASER2Protocol::parse_my_tag(), core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), protocols::peptide_deriver::PeptideDeriverFilter::PeptideDeriverFilter(), protocols::simple_moves::PeriodicBoxMover::PeriodicBoxMover(), protocols::nmr::pre::PREMover::PREMover(), protocols::design_opt::Supercharge::prepack_input_structure(), protocols::glycopeptide_docking::GlycopeptideDockingProtocol::prepare_score_function(), protocols::match::MatcherMover::process_pose(), protocols::denovo_design::DisulfidizeMover::process_pose(), protocols::loop_modeling::LoopProtocol::ramp_score_function(), core::util::rebuild_disulfide(), protocols::glycopeptide_docking::record_pose_metrics(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::tcr::refine_tcr_cdr_loops(), protocols::antibody_legacy::AntibodyModeler::relax_cdrs(), protocols::tcr::remodel_tcr_cdr_loops(), protocols::forge::remodel::RemodelEnzdesCstModule::RemodelEnzdesCstModule(), protocols::forge::remodel::RemodelMover::RemodelMover(), protocols::enzdes::RemoveLigandFilter::RemoveLigandFilter(), protocols::features::HBondFeatures::report_features(), protocols::forge::methods::restore_residues(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::abinitio::run_boinc_debug(), protocols::farnesyl::SampleFarnesylMover::sample_farnesyl(), protocols::farnesyl::InstallFarnesylMover::sample_first(), protocols::farnesyl::InstallFarnesylMover::sample_second(), protocols::farnesyl::InstallFarnesylMover::sample_third(), protocols::matdes::SchemePlaceMotifsMover::SchemePlaceMotifsMover(), protocols::rotamer_recovery::RotamerRecoveryMover::score_function(), protocols::ncbb::SecStructFinder::SecStructFinder(), protocols::antibody::H3RefineCCD::set_default(), protocols::antibody_legacy::CDRH3Modeler::set_default(), protocols::antibody_legacy::LoopRlxMover::set_default(), protocols::ub_e2c::ubi_e2c_modeler::set_default(), protocols::docking::DockMCMCycle::set_default(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::symmetric_docking::SymDockProtocol::set_default(), protocols::tcr::TCRmodel::set_default(), protocols::grafting::AnchoredGraftMover::set_default_fa_scorefunction(), protocols::symmetric_docking::SymSidechainMinMover::set_default_options(), protocols::antibody::design::MutateFrameworkForCluster::set_defaults(), protocols::relax::CentroidRelax::set_defaults(), protocols::relax::RangeRelaxMover::set_defaults(), protocols::minimization_packing::SaneMinMover::set_defaults_(), protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::set_up_scorefunction(), protocols::surface_docking::FullatomRelaxMover::setup_defaults(), protocols::antibody::AntibodyModelerProtocol::setup_objects(), protocols::antibody::GraftCDRLoopsProtocol::setup_objects(), protocols::antibody::GraftedStemOptimizer::setup_protocol(), protocols::carbohydrates::GlycanSampler::setup_score_function(), protocols::carbohydrates::GlycanTreeModeler::setup_score_function(), protocols::simple_moves::CyclizationMover::setup_scorefunction(), protocols::analysis::InterfaceAnalyzerMover::setup_scorefxn(), protocols::glycan_docking::GlycanDockProtocol::setup_scorefxn(), protocols::docking::SidechainMinMover::SidechainMinMover(), protocols::loop_modeling::LoopProtocol::start_protocol(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::simple_moves::SwitchChainOrderMover::SwitchChainOrderMover(), protocols::symmetric_docking::SymDockBaseProtocol::SymDockBaseProtocol(), protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes(), core::simple_metrics::metrics::TotalEnergyMetric::TotalEnergyMetric(), and protocols::chemically_conjugated_docking::UBQ_GTPaseMover::UBQ_GTPaseMover().
| core::scoring::ScoreFunctionOP core::scoring::get_score_function | ( | pose::Pose const & | pose, |
| bool const | is_fullatom | ||
| ) |
Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose.
References get_score_function().
| core::scoring::ScoreFunctionOP core::scoring::get_score_function | ( | pose::Pose const & | pose, |
| utility::options::OptionCollection const & | options, | ||
| bool const | is_fullatom | ||
| ) |
Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. Local Options collection.
References get_score_function(), and core::pose::symmetry::is_symmetric().
| core::scoring::ScoreFunctionOP core::scoring::get_score_function | ( | utility::options::OptionCollection const & | options, |
| bool const | is_fullatom | ||
| ) |
A helper function which creates a scoring function held in an owning pointer reading from the input OptionCollection.
References CENTROID_WTS, core::scoring::ScoreFunctionFactory::create_score_function(), fa_intra_rep_xover4, metalbinding_constraint, sugar_bb, and TR().
| core::scoring::ScoreFunctionOP core::scoring::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.
Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::antibody::LHSnugFitLegacy::apply(), protocols::minimization_packing::SetReturningPackRotamersMover::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::minimization_packing::MinPackMover::apply(), protocols::sasa_scores::compute_avge_scores(), protocols::antibody::get_Pack_ScoreFxn(), protocols::motifs::IRCollection::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::antibody::RefineBetaBarrel::init(), protocols::docking::TemperedDocking::init_from_options(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::antibody::LHRepulsiveRampLegacy::set_default(), protocols::ub_e2c::ubi_e2c_modeler::set_default(), protocols::minimization_packing::PackRotamersMover::setup(), protocols::simple_moves::ShakeStructureMover::setup_for_run(), protocols::symmetry::SymShakeStructureMover::setup_for_run(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol(), protocols::motifs::IRCollection::successful_loop_closure(), and protocols::motifs::IRCollection::try_for_more().
| core::scoring::ScoreFunctionOP core::scoring::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 | ||
| ) |
| std::string core::scoring::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.
References get_score_function_name().
| std::string core::scoring::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.
Referenced by get_score_function_name(), protocols::buns::BuriedUnsatHbondFilter2::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), and protocols::calc_taskop_movers::DesignRepackMover::parse_my_tag().
| std::string core::scoring::get_score_functionName | ( | bool const | is_fullatom | ) |
use the logic of get_score_function to get the name. The name format is <weights_tag>[_<patch_tag> ... ]
References CENTROID_WTS, PRE_TALARIS_2013_STANDARD_WTS, and SCORE12_PATCH.
Referenced by protocols::relax::FastRelax::get_possible_relax_script_names().
| std::map< id::AtomID, utility::vector1< Real > > core::scoring::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.
Pose will be rescored with the scorefunction (hence it being non-const) Not all energies are atomistic
References protocols::cluster::calibur::aa, core::scoring::ScoreFunction::all_energies_begin(), core::scoring::ScoreFunction::all_energies_end(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::EMapVector::sum(), core::id::to_string(), and core::scoring::ScoreFunction::weights().
Referenced by get_atomistic_energies().
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intraresidue atom pair energy evaluations
References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), fa_atr, fa_rep, fa_sol, core::chemical::AtomType::is_virtual(), core::conformation::Residue::nheavyatoms(), residue_fast_pair_energy_attached_H(), and core::conformation::Residue::seqpos().
Referenced by core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >::residue_atom_pair_energy().
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templated atom pair energy calculations
loops over the heavy atoms of residue1 and the heavy atoms of residue2, evaluates their energies, and if a pair of heavy atoms is close enough, descendes into the attached hydrogen atoms for each.
Templates are for count_pair type resolution and etable type resolution: there are no polymorphic lookups within these functions
class T must define class T_Etable must define atom_pair_energy( Atom const &, Atom const &, Real, EnergyMap &, Distance ) and
References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), fa_atr, fa_rep, fa_sol, core::scoring::EMapVector::get(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::name(), residue_fast_pair_energy_attached_H(), core::conformation::Residue::seqpos(), and core::scoring::EMapVector::set().
Referenced by inline_residue_atom_pair_energy(), inline_residue_atom_pair_energy_backbone_backbone(), inline_residue_atom_pair_energy_sidechain_backbone(), inline_residue_atom_pair_energy_sidechain_sidechain(), inline_residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy(), core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy().
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References inline_residue_atom_pair_energy(), and core::conformation::Residue::last_backbone_atom().
Referenced by core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_backbone_backbone(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_backbone_backbone(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_backbone_backbone(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_backbone_backbone().
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References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), core::conformation::Residue::last_backbone_atom(), and core::conformation::Residue::nheavyatoms().
Referenced by core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_backbone(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_backbone(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_backbone(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_backbone().
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References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().
Referenced by core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_sidechain(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_sidechain(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_sidechain(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_sidechain().
