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IMP Reference Guide  2.5.0
The Integrative Modeling Platform
Class Index
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X
  A  
CysteineCrossLinkData (IMP::isd)   ImageHeader (IMP::em)   ParticleStates (IMP::domino)   SGEQsubSlaveArray (IMP.parallel)   
CysteineCrossLinkRestraint (IMP::isd)   ImageReaderWriter (IMP::em2d)   ParticleStatesTable (IMP::domino)   Shift (IMP::score_functor)   
AddBoolFlag (IMP)   
  D  
IMPRestraints (IMP.modeller)   PartitionalClustering (IMP::statistics)   Showable (IMP)   
AddFloatFlag (IMP)   ImproperSingletonScore (IMP::atom)   PartitionalClusteringWithCenter (IMP::statistics)   SigmoidRestraintSphere (IMP::pmi)   
AddIntFlag (IMP)   Database2 (IMP.EMageFit.database)   InBoundingBox3DSingletonPredicate (IMP::core)   PathLocalPlanner (IMP::kinematics)   SimpleAssignmentsTable (IMP::domino)   
AddScores (IMP::score_functor)   DataObject (IMP::core)   InContainerPairFilter (IMP::container)   PCAAligner (IMP::em)   SimpleLoadLink (IMP::rmf)   
AddStringFlag (IMP)   DataPointsAssignment (IMP::multifit)   InContainerQuadFilter (IMP::container)   PCAFitRestraint (IMP::em)   SimpleSaveLink (IMP::rmf)   
AdvancedFlag (IMP)   DecayPairContainerOptimizerState (IMP::misc)   InContainerSingletonFilter (IMP::container)   PCAFitRestraint (IMP::em2d)   Simplex (IMP::gsl)   
Alignment (IMP.pmi.analysis)   Decorator (IMP)   InContainerTripletFilter (IMP::container)   PDBSelector (IMP::atom)   Simulator (IMP::atom)   
AlignmentClustering (IMP.multifit.cluster)   DefaultEmbeddingD (IMP::algebra)   IncrementalScoringFunction (IMP::core)   PermutationStates (IMP::domino)   SingleLinkage (IMP::em2d)   
AlignSymmetric (IMP::cnmultifit)   DegreesOfFreedom (IMP.pmi.dof)   Index (IMP)   Pipe (IMP.isd.utils)   SingletonConstraint (IMP::core)   
AllBipartitePairContainer (IMP::container)   DeltaDistributionFunction (IMP::saxs)   IndexException (IMP)   PivyWriter (IMP::display)   SingletonContainer (IMP)   
AllMol2Selector (IMP::atom)   Demuxer (IMP.isd.demux_trajs)   IndexStates (IMP::domino)   Plane3D (IMP::algebra)   SingletonContainerAdaptor (IMP)   
AllPairContainer (IMP::container)   DenseFloatLogGridKD (IMP::algebra)   IndexVector (IMP)   PlaneGeometry (IMP::display)   SingletonContainerSet (IMP::container)   
AllPDBSelector (IMP::atom)   DenseGrid3D (IMP::algebra)   InitialDockingFromXlinks (IMP.EMageFit.buildxlinks)   Pointer (IMP)   SingletonContainerStatistics (IMP::container)   
AllSamePairPredicate (IMP::core)   DenseGridStorageD (IMP::algebra)   InputAdaptor (IMP)   PointerMember (IMP)   SingletonGeometry (IMP::display)   
AllSameQuadPredicate (IMP::core)   DenseIntLogGrid3D (IMP::algebra)   InternalException (IMP)   PointGeometry (IMP::display)   SingletonModifier (IMP)   
AllSameSingletonPredicate (IMP::core)   DensityDataPoints (IMP::multifit)   IntsOrder (IMP::em2d)   PolarResamplingParameters (IMP::em2d)   SingletonPredicate (IMP)   
AllSameTripletPredicate (IMP::core)   DensityFillingRestraint (IMP::em)   IOException (IMP)   PolygonGeometry (IMP::display)   SingletonRestraint (IMP::core)   
AmbiguousCompositeRestraint (IMP.pmi.restraints.proteomics)   DensityHeader (IMP::em)   IsCollisionPairPredicate (IMP::core)   PPDBSelector (IMP::atom)   SingletonsConstraint (IMP::container)   
AmbiguousNOERestraint (IMP::isd)   DensityMap (IMP::em)   IsosurfaceGeometry (IMP::display)   Precision (IMP.pmi.analysis)   SingletonScore (IMP)   
AmbiguousRestraint (IMP::isd)   DependencyScoreState (IMP::domino)   
  J  
PredicatePairsRestraint (IMP::container)   SingletonsGeometry (IMP::display)   
Analysis (IMP.isd.Analysis)   DerivativeAccumulator (IMP)   PredicateQuadsRestraint (IMP::container)   SingletonsOptimizerState (IMP::container)   
