All Classes

AbInitio AbInitio.AbInitioLogger AbitSmarterLoopBuilder AbitSmarterLoopBuilder.Loop AbitSmarterLoopBuilder.Loop.End AbitSmarterLoopBuilder.LoopComperator AbstractEnergy AbstractEnergy.IsEnergy AbstractHydrogenBond AbstractHydrogenBondList AbstractPunishAngleEnergy AbstractPunishAngleEnergyElement AcceptAll AccesibilitySequence AccesibilitySequence.AccesibilitySequenceCharFilter AddAtomsFlag Ala AlignmentCell AlignmentColumn AlignmentTools AlphaAngleCreator AlphaAngleEnergy AlphaAngleEnergyElement AlphaAngleParameters AlphaAngleParametersList AlphaTorsionCreator AlphaTorsionEnergy AlphaTorsionEnergyElement AlphaTorsionParameters AlphaTorsionParametersList AminoAcidSubstitutionMatrix Angle AngleCreator AngleEnergy AngleEnergyElement AngleList AngleParameters AngleParametersList ArcCos Arg Asn Asp Atom AtomAlignment AtomAlignment.IsAlignmentColumn AtomAlignmentCell AtomAlignmentColumn AtomComparator AtomCore AtomicPairwisePMFSumma AtomicPairwisePMFSummaCreator AtomicPairwisePMFSummaParameters AtomList AtomList.AcceptChainFilter AtomList.BackboneFilter AtomList.IsAtom AtomList.IsDefrostedFilter AtomList.IsFrozenFilter AtomList.NonHydrogen AtomList.RejectChainFilter AtomPair AtomPairList AtomPairList.IsAtomPair AtomStatus AtomType Attributable AttributesRack BackboneCompleterAndMinimizer BackboneFilter BackboneMCM BackboneResidue BasicLoopResult BBatom Beautify Beautify.BeautifyLogger BeautifyAttribute BetaParametersList BetaParametersList.IsHydrogenBondsPairsParameters BFGS BondCreator BondedDistance BondedFrozenDistance BondEnergy BondEnergyElement BondParameters BondParametersList BoundariesMap CaAtomFilter CaFilter CalcGDT CalculateEnergyFromStructuresListAverages CalculateEnergyFromStructuresListAverages.AveragesAndMaxs CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute CalculateEnergyFromStructuresListAverages.GaussianAttribute CalculateEnergyFromStructuresListAverages.GaussianAttributes CaResidue Cell CellScorer Chain Chain.IsResidue ChainList ChainList.IsChain CholeskyDecomposition ChooseTemplate Classes CoefficientsMatrixForAtomPairSpline ColorByEnergy ColorByEnergy.DistanceFromCatalyticAttribute ColorByEnergy.GaussianAttribute ColorByEnergy.GaussianAttributes Command CommandList CommandListGenerator CommandsException CompositePropensity2DCreator CompositePropensity2DEnergy CompositePropensity2DEnergyElement CompositePropensity2DParameters CompositePropensity2DParametersList CompositePropensityCreator CompositePropensityEnergy CompositePropensityEnergyElement CompositePropensityParameters CompositePropensityParametersList CompositeTorsionsDefinitions ConjugateGradient CooperativeAtomicPairwisePMFSumma CooperativeAtomicPairwisePMFSummaCreator CooperativeAtomicPairwisePMFSummaParameters CooperativeEnergyTerm CooperativePerAtomSumma CooperativePerAtomSummaCreator CooperativePerAtomSummaParameters CooperativePropensityCreator CooperativePropensityEnergy CooperativePropensityParameters CooperativeRamachandran CooperativeRamachandranCreator CooperativeRamachandranParameters CooperativeZParameters CooperativeZPropensityCreator CooperativeZPropensityEnergy CooperativeZPropensityParameters CooperativeZRamachandran CooperativeZRamachandranCreator CooperativeZRamachandranParameters CooperativeZSumma