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References core::conformation::Residue::first_sidechain_atom(), inline_residue_atom_pair_energy(), and core::conformation::Residue::nheavyatoms().
Referenced by core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >::residue_atom_pair_energy_sidechain_whole(), core::scoring::etable::count_pair::CountPairAll::residue_atom_pair_energy_sidechain_whole(), and core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_whole().
| void core::scoring::input_sasa_dats | ( | ) |
Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above.
References angles(), core::init::init(), masks(), num_bytes, num_orientations, num_overlaps, num_phi, and num_theta.
Referenced by calc_per_atom_sasa(), core::scoring::packstat::compute_sasa(), get_angles(), and get_masks().
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Referenced by core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_axis_score(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_backbone_backbone_score(), and core::scoring::rna::RNA_LowResolutionPotential::get_rna_stagger_score().
| ResidueSelection core::scoring::invert_exclude_residues | ( | core::Size | nres, |
| utility::vector1< int > const & | exclude_list | ||
| ) |
Referenced by native_CA_gdtmm(), and native_CA_rmsd().
| void core::scoring::invert_exclude_residues | ( | Size | nres, |
| utility::vector1< int > const & | exclude_list, | ||
| ResidueSelection & | residue_selection | ||
| ) |
References core::pose::motif::a(), protocols::match::upstream::b, XX, YY, and ZZ.
| bool core::scoring::is_any_atom | ( | core::pose::Pose const & | , |
| core::pose::Pose const & | , | ||
| core::Size | , | ||
| core::Size | |||
| ) |
Returns true always.
Referenced by all_atom_rmsd_incl_hydrogens().
| bool core::scoring::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.
This is a "predicate" function intended for use with glycan-RMSD-calculating functions
References core::chemical::ResidueType::is_ring_atom(), core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), and core::conformation::Residue::type().
Referenced by protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics().
| bool core::scoring::is_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_is_hydrogen(), and core::pose::Pose::residue().
Referenced by all_atom_rmsd(), all_atom_rmsd_nosuper(), biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::docking::calc_Irmsd(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_with_super(), and sym_rmsd_with_super_subset().
| bool core::scoring::is_ligand_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().
Referenced by biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::ligand_docking::get_multi_residue_ligand_RMSDs(), rmsd_no_super(), rmsd_with_super(), and sym_rmsd_with_super_subset().
| bool core::scoring::is_ligand_heavyatom_residues | ( | core::conformation::Residue const & | residue1, |
| core::conformation::Residue const & | , | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_is_hydrogen(), and core::conformation::Residue::is_polymer().
Referenced by protocols::ligand_docking::check_RMSD(), and rmsd_no_super().
| bool core::scoring::is_nbr_atom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
| bool core::scoring::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.
This is a "predicate" function intended for use with RMSD-calculating functions.
References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by non_peptide_heavy_atom_RMSD().
| bool core::scoring::is_polymer_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::is_polymer(), and core::pose::Pose::residue().
Referenced by biggest_residue_deviation_no_super(), biggest_residue_deviation_no_super_subset(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), rmsd_with_super(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), and sym_rmsd_with_super_subset().
| bool core::scoring::is_protein_backbone | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), bb_rmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::docking::calc_Lrmsd(), protocols::docking::calc_P1rmsd(), protocols::docking::calc_P2rmsd(), protocols::loop_modeling::utilities::TrajectoryLogger::calc_rmsd_to_native(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_with_super(), core::scoring::IsProteinBackbonePredicate::operator()(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| bool core::scoring::is_protein_backbone_including_O | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by bb_rmsd_including_O(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_and_save(), protocols::rpc::JSON_RPC::get_irms(), protocols::antibody::global_loop_rmsd(), core::scoring::IsProteinBackboneIncludingOPredicate::operator()(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features().
| bool core::scoring::is_protein_CA | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::symmetry::SymmetricRMSMover::apply(), CA_gdtmm(), CA_gdttm(), CA_maxsub(), CA_maxsub_by_subset(), CA_rmsd_symmetric(), protocols::docking::calc_CA_Irmsd(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::antibody_legacy::AntibodyModeler::global_loop_rmsd(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd(), core::scoring::IsProteinCAPredicate::operator()(), protocols::glycopeptide_docking::record_pose_metrics(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| bool core::scoring::is_protein_CA_or_CB | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().
Referenced by protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::features::ProteinRMSDFeatures::report_features(), and protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features().
| bool core::scoring::is_protein_CA_or_equiv | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::is_carbohydrate(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), and core::pose::Pose::residue().
Referenced by core::scoring::IsMainAtomPredicate::operator()().
| bool core::scoring::is_protein_sidechain_heavyatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueTypeBase::is_protein(), and core::pose::Pose::residue_type().
Referenced by protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::features::ProteinRMSDFeatures::report_features(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| bool core::scoring::is_scatom | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | , | ||
| core::Size | resno, | ||
| core::Size | atomno | ||
| ) |
References core::conformation::Residue::atom_is_backbone(), and core::pose::Pose::residue().
Referenced by all_scatom_rmsd_nosuper(), and protocols::pose_metric_calculators::compute_rmsd().
| void core::scoring::jacobi | ( | ResidualDipolarCoupling::Tensor5 & | a, |
| ResidualDipolarCoupling::rvec5 & | d, | ||
| ResidualDipolarCoupling::Tensor5 & | v, | ||
| int & | nrot | ||
| ) |
References core::pose::motif::a(), protocols::match::upstream::b, ROTATE(), and protocols::hybridization::t.
Referenced by protocols::evaluation::PCA::calc_fit_R(), and m_inv_gen().
| void core::scoring::jacobi3 | ( | ResidualDipolarCoupling::Tensor & | a, |
| ResidualDipolarCoupling::rvec & | d, | ||
| ResidualDipolarCoupling::Tensor & | v, | ||
| int & | nrot | ||
| ) |
References core::pose::motif::a(), protocols::match::upstream::b, ROTATE(), and protocols::hybridization::t.
Referenced by core::scoring::ResidualDipolarCoupling::compute_tensor_stats().
| core::Real core::scoring::lddt | ( | core::pose::Pose const & | ref, |
| core::pose::Pose const & | model, | ||
| bool | consider_alt | ||
| ) |
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)
References core::scoring::lDDT_Calculator::consider_alt_states(), and ref.
| void core::scoring::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.
References core::scoring::ScoreFunctionFactory::list_read_options().
Referenced by protocols::rosetta_scripts::RosettaScriptsParser::list_options_read().
| void core::scoring::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.
References core::scoring::ScoreFunctionFactory::list_read_options().
| int core::scoring::m_inv_gen | ( | ResidualDipolarCoupling::Tensor5 const & | m, |
| int | n, | ||
| ResidualDipolarCoupling::Tensor5 & | minv | ||
| ) |
References jacobi().
Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore().
| ObjexxFCL::FArray2D_ubyte core::scoring::masks | ( | num_bytes | , |
| num_overlaps * | num_orientations | ||
| ) |
Referenced by calc_atom_masks(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), get_masks(), core::scoring::packstat::old::input_sasa_dats(), input_sasa_dats(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().
| std::string const core::scoring::MEMB_HIGHRES_WTS | ( | "membrane_highres" | ) |
| Membrane_FAEmbed const & core::scoring::Membrane_FAEmbed_from_pose | ( | pose::Pose const & | pose | ) |
Return a Const Reference to the Embedding Object from the Pose Cache.
Grab Const MP Fa Embedding data from the pose cache.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.
Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::energy_methods::Fa_MbenvEnergy::residue_energy(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().
| MembraneEmbed const & core::scoring::MembraneEmbed_from_pose | ( | pose::Pose const & | pose | ) |
Add Const Membrane Embedding to the pose cache.
Pose must already contain a cenlist object or this method will fail.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.
Referenced by protocols::rigid::MovePoseToMembraneCenterMover::apply(), protocols::rigid::MembraneCenterPerturbationMover::apply(), protocols::rigid::MembraneNormalPerturbationMover::apply(), core::energy_methods::MembraneEnvSmoothEnergy::calc_energy(), core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::evaluate_env(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().
| MembraneTopology const & core::scoring::MembraneTopology_from_pose | ( | pose::Pose const & | pose | ) |
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.
Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MembranePotential::check_spanning(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::MembranePotential::init_membrane_center_normal(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::MembranePotential::score_normal_center(), core::scoring::MembranePotential::termini_penalty(), and core::scoring::MembranePotential::tm_projection_penalty().
| std::string const core::scoring::MM_STD_WTS | ( | "mm_std" | ) |
References core::pose::motif::a(), XX, YY, and ZZ.
| std::string core::scoring::name_from_score_type | ( | ScoreType | score_type | ) |
Returns the name of the ScoreType <score_type>
example(s): name_from_score_type(fa_sol) See also: ScoreFunction ScoreType Energies Energies.residue_total_energies score_type_from_name
References core::scoring::ScoreTypeManager::name_from_score_type().