AnalysisReplicaExchange0 (IMP.pmi.macros)   DerivativeCalculator (IMP::saxs)   JeffreysRestraint (IMP::isd)   PredicateSingletonScore (IMP::core)   SingletonsRestraint (IMP::container)   
AnchorsData (IMP::multifit)   DerivativesFromRefined (IMP::core)   Joint (IMP::kinematics)   PredicateSingletonsRestraint (IMP::container)   SingletonStatistical (IMP::score_functor)   
AndPDBSelector (IMP::atom)   DerivativesToRefined (IMP::core)   JPGImageReaderWriter (IMP::em2d)   PredicateTripletsRestraint (IMP::container)   SkinSurfaceGeometry (IMP::display)   
Angle (IMP::atom)   DiameterRestraint (IMP::core)   
  K  
PrincipalComponentAnalysisD (IMP::algebra)   Slave (IMP.parallel)   
AngleRestraint (IMP::core)   Diffusion (IMP::atom)   PrismaticJoint (IMP::kinematics)   SlaveArray (IMP.parallel)   
AngleSingletonScore (IMP::atom)   Dihedral (IMP::atom)   KClosePairsPairScore (IMP::core)   ProbabilisticAnchorGraph (IMP::multifit)   Slice (IMP::domino)   
AngleTripletScore (IMP::core)   DihedralAngleRevoluteJoint (IMP::kinematics)   KernelParameters (IMP::em)   ProbabilisticSubsetFilterTable (IMP::domino)   SmoothingFunction (IMP::atom)   
AngularVelocity (IMP::atom)   DihedralRestraint (IMP::core)   Key (IMP)   ProcessOutput (IMP.pmi.output)   Soap (IMP::score_functor)   
ApplicationTestCase (IMP.test)   DihedralSingletonScore (IMP::atom)   KinematicForest (IMP::kinematics)   Profile (IMP::saxs)   SoapPairFilter (IMP::atom)   
Array (IMP)   DirectorObjectChecker (IMP.test)   KinematicForestScoreState (IMP::kinematics)   ProfileClustering (IMP::saxs)   SoftCylinderPairScore (IMP::misc)   
AssemblyHeader (IMP::multifit)   DiscreteSampler (IMP::domino)   KinematicNode (IMP::kinematics)   ProfileFitter (IMP::saxs)   SoftSpherePairScore (IMP::core)   
Assignment (IMP::domino)   DisjointSetsSubsetFilterTable (IMP::domino)   KMeans (IMP::kmeans)   Profiler (IMP::benchmark)   SolventAccessibleSurface (IMP::saxs)   
AssignmentContainer (IMP::domino)   DistanceFilter (IMP::em2d)   
  L  
ProjectingOptions (IMP::em2d)   SparseGrid3D (IMP::algebra)   
AssignmentsTable (IMP::domino)   DistanceFilterTable (IMP::em2d)   ProjectingParameters (IMP::em2d)   SparseGridStorageD (IMP::algebra)   
Atom (IMP::atom)   DistanceMask (IMP::em)   LabelGeometry (IMP::display)   ProjectionFinder (IMP::em2d)   SparseSymmetricPairMemoizer (IMP)   
AtomicCrossLinkMSRestraint (IMP::isd)   DistancePairScore (IMP::core)   LangevinThermostatOptimizerState (IMP::atom)   ProjectionMask (IMP::em2d)   SparseUnboundedGrid3D (IMP::algebra)   
ATOMPDBSelector (IMP::atom)   DistancePairScore (IMP::score_functor)   LeavesRefiner (IMP::core)   ProjectionParameters (IMP::em2d)   SparseUnboundedGridD (IMP::algebra)   
AtomType (IMP::atom)   DistanceRestraint (IMP::core)   LennardJones (IMP::atom)   ProjectionParametersScoreState (IMP::em2d)   SphereD (IMP::algebra)   
AttributeOptimizer (IMP)   DistributePairsScoreState (IMP::container)   LennardJonesPairScore (IMP::atom)   ProjectionStates (IMP::em2d)   SphereDistance (IMP::score_functor)   
AttributeSingletonPredicate (IMP::core)   DistributeQuadsScoreState (IMP::container)   LessPairBySecond (IMP::em2d)   ProteinKinematics (IMP::kinematics)   SphereDistancePairScore (IMP::core)   
AverageDistanceLinkage (IMP::em2d)   DistributeSingletonsScoreState (IMP::container)   Linear (IMP::core)   ProteinLigandAtomPairScore (IMP::atom)   SphereDistanceToSingletonScore (IMP::core)   
  B  
DistributeTripletsScoreState (IMP::container)   Linear1DFunction (IMP::isd)   ProteinLigandRestraint (IMP::atom)   SphereGeometry (IMP::display)   
Distribution (IMP::saxs)   LinearFit2D (IMP::algebra)   ProteinsAnchorsSamplingSpace (IMP::multifit)   SpherePatch3D (IMP::algebra)   
BackbonePDBSelector (IMP::atom)   DockOrder (IMP.EMageFit.buildxlinks)   LinearLowerBound (IMP::score_functor)   ProteomicsData (IMP::multifit)   SphericalVector3D (IMP::algebra)   