CooperativeZSummaCreator Coordinates CoordinatesAssigner Corpus CorrectRottenRamachandrans CoulombElectrostaticCreator CoulombElectrostaticEnergyElement CoulombElectrostatics CylinderCreator CylinderEnergy CylinderEnergyElement CylinderParameters CylinderParametersList Cys DahiyatImplementationConstants Differs Distance DistanceConstrainsDialog DistanceConstrainsDialogLayout DistanceList DistanceList.DistanceIterator DistanceMatrix DistanceMatrixBondedOnly DistanceMatrixCaOnly DistanceMatrixNoImageAtoms DistanceMatrixWhichUpdateOnlyMovingAtoms DistanceMirror DistanceMode DoNothingExceptionHandler DpMatrix DresserFullFrag DSSP DunbrackLib EDMEnergy EDMEnergyCreator EDMEnergyElement EDMEnergyParameters EDMEnergyParametersList EDMSplinedPolynomial EigenvalueDecomposition Element EnergyCreator EnergyElement EnergyStatistics EnergyStatisticsForAtom Equals EVRot1BBCreator EVRot1BBEnergy EVRot1BBParameterList EVRot1BBParameters ExceptionHandler ExcludedVol ExcludedVol ExcludedVolCreator ExcludedVolCreator ExcludedVolCreatorOLD ExcludedVolEnergyElement ExcludedVolEnergyElement ExcludedVolEnergyElementOLD ExcludedVolOLD ExcludedVolParameters ExcludedVolParametersList ExtendedAtomsProtein ExtractChain FastaList FastaReader Fdouble File2StringArray FileToString Filter FiniteExcludedVol FiniteExcludedVolCreator FiniteExcludedVolEnergyElement Fint Format FreeDistance FrozenCoordinates FrozenDistance FullModeller FWriter GDTcalculator GJFilters GJFilters.AcceptChainFilter GJFilters.AndFilter GJFilters.RejectChainFilter GJFilters.ResidueRangeFilter GJModeller GJModeller.HBRangesAndGoodResiduesFilter GJModeller.HBRangesFilter GJModeller.SpecialHBPairs GJUtils Gln Glu Gly GoodBonds GoodResiduesForHB GoodResiduesForHB.GoodSS GoodResiduesForHB.IsNot13 Grid GridCell HB_AtomAttribute HB_DistanceAttribute HBdistanceList HBondList HBondList.IsAlive HBondList.IsWithInRmax HbondsPunishHOCAngleCreator HbondsPunishHOCAngleEnergy HbondsPunishHOCAngleEnergyElement HBondsPunishOHNAngleCreator HBondsPunishOHNAngleEnergy HBondsPunishOHNAngleEnergyElement HeavyAtomsFilter HeliumClusterMinimization HeliumClusterMinimization.HeliumLennardJonesCreator HelixParametersList HelixParametersList.IsHydrogenBondsPairsParameters His Histogram Histogram.BinCreator Histogram.IsBin HistogramBin HomologyFileFilter HomologyFrame HomologyFrame11Layout HomologyModeling HomologyModeling.HomologyLogger HomologyModeling.Loop HomologyModeling.LoopAttribute HomologyModeling.LoopComperator HomologyModeling.LoopMode HomologyModeling.Three HomologyModeling.TimeTerminator HubbardPosition HydrogenBondDahiyat HydrogenBondDahiyatList HydrogenBondsCreator HydrogenBondsEnergy HydrogenBondsEnergyElement HydrogenBondsPairsCreator HydrogenBondsPairsEnergy HydrogenBondsPairsEnergyElement HydrogenBondsPairsParameters HydrogenBondsPairsParametersList HydrogenBondsPairsParametersList.NoElements HydrogenBondsParameters HydrogenBondsParametersList HydrogenTest HydrogenTest.PolyAla HydrogenTest.ResWithSSFilter Identity Ile ImageAtom ImageAtomList ImageChain ImageChain.IsImageChain ImageResidue InflateParameters InflateParametersDialog InflateParametersLayout InflateParametersList InitialEvaluation isAPdbFile IsClass IsHO Key KeyWords KolDichfin LBFGS LennardJones