Referenced by core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::docking::SlideIntoContact::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::calculate(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), core::scoring::ScoreFunction::check_methods(), protocols::optimize_weights::IterativeOptEDriver::converged(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::io::silent::SilentStruct::energies_from_pose(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::get_metric_names(), protocols::ddg::ddGMover::get_scorefunction_header(), protocols::ligand_docking::InterfaceScoreCalculator::get_scores(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::optimize_weights::WrapperOptEMultifunc::init(), protocols::optimize_weights::IterativeOptEDriver::initialize_free_and_fixed(), protocols::optimize_weights::IterativeOptEDriver::IterativeOptEDriver(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::scoring::methods::EnergyMethodOptions::method_weights(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::ligand_docking::output_interface_deltas(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), core::scoring::ScoreFunction::perturb_weights(), protocols::rpc::pose_energies_to_json(), core::scoring::EMapVector::print(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::process_score(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::provide_xml_schema(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::moves::PyMOLMover::send_energy(), protocols::abinitio::ClassicAbinitio::set_score_weight(), protocols::abinitio::FragmentSampler::set_score_weight(), protocols::abinitio::MembraneAbinitio::set_score_weight(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_scorefxn(), core::scoring::Energies::show(), protocols::mainchain_potential::GenerateMainchainPotential::write_last_generated_to_disk(), protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile(), protocols::optimize_weights::IterativeOptEDriver::write_parameters_to_std_out(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file(), and protocols::optimize_weights::OptEData::write_to_file().
| core::Real core::scoring::native_CA_gdtmm | ( | const core::pose::Pose & | native_pose, |
| const core::pose::Pose & | pose | ||
| ) |
References CA_gdtmm(), invert_exclude_residues(), and core::pose::Pose::size().
Referenced by protocols::relax::FastRelax::batch_apply().
| core::Real core::scoring::native_CA_rmsd | ( | const core::pose::Pose & | native_pose, |
| const core::pose::Pose & | pose | ||
| ) |
References CA_or_equiv_rmsd(), CA_rmsd(), invert_exclude_residues(), and core::pose::Pose::size().
Referenced by protocols::relax::FastRelax::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::relax::FastRelax::inner_loop_accept_to_best_command(), protocols::jobdist::main_plain_pdb_mover(), and protocols::jobdist::universal_main().
| core::Real core::scoring::nbr_atom_rmsd | ( | const core::pose::Pose & | pose1, |
| const core::pose::Pose & | pose2 | ||
| ) |
References is_nbr_atom(), rms, and rmsd_with_super().
| core::DistanceSquared core::scoring::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.
This does NOT perform a superimposition first.
References is_non_peptide_heavy_atom(), and rmsd_no_super().
| Membrane_FAEmbed & core::scoring::nonconst_Membrane_FAEmbed_from_pose | ( | pose::Pose & | pose | ) |
Return a Non Const Reference to the Embedding Object from the Pose Cache.
Grab Const MP Fa embedding data from the pose cache.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.
Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::Membrane_FAPotential::fa_projection(), and core::scoring::Membrane_FAPotential::finalize().
| MembraneEmbed & core::scoring::nonconst_MembraneEmbed_from_pose | ( | pose::Pose & | pose | ) |
Add a non const membrane embedding object to the pose cache.
Add Non Const Membrane Embedding to the pose cache.
Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.
Referenced by core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::Membrane_FAPotential::finalize(), core::scoring::MembranePotential::finalize(), and protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_embed().
| MembraneTopology & core::scoring::nonconst_MembraneTopology_from_pose | ( | pose::Pose & | pose | ) |
Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenlist object, places it in the pose, and returns a non-const reference to it.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.
Referenced by core::scoring::MembranePotential::compute_membrane_embedding().
| Real core::scoring::normalizing_area | ( | char const | res | ) |
Get the area of the sidechain.
Threadsafe now, but these values are suspect.
Referenced by calc_per_atom_sasa_sc().
| Real core::scoring::normalizing_area_total | ( | char const | res | ) |
Given a one-letter code for a canonical amino acid, return its total surface area.
Threadsafe now, but these values are suspect.
| Real core::scoring::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.
Threadsafe now. Based on Gabe Rocklin's values (grocklin@gmail.com).
Threadsafe now.
Referenced by protocols::simple_filters::BuriedSurfaceAreaFilter::compute().
| Real core::scoring::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.
Threadsafe. Based on Gabe Rocklin's values (grocklin@gmail.com).
Referenced by protocols::simple_filters::BuriedSurfaceAreaFilter::compute().
|
inline |
References core::scoring::DerivVectorPair::f1(), and core::scoring::DerivVectorPair::f2().
|
inline |
References core::scoring::DerivVectorPair::f1(), and core::scoring::DerivVectorPair::f2().
| std::ostream& core::scoring::operator<< | ( | std::ostream & | os, |
| PolymerBondedEnergyContainer const & | t | ||
| ) |
Operator to allow object to be summarized.
| std::ostream & core::scoring::operator<< | ( | std::ostream & | os, |
| ScoreType const & | score_type | ||
| ) |
output operator for ScoreType enum type
example usage: std::cout << score_type_gly << std::endl;
References core::scoring::ScoreTypeManager::name_from_score_type().
| std::ostream & core::scoring::operator<< | ( | std::ostream & | os, |
| ScoreTypes const & | score_types | ||
| ) |
output operator for ScoreTypes list type
output operator for ScoreTypes list
| std::ostream & core::scoring::operator<< | ( | std::ostream & | ost, |
| EMapVector const & | emap | ||
| ) |
output operator (index;value)
References n_score_types.
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| ChemicalShiftAnisotropy const & | csa | ||
| ) |
References csa, and core::conformation::membrane::out.
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| const Energies & | e | ||
| ) |
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| CSA const & | csa | ||
| ) |
References csa, and core::conformation::membrane::out.
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| DC const & | dc | ||
| ) |
References dc, and core::conformation::membrane::out.
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| DipolarCoupling const & | dc | ||
| ) |
References dc, and core::conformation::membrane::out.
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Hairpin const & | s | ||
| ) |
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Hairpins const & | |||
| ) |
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Helices const & | s | ||
| ) |
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| RDC const & | rdc | ||
| ) |
References core::conformation::membrane::out, and rdc.
| std::ostream & core::scoring::operator<< | ( | std::ostream & | out, |
| ResidualDipolarCoupling const & | rdc | ||
| ) |
References core::conformation::membrane::out, and rdc.
|
inline |
References core::conformation::membrane::out, and core::scoring::ScoreFunction::show().
| std::ostream& core::scoring::operator<< | ( | std::ostream & | out, |
| Strands const & | s | ||
| ) |
| bool core::scoring::operator== | ( | ScoreFunctionInfo const & | a, |
| ScoreFunctionInfo const & | b | ||
| ) |
| std::istream & core::scoring::operator>> | ( | std::istream & | is, |
| ScoreType & | score_type | ||
| ) |
input operator for ScoreType enum type
read in a string name from a file or std::cin and directly convert it to an ScoreType enum type, for example, std::cin >> ScoreType. This will first check if the lookup map has been set up already. If the string name cannot be converted properly, it will flag the input stream as failure (e.g., istream.fail() is true) and set ScoreType enum type to total_score.
References core::scoring::ScoreTypeManager::is_score_type(), core::scoring::ScoreTypeManager::score_type_from_name(), and total_score.
| core::scoring::ScoreFunctionOP core::scoring::parse_score_function | ( | utility::tag::TagCOP | tag, |
| basic::datacache::DataMap const & | data, | ||
| std::string const & | dflt_key | ||
| ) |
Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Defaults to 'commandline'.
Utility function to find a scorefunction from parser-provided data for the option 'scorefxn'.
References parse_score_function().
| core::scoring::ScoreFunctionOP core::scoring::parse_score_function | ( | utility::tag::TagCOP | tag, |
| std::string const & | option_name, | ||
| basic::datacache::DataMap const & | data, | ||
| std::string const & | dflt_key | ||
| ) |
Look up the score function defined in the <SCOREFXNS> through the given option. Defaults to 'commandline'.
Utility function to find a scorefunction from parser-provided data.
References check_score_function_sanity().
Referenced by protocols::cyclic_peptide::PeptideInternalHbondsMetric::configure_from_filter_tag(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::antibody::design::get_ab_design_global_scorefxn(), protocols::parser::MonteCarloLoader::load_data(), protocols::antibody::design::MutateFrameworkForCluster::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), protocols::minimization_packing::BoltzmannRotamerMover::parse_my_tag(), protocols::simple_ddg::SSElementBisectddGFilter::parse_my_tag(), protocols::splice::TailSegmentMover::parse_my_tag(), protocols::coupled_moves::CoupledMovesProtocol::parse_my_tag(), protocols::minimization_packing::RotamerTrialsMinMover::parse_my_tag(), protocols::minimization_packing::TaskAwareMinMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::recon_design::FindConsensusSequence::parse_my_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::enzdes::BackboneSampler::parse_my_tag(), protocols::enzdes::LigInterfaceEnergyFilter::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::enzdes::RepackWithoutLigandFilter::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::enzdes::PackRotamersMoverPartGreedy::parse_my_tag(), protocols::evolution::NucleotideMutation::parse_my_tag(), protocols::hbnet::HBNet::parse_my_tag(), protocols::helical_bundle::BundleReporterFilter::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::relax::loop::LoopRelaxMover::parse_my_tag(), protocols::score_filters::ScoreTypeFilter::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::seeded_abinitio::SegmentHybridizer::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::simple_ddg::AlaScan::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::simple_ddg::DdGScan::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::simple_filters::InterfaceHbondsFilter::parse_my_tag(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_moves::DumpPdb::parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceInTail::parse_my_tag(), protocols::splice::SpliceOut::parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), protocols::symmetric_docking::SymDockProtocol::parse_my_tag(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::InteractionEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag(), protocols::abinitio::abscript::AbscriptLoopCloserCM::parse_my_tag(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::parse_my_tag(), protocols::antibody::AntibodyCDRGrafter::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::parse_my_tag(), protocols::calc_taskop_movers::CreateSequenceMotifMover::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::carbohydrates::CreateGlycanSequonMover::parse_my_tag(), protocols::carbohydrates::GlycanSampler::parse_my_tag(), protocols::carbohydrates::GlycanTreeModeler::parse_my_tag(), protocols::cryst::ReportGradientsMover::parse_my_tag(), protocols::cryst::SetCrystWeightMover::parse_my_tag(), protocols::cryst::CrystRMS::parse_my_tag(), protocols::cryst::DockLatticeMover::parse_my_tag(), protocols::cyclic_peptide::CrosslinkerMover::parse_my_tag(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::parse_my_tag(), protocols::denovo_design::movers::BridgeChainsMover::parse_my_tag(), protocols::denovo_design::DisulfidizeMover::parse_my_tag(), protocols::evolution::AlignmentAAFinder::parse_my_tag(), protocols::evolution::AlignmentGapInserter::parse_my_tag(), protocols::farnesyl::SampleFarnesylMover::parse_my_tag(), protocols::features::InterfaceDdGMover::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::parse_my_tag(), protocols::fold_from_loops::NubInitioMover::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::parse_my_tag(), protocols::loop_modeler::LoopModeler::parse_my_tag(), protocols::mean_field::GenMeanFieldMover::parse_my_tag(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::parse_my_tag(), protocols::membrane_benchmark::PeptideOrientationMover::parse_my_tag(), protocols::minimization_packing::DisulfideOptimizationMover::parse_my_tag(), protocols::minimization_packing::PertMinMover::parse_my_tag(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::parse_my_tag(), protocols::ncbb::ResidueReplacementRebuildMover::parse_my_tag(), protocols::peptide_deriver::PeptideDeriverFilter::parse_my_tag(), protocols::pose_creation::SliceToMiniProteinMover::parse_my_tag(), protocols::pose_sewing::movers::BlockwiseAnalysisMover::parse_my_tag(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::quantum_annealing::InteractionGraphSummaryMetric::parse_my_tag(), protocols::relax::AcceptToBestMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::rna::movers::ERRASER2Protocol::parse_my_tag(), protocols::simple_filters::SimpleHbondsToAtomFilter::parse_my_tag(), protocols::simple_moves::AddChainMover::parse_my_tag(), protocols::simple_moves::BackboneMover::parse_my_tag(), protocols::simple_moves::DisulfideInsertionMover::parse_my_tag(), protocols::simple_moves::ExplicitWaterMover::parse_my_tag(), protocols::simple_moves::PeriodicBoxMover::parse_my_tag(), protocols::simple_moves::SimpleThreadingMover::parse_my_tag(), protocols::simple_moves::SwitchChainOrderMover::parse_my_tag(), protocols::calc_taskop_movers::ConsensusDesignMover::parse_my_tag(), protocols::calc_taskop_movers::ForceDisulfidesMover::parse_my_tag(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), core::pack::task::residue_selector::ClashBasedShellSelector::parse_my_tag(), protocols::hbnet::UnsatSelector::parse_my_tag(), protocols::matdes::SchemePlaceMotifsMover::parse_my_tag(), protocols::nmr::ParaNMRScoreMover::parse_my_tag(), protocols::nmr::pcs::PCSLigandTransformMover::parse_my_tag(), protocols::nmr::pre::PREMover::parse_my_tag(), protocols::relax::RepeatProteinRelax::parse_my_tag(), protocols::residue_selectors::HBondSelector::parse_my_tag(), protocols::moves::RampingMover::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::calc_taskop_movers::DesignRepackMover::parse_my_tag(), protocols::ncbb::SecStructMinimizeMover::parse_my_tag(), protocols::protein_interface_design::movers::SecretionOptimizationMover::parse_my_tag(), protocols::simple_ddg::ddG::parse_my_tag(), protocols::stepwise::monte_carlo::mover::AddMover::parse_my_tag(), protocols::stepwise::monte_carlo::mover::FromScratchMover::parse_my_tag(), protocols::stepwise::monte_carlo::mover::ResampleMover::parse_my_tag(), protocols::minimization_packing::MinMover::parse_opts(), protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag(), protocols::minimization_packing::MinPackMover::parse_score_function(), protocols::minimization_packing::PackRotamersMover::parse_score_function(), protocols::minimization_packing::RepackSidechainsMover::parse_score_function(), protocols::switches::GraftSwitchMover::parse_score_function(), parse_score_function(), protocols::task_operations::SelectByDeltaScoreOperation::parse_tag(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::parse_tag(), and protocols::loop_modeling::utilities::set_scorefxn_from_tag().
| utility::vector1< core::Real > core::scoring::per_res_lddt | ( | core::pose::Pose const & | ref, |
| core::pose::Pose const & | model, | ||
| bool | consider_alt | ||
| ) |
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)
References core::scoring::lDDT_Calculator::consider_alt_states(), ref, and core::scoring::lDDT_Calculator::residue_lDDT().
| std::map< core::Size, core::Real > core::scoring::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.
Calculate RMS for each residue in mask, return a map of res to value.
Mask and result corresponds to MOD POSE, not the reference pose!
References core::id::AtomID::atomno(), core::conformation::Residue::is_virtual(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::size(), core::simple_metrics::metrics::sum, and core::pose::Pose::xyz().
Referenced by core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate().
|
inline |
References core::conformation::Residue::connection_incomplete(), and core::conformation::Residue::n_polymeric_residue_connections().
Referenced by core::scoring::Ramachandran::defines_score_for_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), and core::scoring::Ramachandran2B::RamaE_Upper().
| std::string const core::scoring::PRE_TALARIS_2013_STANDARD_WTS | ( | "pre_talaris_2013_standard" | ) |
| std::string const core::scoring::REF_2015 | ( | "ref2015" | ) |
|
inline |
class T must define
References core::conformation::Residue::atom(), protocols::antibody::H1, and protocols::antibody::H2.
Referenced by inline_intraresidue_atom_pair_energy(), and inline_residue_atom_pair_energy().
| core::Real core::scoring::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.
References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by protocols::drug_design::align_residues(), and automorphic_rmsd().
| core::Real core::scoring::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.)
References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by protocols::drug_design::align_residues(), automorphic_rmsd(), and protocols::drug_design::place_new_restype_rotamer_align().
| core::Real core::scoring::residue_sc_rmsd_no_super | ( | core::conformation::ResidueCOP | res1, |
| core::conformation::ResidueCOP | res2, | ||
| bool const | fxnal_group_only | ||
| ) |
utility function to calculate per-residue sidechain rmsd without superposition
Iterates over all non-hydrogen sidechain atoms of two residues and returns their rmsd without superposition.
References core::pose::num_atoms().