LennardJonesCreator LennardJonesCreatorCa LennardJonesEnergyElement LennardJonesParameters LennardJonesParametersList Leu LinearRgCreator LinearRgEnergy LineSearch LineSearchException LocalFragmentLib Logger Loop LoopResults LoopResultVector LoopUtils LoopUtils.Line LoopUtils.Point LUDecomposition Lys Maths Matrix Matrix Matrix1D MatrixRow MatrixRowCaOnly MatrixRowNoImageAtoms MCM MergeCorpora MeshiAttribute MeshiException MeshiInitException MeshiLineReader MeshiPotential MeshiProgram MeshiProgram.GlobalElement MeshiProgram.GlobalElementList MeshiWriter Met MinimizeParametersFullDialog MinimizeParametersFullDialogLayout MinimizeParametersShortDialog MinimizeParametersShortLayout MinimizeProtein Minimizer ModelData ModelData.TermComparator ModelRanker MolecularSystem NoConvergenceException NonBondedEnergyElement NonBondedEnergyTerm NonFrozenRangeDialog NonFrozenRangeDialogLayout NonFrozensRadiusFilter NotEnoughBoundAtomsException OldDistanceMatrix OldGrid OneOfTwenty Optimize Optimize.OptimizeLogger Optimizer Optimizer.OptimizerStatus OptimizerException OptionDialog OptionDialog3Layout OriginalAtom OriginalAtom.OriginalAtomFilter OriginalAtoms OutOfPlaneCreator OutOfPlaneEnergy OutOfPlaneEnergyElement OutOfPlaneParameters OutOfPlaneParametersList Overlap Pair PairOfHydrogenBondsElements PairsOfHBEElementsList PairsOfHBEElementsList.IsWithInRmax Parameters ParametersForChainCompletion ParametersForChainCompletionLayout ParametersList Pdb2Fasta Pdb2Fasta.MyAtom Pdb2Fasta.MyChain Pdb2Fasta.MyFilter Pdb2Fasta.MyResidue PdbLine PdbLineATOM PdbLineATOMorHETATOM PdbLineFilter PdbLineSEQRES PdbReader Perturbation Phe PlaneCreator PlaneEnergy PlaneEnergyElement PlaneParameters PlaneParametersList PredictionSequenceAlignment PredictionSequenceAlignment.TemplateAlignmentException Pro Protein Protein.BackboneFilter PutHpos PutHposLog QRDecomposition QuickAndDirtyAngle QuickAndDirtyAngleList QuickAndDirtyTorsion QuickAndDirtyTorsionList RamachandranCreator RamachandranEnergy RamachandranEnergyElement RamachandranParameters RamachandranParametersList RamachandranSidechainEnergy RamachandranSidechainEnergyCreator RamachandranSidechainEnergyElement RamachandranSidechainEnergyElementChi0 RamachandranSidechainEnergyElementChi1 RamachandranSidechainEnergyElementChi2 RamachandranSidechainEnergyElementChi3 RamachandranSidechainEnergyElementChi4 RamachandranSidechainParameters RamachandranSidechainParametersChi0 RamachandranSidechainParametersChi1 RamachandranSidechainParametersChi2 RamachandranSidechainParametersChi3 RamachandranSidechainParametersChi4 RamachandranSidechainParametersList Ramp Refine Refine.RefineLogger Residue ResidueAlignment ResidueAlignmentCell ResidueAlignmentColumn ResidueAlignmentOfModels ResidueBuilder ResidueCreator ResidueExtendedAtoms ResidueExtendedAtomsCreator ResidueIdentifier ResidueList ResidueList.NonDummyFilter ResidueMode ResidueNameConvertor ResidueSequence ResidueSequence.ResidueSequenceCharFilter ResidueTorsions ResidueTorsionsAttribute ResidueTorsionsList ResidueTorsionsList.CompleteResidueFilter ResidueTorsionsList.IncompleteResidueFilter ResidueTorsionsList.PhiPsiResidueFilter ResidueTorsionsPropensityAttribute ResidueType ResidueTypeException RgCalculator RgCreator RgEnergy Rms RmsException