Referenced by protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::hbnet::HBNet::monte_carlo_net_clash(), protocols::hbnet::HBNet::net_clash(), protocols::hbnet::HBNet::network_already_stored(), and protocols::hotspot_hashing::residue_sc_rmsd_no_super().
| SS_Info const& core::scoring::retrieve_const_ss_info_from_pose | ( | pose::Pose const & | pose | ) |
| void core::scoring::retrieve_coordinates | ( | const core::pose::Pose & | pose, |
| const utility::vector1< core::Size > & | residues, | ||
| FArray2D< core::Real > * | coords | ||
| ) |
Populates the output parameter with the xyz coordinates of a subset of <pose>'s CA atoms, which are specified in <residues>
References protocols::simple_filters::coords(), core::pose::Pose::xyz(), and protocols::kinmatch::xyz().
Referenced by CA_gdtmm(), CA_gdttm(), and CA_rmsd().
| ChemicalShiftAnisotropyOP core::scoring::retrieve_CSA_from_pose | ( | core::pose::Pose & | pose | ) |
| ChemicalShiftAnisotropyCOP core::scoring::retrieve_CSA_from_pose | ( | core::pose::Pose const & | pose | ) |
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
Referenced by core::energy_methods::ChemicalShiftAnisotropyEnergy::csa_from_pose(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), and core::energy_methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing().
| DipolarCouplingOP core::scoring::retrieve_DC_from_pose | ( | core::pose::Pose & | pose | ) |
| DipolarCouplingCOP core::scoring::retrieve_DC_from_pose | ( | core::pose::Pose const & | pose | ) |
References core::pose::datacache::CacheableDataType::CHEMICAL_SHIFT_ANISOTROPY_DATA, and core::pose::Pose::data().
Referenced by core::energy_methods::DipolarCouplingEnergy::dc_from_pose(), core::energy_methods::DipolarCouplingEnergy::eval_atom_derivative(), and core::energy_methods::DipolarCouplingEnergy::setup_for_minimizing().
| SS_Info& core::scoring::retrieve_nonconst_ss_info_from_pose | ( | pose::Pose & | pose | ) |
helper function
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SS_INFO.
Referenced by core::scoring::SecondaryStructurePotential::setup_for_scoring().
| ResidualDipolarCouplingOP core::scoring::retrieve_RDC_from_pose | ( | core::pose::Pose & | pose | ) |
| ResidualDipolarCouplingCOP core::scoring::retrieve_RDC_from_pose | ( | core::pose::Pose const & | pose | ) |
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::RESIDUAL_DIPOLAR_COUPLING_DATA.
Referenced by core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::rdc_from_pose(), and core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing().
| ResidualDipolarCoupling_RohlOP core::scoring::retrieve_RDC_ROHL_from_pose | ( | core::pose::Pose & | pose | ) |
| ResidualDipolarCoupling_RohlCOP core::scoring::retrieve_RDC_ROHL_from_pose | ( | core::pose::Pose const & | pose | ) |
| Real core::scoring::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 | ||
| ) |
Calculates RMSD of all atoms in AtomID map, no need for the poses to be the same length.
References core::conformation::Residue::atom_name(), core::conformation::Residue::name(), core::pose::Pose::residue(), TR(), and core::pose::Pose::xyz().
Referenced by protocols::fldsgn::MatchResidues::compute_comb().
| Real core::scoring::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 | ||
| ) |
Should be more robust to crazy variant type mismatches. Both poses must have the same length.
References core::pose::Pose::size().
Referenced by protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::check_for_closeness(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::check_for_closeness(), protocols::stepwise::legacy::screener::SimpleRMSD_Screener::check_screen(), protocols::stepwise::legacy::modeler::protein::output_silent_struct(), and rms_at_corresponding_heavy_atoms().
| Real core::scoring::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 | ||
| ) |
Should be more robust to crazy variant type mismatches. Both poses must have the same length.
References core::conformation::Residue::atom_name(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::pose::Pose::xyz().
| Real core::scoring::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 | ||
| ) |
References core::pose::Pose::size().
Referenced by protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), core::simple_metrics::metrics::RMSDMetric::calculate(), protocols::antibody::cdr_backbone_rmsds(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::check_for_closeness(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::check_for_closeness(), protocols::stepwise::legacy::screener::SimpleRMSD_Screener::check_screen(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_superimposition(), protocols::rna::AlignmentEnergy::eval_atom_derivative(), protocols::rna::AlignmentEnergy::finalize_total_energy(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_no_superimpose(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(), protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_stems_no_superimpose(), and protocols::stepwise::legacy::modeler::protein::output_silent_struct().
| Real core::scoring::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 | ||
| ) |
| Real core::scoring::rms_at_corresponding_heavy_atoms | ( | pose::Pose const & | mod_pose, |
| pose::Pose const & | ref_pose | ||
| ) |
| core::Real core::scoring::rmsd_no_super | ( | core::conformation::ResidueCOPs const & | residues1, |
| core::conformation::ResidueCOPs const & | residues2, | ||
| T * | predicate | ||
| ) |
References is_ligand_heavyatom_residues(), and core::pose::num_atoms().
| core::Real core::scoring::rmsd_no_super | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| T * | predicate | ||
| ) |
Select atoms for RMS via a predicate function/functor.
Calculates minimal rms, NOT allowing rotation/translation – uses current coordinates as-is. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:
bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);
It should return true if the atom should be included and false otherwise.
Example of use, to calculate C-alpha RMSD: rmsd_no_super(pose1, pose2, is_protein_CA);
References rmsd_no_super(), and core::pose::Pose::size().
| core::Real core::scoring::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.
Calculates rms, NOT allowing rotation/translation – uses current coordinates as-is. The two vectors should be the same length, and taken pairwise should be a mapping. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:
bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);
It should return true if the atom should be included and false otherwise.
The "resno" and "atomno" are calculated based on pose1 (which is what most predicates expect)
References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by all_atom_rmsd_nosuper(), all_scatom_rmsd_nosuper(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), protocols::ligand_docking::check_RMSD(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::ligand_docking::get_multi_residue_ligand_RMSDs(), non_peptide_heavy_atom_RMSD(), protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_no_super(), and rmsd_no_super_subset().
| core::Real core::scoring::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...
References rmsd_no_super(), and core::pose::Pose::size().
| core::Real core::scoring::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.
Calculates minimal rms over a subset of residues, NOT allowing rotation/translation – uses current coordinates as-is. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:
bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno); the subset is a vector of all the residues, with true for those over which to calculate the rms
It should return true if the atom should be included and false otherwise.
Example of use, to calculate C-alpha RMSD: rmsd_no_super_subset(pose1, pose2, subset, is_protein_CA);
References rmsd_no_super(), and core::pose::Pose::size().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::best_Kmer_rms(), protocols::docking::calc_Lrmsd(), protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(), protocols::loop_modeling::utilities::TrajectoryLogger::calc_rmsd_to_native(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::pose_metric_calculators::compute_rmsd(), protocols::antibody_legacy::AntibodyModeler::global_loop_rmsd(), protocols::antibody::global_loop_rmsd(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd(), protocols::glycopeptide_docking::record_pose_metrics(), protocols::features::ProteinRMSDNoSuperpositionFeatures::report_features(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| core::Real core::scoring::rmsd_with_super | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| std::list< core::Size > const & | subset_residues, | ||
| T * | predicate | ||
| ) |
References rmsd_with_super().
| core::Real core::scoring::rmsd_with_super | ( | core::pose::Pose const & | pose1, |
| core::pose::Pose const & | pose2, | ||
| T * | predicate | ||
| ) |
Select atoms for RMS via a predicate function/functor.
Calculates minimal rms, allowing rotation/translation for best fit. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:
bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);
It should return true if the atom should be included and false otherwise.
Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA);
References rmsd_with_super(), and core::pose::Pose::size().
| core::Real core::scoring::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.
Calculates minimal rms, allowing rotation/translation for best fit. The two vectors should be the same length, and taken pairwise should be a mapping. Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:
bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);
It should return true if the atom should be included and false otherwise.
The "resno" and "atomno" are calculated based on pose1 (which is what most predicates expect)
References is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), all_atom_rmsd(), all_atom_rmsd_incl_hydrogens(), bb_rmsd(), bb_rmsd_including_O(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_and_save(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::rpc::JSON_RPC::get_irms(), protocols::ligand_docking::get_multi_residue_ligand_RMSDs(), nbr_atom_rmsd(), protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics(), protocols::features::ProteinRMSDFeatures::report_features(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), rmsd_with_super(), rmsd_with_super_subset(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| core::Real core::scoring::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...
References rmsd_with_super(), and core::pose::Pose::size().
| core::Real core::scoring::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.
Calculates minimal rms, allowing rotation/translation for best fit. Same as above function, but allows a subset of residues over which to superposition to be passed in Parameter "predicate" should be a function pointer [ or class that defines operator() ] with the following signature:
bool my_pred_func(Pose const & pose1, Pose const & pose2, Size resno, Size atomno);
It should return true if the atom should be included and false otherwise.
Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);
References rmsd_with_super(), and core::pose::Pose::size().
Referenced by protocols::symmetry::SymmetricRMSMover::apply(), protocols::docking::calc_CA_Irmsd(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::docking::calc_P1rmsd(), protocols::docking::calc_P2rmsd(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::membrane::mem_bb_rmsd_with_super(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| std::string const core::scoring::RNA_HIRES_WTS | ( | "rna/denovo/rna_hires" | ) |
| std::string const core::scoring::RNA_LORES_PLUS_HIRES_WTS | ( | "rna/denovo/rna_lores_plus_hires" | ) |
| std::string const core::scoring::RNA_LORES_WTS | ( | "rna/denovo/rna_lores" | ) |
| void core::scoring::ROTATE | ( | T & | a, |
| int | i, | ||
| int | j, | ||
| int | k, | ||
| int | l, | ||
| Real | s, | ||
| Real | tau | ||
| ) |
References core::pose::motif::a().
|
inline |
References core::scoring::MultipoleElecResidueInfo::const_my_group(), and core::conformation::Residue::seqpos().
Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().
| bool core::scoring::SASAShouldItCount | ( | conformation::Residue const & | rsd, |
| Size const & | atm | ||
| ) |
| std::string const core::scoring::SCORE12_PATCH | ( | "score12" | ) |
| std::string const core::scoring::SCORE13 | ( | "score13" | ) |
| std::string const core::scoring::SCORE4_SMOOTH_CART | ( | "score4_smooth_cart" | ) |
| ScoreType core::scoring::score_type_from_name | ( | std::string const & | name | ) |
give a ScoreType string name and return its enum type
Returns the ScoreType titled <name>
example(s): score_type_from_name("fa_sol") See also: ScoreFunction ScoreType Energies Energies.residue_total_energies name_from_score_type
References core::scoring::ScoreTypeManager::score_type_from_name().
Referenced by protocols::docking::SlideIntoContact::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::relax::FastRelax::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), apply_set_weights(), protocols::relax::FastRelax::batch_apply(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), core::io::silent::SilentStruct::energies_into_pose(), core::pose::energy_from_pose(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::loop_grower::LoopGrower::full_atom_beam(), protocols::ddg::ddGMover::get_scorefunction_header(), protocols::relax::FastRelax::inner_loop_reference_command(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::helical_bundle::BundleReporterFilter::parse_my_tag(), protocols::score_filters::ScoreTypeFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), core::simple_metrics::metrics::InteractionEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag(), core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), protocols::task_operations::SelectByDeltaScoreOperation::parse_tag(), protocols::optimize_weights::OptEData::read_from_file(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), protocols::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::docking::SlideIntoContact::scorefunction(), protocols::simple_moves::ShakeStructureMover::setup_for_run(), protocols::symmetry::SymShakeStructureMover::setup_for_run(), and protocols::ddg::ddGMover::store_energies().
| void core::scoring::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 | ||
| ) |
References core::conformation::Residue::atom_index(), core::chemical::ResidueType::has(), core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().
Referenced by setup_matching_CA_atoms(), and setup_matching_protein_backbone_heavy_atoms().
| void core::scoring::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 | ||
| ) |
References setup_matching_atoms_with_given_names().
Referenced by protocols::stepwise::legacy::modeler::protein::output_silent_struct().
| void core::scoring::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 | ||
| ) |
References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::has(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::size().
Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_no_superimpose(), protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_stems_no_superimpose(), protocols::stepwise::legacy::screener::SimpleRMSD_Screener::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_corresponding_atom_id_map(), protocols::stepwise::legacy::modeler::protein::output_silent_struct(), and rms_at_corresponding_heavy_atoms().
| void core::scoring::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 | ||
| ) |
References setup_matching_atoms_with_given_names().
Referenced by protocols::stepwise::legacy::screener::SimpleRMSD_Screener::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_corresponding_atom_id_map(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_corresponding_atom_id_map(), and protocols::stepwise::legacy::modeler::protein::output_silent_struct().
| std::map< rmsd_atoms, utility::vector1< std::string > > core::scoring::setup_rmsd_atom_names | ( | ) |
@breif Returns a map of the rmsd_atom enum and a list of atom names for which this RMSD setting selects for the calculation
References rmsd_all, rmsd_protein_bb_ca, rmsd_protein_bb_heavy, and rmsd_protein_bb_heavy_including_O.
Referenced by core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::setup_name_mapping().
| bool core::scoring::ShouldItCount | ( | conformation::Residue const & | rsd, |
| Size const & | atm | ||
| ) |
| std::string const core::scoring::SOFT_REP_DESIGN_WTS | ( | "soft_rep_design" | ) |
| std::string const core::scoring::SOFT_REP_WTS | ( | "soft_rep" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_BOLTZ | ( | "SPLIT_UNFOLDED_BOLTZ" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_ELE | ( | "SPLIT_UNFOLDED_ELE" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_MEAN | ( | "SPLIT_UNFOLDED_MEAN" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_MEDIAN | ( | "SPLIT_UNFOLDED_MEDIAN" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_MM | ( | "SPLIT_UNFOLDED_MM" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_MODE | ( | "SPLIT_UNFOLDED_MODE" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_PDB | ( | "SPLIT_UNFOLDED_PDB" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_ROSETTA | ( | "SPLIT_UNFOLDED_ROSETTA" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_UNIQUE | ( | "SPLIT_UNFOLDED_UNIQUE" | ) |
| std::string const core::scoring::SPLIT_UNFOLDED_USER_DEFINED | ( | "SPLIT_UNFOLDED_USER_DEFINED" | ) |
| void core::scoring::store_CSA_in_pose | ( | ChemicalShiftAnisotropyOP | csa_info, |
| core::pose::Pose & | pose | ||
| ) |
| void core::scoring::store_DC_in_pose | ( | DipolarCouplingOP | dc_info, |
| core::pose::Pose & | pose | ||
| ) |
| void core::scoring::store_RDC_in_pose | ( | ResidualDipolarCouplingOP | rdc_info, |
| core::pose::Pose & | pose | ||
| ) |
| void core::scoring::store_RDC_ROHL_in_pose | ( | ResidualDipolarCoupling_RohlOP | rdc_info, |
| core::pose::Pose & | pose | ||
| ) |
| core::Real core::scoring::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.
General, for any heteropolymer. Ignores ligands and hydrogen atoms.
References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::atom_is_sidechain(), core::chemical::ResidueType::atom_name(), core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::ResidueType::has(), core::pose::initialize_atomid_map(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::is_virtual_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::set(), superimpose_pose(), core::id::to_string(), and core::pose::Pose::total_residue().
| Real core::scoring::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.
The rms_calc_offset_val is a small constant value used by the numerical machinery to ensure a nonzero determinant. This defaults to 1.0e-7. Realign determines whether this is subtracted off again (default false). If throw_on_failure is true, this function throws if the RMSD calculation fails; otherwise it fails silently and returns 0.0 for the RMSD.
WARNING: this will give you errors if you try to superimpose a non-symmetric pose onto a symmetric one, even with the correct atom_map. It will not fail, but the superposition will be bad and any subsequent RMSD calculation will be wrong.
References core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rms, core::pose::Pose::set_xyz(), core::pose::Pose::size(), core::id::to_string(), core::pose::MiniPose::xyz(), and core::conformation::Residue::xyz().
| Real core::scoring::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, | ||
| bool const | realign, | ||
| bool const | throw_on_failure | ||
| ) |
Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by atom_map.
Superimpose mod_pose onto ref_pose using the AtomID mapping, which maps atoms in mod_pose onto atoms in ref_pose. Returns rmsd over alignment.
Usage example: superimpose pose1 onto pose2 by mapping C-alphas of residue 10-30 onto residues 20-40
id::AtomID_Map< id::AtomID > atom_map; id::initialize( atom_map, pose1, id::AtomID::BOGUS_ATOM_ID() ); // maps every atomid to bogus atom
for ( Size i=10; i<=30; ++i ) { id::AtomID const id1( pose1.residue(i).atom_index("CA"), i ); id::AtomID const id2( pose2.residue(i+10).atom_index("CA"), i+10 ); atom_map[ id1 ] = id2; } superimpose_pose( pose1, pose2, atom_map );
The rms_calc_offset_val is a small constant value used by the numerical machinery to ensure a nonzero determinant. This defaults to 1.0e-7. Realign determines whether this is subtracted off again (default false). If throw_on_failure is true, this function throws if the RMSD calculation fails; otherwise it fails silently and returns 0.0 for the RMSD.