RoisFirstMeshiProgram Rot1Arrays RotamericTools RunBackboneCompleterAndMinimizer RunBackboneMCM RunFullModeller RunThreadingExperiment Scmod SCMOD SecondaryStructure SecondaryStructureSequence SecondaryStructureSequence.SecondaryStructureSequenceCharFilter SelectForCASP SelectModels SelectModels.ModelComparator Sequence Sequence.kolDichfin SequenceAlignment SequenceAlignmentCell SequenceAlignmentColumn SequenceCharFilter SequenceList SequenceList.AcceptAll SequenceList.IsSequenceFilter Ser SideChainSolvateCreator SideChainSolvateDistanceAttribute SideChainSolvateEnergy SideChainSolvateHBAngle SideChainSolvateParametersList Sigma SigmaParameters SimpleEnergyCreator SimpleEnergyCreator.HaveParametersFilter SimpleEnergyTerm SimpleInflate SimpleInflate.TargetFilter SimpleInflateCreator SimpleInflateEnergyElement SimpleStepLength SimplestMinimizeProtein SingleAxisRotationTransformation SingularValueDecomposition SmoothRotamerLibraryEnergy SmoothRotamerLibraryEnergyCreator SmoothRotamerLibraryEnergyElement SmoothRotamerLibraryEnergyElementChi0 SmoothRotamerLibraryEnergyElementChi1 SmoothRotamerLibraryEnergyElementChi2 SmoothRotamerLibraryEnergyElementChi3 SmoothRotamerLibraryEnergyElementChi4 SmoothRotamerLibraryParameters SmoothRotamerLibraryParametersChi0 SmoothRotamerLibraryParametersChi1 SmoothRotamerLibraryParametersChi2 SmoothRotamerLibraryParametersChi3 SmoothRotamerLibraryParametersChi4 SmoothRotamerLibraryParametersList SolvateCreatorHBforMinimization SolvateCreatorLongHB SolvateCreatorRegularHB SolvateDistanceAttribute SolvateDistanceAttributeBetweenPolars SolvateDistanceAttributeCreator SolvateDistanceAttributeNonPolarPolar SolvateDistanceAttributePolarNonPolar SolvateDistanceAttributeWithAhydrogen SolvateDistanceAttributeWithNonPolar SolvateDistanceType SolvateEnergy SolvateEnergy.SuperType SolvateParametersList SolvateRot1Creator SolvateRot1DistanceAttribute SolvateRot1Energy SolvateRot1ParametersList Spline1D Spline2D SplinedPolynomial SplinedPolynomialsLoader SteepestDecent StringFilter StringFilterEndsWith StringFilterEquals StringFilterGrep StringFilterStartsWith StringList StringList.IsString StringParser StructureBasedMatrix SubstitutionMatrix SummaAttribute SymmetricComplex SymmetricComplexCompleter SymmetryCreator SymmetryEnergy SymmetryEnergyElement SynchronizedUpdateException TemperatureGenerator TemplateEnergy TemplateEnergyCreator TemplateEnergyCreator.Template TemplateEnergyElement TemplateEnergyElementsList Terminator TestElectrostatics TetherCreator TetherEnergy TetherEnergyElement Thr Topology Torsion TorsionList TorsionList.FilterChi1 TorsionList.FilterChi2 TorsionList.FilterChi3 TorsionList.FilterChi4 TorsionList.FilterOOP TorsionList.FilterPhi TorsionList.FilterPsi TorsionList.FilterSideChain TorsionPair TorsionPairList TotalEnergy TotalEnergy.EnergyComparator TotalEnergy.FreeAtom TotalEnergy.IsEnergy Transformation Trp Tyr UnknownAtomTypeException UnWarpEnergy UnWarpEnergyCreator UnWarpEnergyElement UnWarpEnergyElementsList Updateable UpdateableException Utils Utils.DefaultExceptionHandler Utils.DoNothingExceptionHandler Val Verbose ViewAt WarpEnergy WarpEnergyCreator WarpEnergyElement WarpEnergyElementsList WeightsForEnergyTerms WeightsForEnergyTermsLayout WolfConditionLineSearch