WARNING: This will give you errors if you try to superimpose a non-symmetric pose onto a symmetric one, even with the correct atom_map. It will not fail, but the superposition will be bad and any subsequent RMSD calculation will be wrong.
Referenced by protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::loops::addScoresForLoopParts(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::align_cycpep_pose_to_original_pose(), protocols::helical_bundle::align_mainchain_atoms(), protocols::helical_bundle::align_mainchain_atoms_of_residue_range(), core::scoring::motif::align_motif_pose_NCAC_super(), core::scoring::motif::align_motif_pose_super(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_pose(), protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose(), protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_poses(), core::import_pose::libraries::RNA_ChunkLibrary::align_to_chunk(), protocols::antibody_legacy::Antibody::align_to_native(), protocols::antibody::align_to_native(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::align_with_offset(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_working_pose(), core::fragment::rna::analyze_for_homology(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::apply_current_pose_segment(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), core::simple_metrics::metrics::RMSDMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::antibody::cdr_backbone_rmsds(), protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_superimposition(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::tcr::orient_tcr_chain(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::fldsgn::MatchResidues::superimpose_comb(), protocols::grafting::superimpose_overhangs_heavy(), superimpose_polymer_heavyatoms(), superimpose_pose(), protocols::stepwise::modeler::align::superimpose_pose_legacy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), and protocols::docking::ConformerSwitchMover::switch_conformer().
| Real core::scoring::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, |
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| bool const | realign = false, |
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| bool const | throw_on_failure = true |
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Superimpose mod_pose onto ref_pose using the mapping of atoms from mod_pose to ref_pose given by map< AtomID, AtomID >
The rms_calc_offset_val is a small constant value used by the numerical machinery to ensure a nonzero determinant. This defaults to 1.0e-7. Realign determines whether this is subtracted off again (default false). If throw_on_failure is true, this function throws if the RMSD calculation fails; otherwise it fails silently and returns 0.0 for the RMSD.
References core::pose::convert_from_std_map(), core::conformation::symmetry::is_symmetric(), superimpose_pose(), and TR().
| core::Real core::scoring::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);.
References core::pose::Pose::conformation(), create_shuffle_map_recursive_rms(), is_heavyatom(), is_ligand_heavyatom(), is_polymer_heavyatom(), core::chemical::element::N, core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), rms, core::pose::Pose::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::conformation::Residue::xyz().
Referenced by protocols::protein_interface_design::filters::RmsdFilter::compute().
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Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::Ramachandran2B::eval_rama_score_all(), get_minval_binwidth(), core::scoring::loop_graph::evaluator::get_minval_binwidth(), core::scoring::nmr::pre::PREMultiSet::PRE_Curie_prefactor(), core::scoring::Ramachandran2B::read_rama(), and core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives().
| std::string const core::scoring::TALARIS_2013 | ( | "talaris2013" | ) |
| std::string const core::scoring::TALARIS_2013_CART | ( | "talaris2013_cart" | ) |
| std::string const core::scoring::TALARIS_2014 | ( | "talaris2014" | ) |
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Referenced by abego3aa_to_index(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::add_coordinatecst_for_hotspot_packing(), core::scoring::GenBondedExclInfo::add_residue_exclude_torsions(), core::scoring::lDDT_Calculator::lDDT_Cache::add_states_from_automorphisms(), core::scoring::sc::MolecularSurfaceCalculator::AddAtom(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::MultipoleElecPotential::align_multipole_axes(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::scoring::VdWTinkerPotential::amoeba_type_lookup(), core::scoring::MultipoleElecPotential::amoeba_type_lookup(), core::scoring::APBSWrapper::APBSWrapper(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::apply(), protocols::simple_moves::MembraneTopology::apply(), protocols::protein_interface_design::filters::HbondsToAtomFilter::apply(), apply_set_weights(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::scoring::sc::MolecularSurfaceCalculator::AssignAtomRadius(), core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), core::scoring::atomic_depth::AtomicDepth::AtomicDepth(), core::scoring::AtomVDW::AtomVDW(), basename_for_score_function(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::scoring::elec::GroupElec::build_groupinfo(), CA_gdtmm(), CA_gdttm(), CA_maxsub(), CA_or_equiv_rmsd(), CA_rmsd(), CA_rmsd_symmetric(), core::scoring::sc::ShapeSimilarityCalculator::Calc(), core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::sc::ContactMolecularSurfaceCalculator::CalcContactArea(), core::scoring::sc::ShapeComplementarityCalculator::CalcNeighborDistance(), core::scoring::sc::ShapeSimilarityCalculator::CalcNeighborDistance(), core::scoring::sc::ShapeSimilarityCalculator::CalcSs(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::scoring::loop_graph::LoopGraph::check_disjoint(), core::scoring::loop_graph::LoopGraph::check_loop_cycles_are_disjoint(), check_score_function_sanity(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::ScoringManager::create_chi_energy_function_instance(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::ScoringManager::create_file_contents_instance(), core::scoring::ScoringManager::create_mhc_csv_contents(), core::scoring::ScoringManager::create_mhc_map_from_db(), core::scoring::ScoringManager::create_mhc_matrix_contents(), core::scoring::ScoringManager::create_nmer_pssm(), core::scoring::ScoringManager::create_nmer_svm_aa_matrix(), core::scoring::ScoringManager::create_nmer_svm_rank(), core::scoring::ScoringManager::create_omega_preferences_function_instance(), core::scoring::ScoringManager::create_rna_lowresolutionpotential_instance(), core::scoring::ScoringManager::create_sixdtransrotpotential_instance(), core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance(), core::scoring::ScoringManager::create_svm_rosetta(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::create_task_for_allhotspot_packing(), core::scoring::ScoringManager::create_unfolded_state_potential_instance(), protocols::ddG_main(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::lDDT_Calculator::do_division(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::MultipoleElecPotential::eval_residue_pair_derivatives(), core::scoring::OneDDistPotential::evaluate(), core::scoring::facts::FACTSPotential::evaluate_nonpolar_energy(), core::scoring::facts::FACTSPotential::evaluate_polar_energy(), core::scoring::TMscore::extend(), core::scoring::loop_graph::LoopGraph::figure_out_loop_cycles_legacy(), core::scoring::rna::chemical_shift::filter_chem_shift_data_list(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), core::scoring::sc::MolecularSurfaceCalculator::GenerateMolecularSurfaces(), core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_best_exp_to_calc_chem_shift_mapping(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), core::scoring::elec::GroupElec::get_group(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::elec::CountPairRepMap::get_map(), core::scoring::sasa::LeGrandSasa::get_overlap(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), core::scoring::GenBondedExclInfo::get_residue_data(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::rna::chemical_shift::get_rosetta_hatom_name(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::get_score(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::get_score(), get_score_function(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::packstat::SimplePDB::get_spheres(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data(), core::scoring::MultipoleElecPotential::induce_polarizable_dipoles(), core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator::initialize(), core::scoring::MultipoleElecResidueInfo::initialize(), core::scoring::MembraneTopology::initialize(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_aa_rna_backbone(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_base_pair(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_pair(), core::scoring::PoissonBoltzmannPotential::load_APBS_potential(), core::scoring::Ramachandran::load_custom_rama_table(), core::scoring::loop_graph::LoopGraph::look_for_cycles_recursively(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), core::scoring::P_AA_ABEGO3::P_AA_ABEGO3_energy(), core::scoring::P_AA_ss::P_AA_ss_energy(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::protein_interface_design::filters::HbondsToAtomFilter::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::simple_moves::MembraneTopology::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), core::scoring::PolymerBondedEnergyContainer::PolymerBondedEnergyContainer(), core::scoring::MembraneTopology::print(), core::scoring::rna::chemical_shift::print_chemical_shift_data(), protocols::print_ddgs(), core::scoring::sasa::LeGrandSasa::print_dot_bit_string(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::process_score(), core::scoring::Ramachandran::Ramachandran(), core::scoring::elec::read_cp_tables_from_db(), core::scoring::HydroxylTorsionPotential::read_database(), core::scoring::SplitUnfoldedTwoBodyPotential::read_database_file(), core::scoring::carbohydrates::read_Gaussian_parameters_from_database_file(), protocols::read_in_mutations(), core::scoring::MembraneTopology::read_in_spanfile(), core::scoring::P_AA_ABEGO3::read_P_AA_ABEGO3(), core::scoring::P_AA::read_P_AA_pp(), core::scoring::dssp::read_pairing_list(), protocols::protein_interface_design::PatchdockReader::read_patchdock(), protocols::protein_interface_design::PatchdockReader::read_patchdock_entry(), protocols::protein_interface_design::PatchdockReader::read_poses(), core::scoring::Ramachandran::read_rama_map_file_shapovalov(), core::scoring::sc::MolecularSurfaceCalculator::ReadScRadii(), core::scoring::loop_graph::LoopGraph::record_loop_cycle(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), rms_at_all_corresponding_atoms(), rms_at_corresponding_atoms(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::RNA_ChemicalShiftPotential(), core::scoring::rna::RNA_TorsionPotential::RNA_TorsionPotential(), core::scoring::facts::FACTSPotential::set_default(), core::scoring::TMscore::set_default(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::set_water_base_atm(), core::scoring::facts::FACTSPotential::setup_for_derivatives(), core::scoring::carbohydrates::CHIEnergyFunction::setup_for_sampling(), core::scoring::carbohydrates::OmegaPreferencesFunction::setup_for_sampling(), core::scoring::facts::FACTSPotential::setup_for_scoring(), core::scoring::PoissonBoltzmannPotential::solve_pb(), superimpose_pose(), core::scoring::P_AA::symmetrize_gly_table(), core::scoring::Ramachandran::symmetrize_gly_table(), core::scoring::loop_graph::LoopGraph::update(), core::scoring::loop_graph::LoopGraph::update_loops_and_cycles(), core::scoring::ScoreFunctionFactory::validate_beta(), core::scoring::ScoreFunctionFactory::validate_talaris(), core::scoring::PoissonBoltzmannPotential::write_config(), core::scoring::PoissonBoltzmannPotential::write_pqr(), and xyz_gdtmm().
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Referenced by core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::GenericBondedPotential::lookup_tors_params(), core::scoring::GenericBondedPotential::modify_tors_params(), core::scoring::GenericBondedPotential::modify_torsion_params_from_cmd_line(), core::scoring::GenericBondedPotential::read_database(), core::scoring::GenericBondedPotential::residue_energy(), and core::scoring::GenericBondedPotential::residue_pair_energy().
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Referenced by core::scoring::ScoreFunction::_add_weights_from_stream(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::do_correct_NH(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::ScoreFunction::extract_weights_from_stream(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_basepair_xy(), core::scoring::ScoreFunction::intersubunit_hbond_energy(), core::scoring::ResidualDipolarCoupling::iterate_tensor_weights(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::ScoreFunction::perturb_weights(), core::scoring::ChemicalShiftAnisotropy::read_CSA_file(), core::scoring::DipolarCoupling::read_DC_file(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), core::scoring::ResidualDipolarCoupling::reserve_buffers(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::scoring::rna::rna_residue_name_to_num(), core::scoring::rna::rna_residue_type_to_num(), core::scoring::Energies::show(), core::scoring::ScoreFunction::show(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), core::scoring::rna::RNA_AtomVDW::vdw_atom_list(), and core::scoring::NeighborList::~NeighborList().
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Referenced by automorphic_rmsd(), gdtha(), and gdtsc().
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| std::string const core::scoring::UNFOLDED_MM_STD | ( | "UNFOLDED_MM_STD" | ) |
| std::string const core::scoring::UNFOLDED_RNA | ( | "UNFOLDED_RNA" | ) |
| std::string const core::scoring::UNFOLDED_SCORE12 | ( | "UNFOLDED_SCORE12" | ) |
| std::string const core::scoring::UNFOLDED_SPLIT_MM_STD | ( | "UNFOLDED_SPLIT_MM_STD" | ) |
| std::string const core::scoring::UNFOLDED_SPLIT_TALARIS2013 | ( | "UNFOLDED_SPLIT_TALARIS2013" | ) |
| std::string const core::scoring::UNFOLDED_SPLIT_USER_DEFINED | ( | "UNFOLDED_SPLIT_USER_DEFINED" | ) |
| bool core::scoring::VdWShouldItCount | ( | conformation::Residue const & | rsd, |
| Size const & | atm | ||
| ) |
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private – handles setting the derived data
References protocols::hybridization::t.
Referenced by core::scoring::ScoreFunction::remove_method().
| core::Real core::scoring::xyz_gdtmm | ( | FArray2D< core::Real > | p1a, |
| FArray2D< core::Real > | p2a | ||
| ) |
| core::Real core::scoring::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 | ||
| ) |
References TR().
| core::Real core::scoring::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.
| core::Real core::scoring::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.
| void core::scoring::xyz_gdttm | ( | FArray2D< core::Real > | p1a, |
| FArray2D< core::Real > | p2a, | ||
| core::Real & | gdttm_score, | ||
| core::Real & | gdtha_score | ||
| ) |
| void core::scoring::xyz_gdttm | ( | ObjexxFCL::FArray2D< core::Real > | p1a, |
| ObjexxFCL::FArray2D< core::Real > | p2a, | ||
| core::Real & | gdttm_score, | ||
| core::Real & | gdtha_score | ||
| ) |
| int core::scoring::xyz_maxsub | ( | FArray2D< core::Real > | p1a, |
| FArray2D< core::Real > | p2a, | ||
| int | natoms | ||
| ) |
| int core::scoring::xyz_maxsub | ( | ObjexxFCL::FArray2D< core::Real > | p1a, |
| ObjexxFCL::FArray2D< core::Real > | p2a, | ||
| int | natoms | ||
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Referenced by basename_for_score_function(), and core::scoring::ScoreFunctionFactory::validate_beta().
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Referenced by basename_for_score_function(), and core::scoring::ScoreFunctionFactory::validate_beta().
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Referenced by basename_for_score_function().
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Referenced by basename_for_score_function(), and core::scoring::ScoreFunctionFactory::validate_beta().
| short const core::scoring::bit_count[] |
Referenced by calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::prune_1pass(), and core::scoring::packstat::prune_hidden_cavity_balls().
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Referenced by basename_for_score_function(), protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), get_score_function(), get_score_functionName(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::symmetry::SymmetrySlider::setup(), protocols::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::symmetry::SymmetrySlider::SymmetrySlider().
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Referenced by basename_for_score_function().
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Referenced by basename_for_score_function().
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Referenced by basename_for_score_function(), protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact(), protocols::symmetry::SymmetrySlider::setup(), protocols::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), and protocols::symmetry::SymmetrySlider::SymmetrySlider().
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Referenced by core::scoring::ScoringManager::etable().
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Referenced by protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), core::scoring::ScoringManager::etable(), and core::scoring::rna::data::RNA_DMS_Potential::get_probe_scorefxn().
| int const core::scoring::maskbits = 162 |
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Referenced by basename_for_score_function().
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Referenced by protocols::ncbb::oop::OopCreatorMover::apply(), and basename_for_score_function().
| int const core::scoring::num_bytes = 21 |
Referenced by calc_atom_masks(), calc_per_atom_sasa(), get_num_bytes(), and input_sasa_dats().
| int const core::scoring::num_orientations = 162 |
Referenced by input_sasa_dats().
| int const core::scoring::num_overlaps = 100 |
Referenced by input_sasa_dats().
| int const core::scoring::num_phi = 64 |
Referenced by get_orientation(), and input_sasa_dats().
| int const core::scoring::num_theta = 64 |
Referenced by get_orientation(), and input_sasa_dats().
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Referenced by protocols::antibody::LHSnugFitLegacy::apply(), protocols::minimization_packing::SetReturningPackRotamersMover::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::minimization_packing::MinPackMover::apply(), basename_for_score_function(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), protocols::sasa_scores::compute_avge_scores(), protocols::antibody::get_Pack_ScoreFxn(), get_score_functionName(), protocols::motifs::IRCollection::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::antibody::RefineBetaBarrel::init(), protocols::docking::TemperedDocking::init_from_options(), protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(), core::scoring::ScoreFunctionFactory::load_score_function_from_disk(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), core::pack::optimize_H_and_notify(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP(), protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::antibody::LHRepulsiveRampLegacy::set_default(), protocols::minimization_packing::PackRotamersMover::setup(), protocols::simple_moves::ShakeStructureMover::setup_for_run(), protocols::symmetry::SymShakeStructureMover::setup_for_run(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol(), protocols::motifs::IRCollection::successful_loop_closure(), and protocols::motifs::IRCollection::try_for_more().
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Referenced by basename_for_score_function().
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Referenced by basename_for_score_function(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), get_score_functionName(), protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(), and core::scoring::ScoreFunctionFactory::load_score_function_from_disk().
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Referenced by basename_for_score_function().
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Referenced by protocols::legacy_sewing::LegacyAssemblyMover::apply(), and basename_for_score_function().
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Referenced by protocols::flxbb::InterlockAroma::apply(), and basename_for_score_function().
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Referenced by protocols::legacy_sewing::LegacyAssemblyMover::apply().
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Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), core::scoring::ScoringManager::create_unfolded_state_potential_instance(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), and protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies().
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1.9.1