BallMover (IMP::core)   DOF (IMP::kinematics)   LinearVelocity (IMP::atom)   ProteomicsEMAlignmentAtomic (IMP::multifit)   SpiderHeader (IMP::em)   
BallMover (IMP::symmetry)   DOFsSampler (IMP::kinematics)   ListAssignmentContainer (IMP::domino)   PseudoAtomicRestraint (IMP.pmi.restraints.stereochemistry)   SpiderImageReaderWriter (IMP::em2d)   
BerendsenThermostatOptimizerState (IMP::atom)   Domain (IMP::atom)   ListAssignmentsTable (IMP::domino)   PymolWriter (IMP::display)   SpiderMapReaderWriter (IMP::em)   
BinormalTerm (IMP::modeller)   DominoModel (IMP.EMageFit.domino_model)   ListPairContainer (IMP::container)   PythonDirectedGraph (IMP)   State (IMP::atom)   
BiStableDistanceRestraint (IMP.pmi.restraints.basic)   DominoSampler (IMP::domino)   ListQuadContainer (IMP::container)   PythonExampleConstraint (IMP.example)   State (IMP.pmi.topology)   
BivariateFunction (IMP::isd)   Dope (IMP::score_functor)   ListSingletonContainer (IMP::container)   PythonExamplePairScore (IMP.example)   StateAdaptor (IMP::misc)   
Bond (IMP::atom)   DopePairScore (IMP::atom)   ListSubsetFilterTable (IMP::domino)   PythonExampleRestraint (IMP.example)   Statistical (IMP::score_functor)   
ForceFieldParameters::Bond (IMP::atom)   DummyRestraint (IMP::em2d)   ListTripletContainer (IMP::container)   PythonExampleSingletonModifier (IMP.example)   StatisticalPairScore (IMP::core)   
BondAngleRevoluteJoint (IMP::kinematics)   DummyRestraint (IMP::multifit)   LoadLink (IMP::rmf)   PythonExampleUnaryFunction (IMP.example)   Statistics (IMP.isd.Statistics)   
Bonded (IMP::atom)   DynamicListPairContainer (IMP::container)   LocalPlanner (IMP::kinematics)   
  Q  
SteepestDescent (IMP::core)   
BondedPairFilter (IMP::atom)   DynamicListQuadContainer (IMP::container)   LocalSlave (IMP.parallel)   StereochemistryPairFilter (IMP::atom)   
BondEndpointsRefiner (IMP::atom)   DynamicListSingletonContainer (IMP::container)   LogEmbeddingD (IMP::algebra)   QuadConstraint (IMP::core)   StructureSource (IMP::atom)   
BondGeometry (IMP::atom)   DynamicListTripletContainer (IMP::container)   LogHolder (IMP.isd.demux_trajs)   QuadContainer (IMP)   Subsequence (IMP.pmi.io)   
BondGraph (IMP::atom)   DynamicNearestNeighbor3D (IMP::algebra)   LognormalAmbiguousRestraint (IMP::isd)   QuadContainerAdaptor (IMP)   SubsequenceData (IMP.pmi.io)   
BondPairContainer (IMP::atom)   
  E  
LognormalRestraint (IMP::isd)   QuadContainerSet (IMP::container)   Subset (IMP::domino)   
BondsGeometry (IMP::atom)   LogPairScore (IMP::misc)   QuadContainerStatistics (IMP::container)   SubsetFilter (IMP::domino)   
BondSingletonScore (IMP::atom)   EdgePairGeometry (IMP::core)   LogWrapper (IMP::isd)   QuadModifier (IMP)   SubsetFilterTable (IMP::domino)   
BoundedGridRangeD (IMP::algebra)   EdgePairsGeometry (IMP::core)   LowestRefinedPairScore (IMP::misc)   QuadPredicate (IMP)   SurfaceMeshGeometry (IMP::display)   
BoundingBoxD (IMP::algebra)   ElasticNetworkRestraint (IMP.pmi.restraints.stereochemistry)   LRUCache (IMP)   QuadraticClosePairsFinder (IMP::core)   SurfaceShellDensityMap (IMP::em)   
BoundingBoxGeometry (IMP::display)   ElementTable (IMP::atom)   
  M  
QuadRestraint (IMP::core)   Switching (IMP::isd)   
BoxSweepClosePairsFinder (IMP::core)   Ellipsoid3D (IMP::algebra)   QuadsConstraint (IMP::container)   Symmetric (IMP::pmi)   
BranchAndBoundAssignmentsTable (IMP::domino)   EllipsoidGeometry (IMP::display)   Manager (IMP.parallel)   QuadScore (IMP)   System (IMP.pmi.topology)   
BranchAndBoundSampler (IMP::domino)   Em2DRestraint (IMP::em2d)   MapDistanceTransform (IMP::em)   QuadsOptimizerState (IMP::container)   SystemBase (IMP.pmi.topology)   
BrownianDynamics (IMP::atom)   Em2DRestraintParameters (IMP::em2d)   MapReaderWriter (IMP::em)   QuadsRestraint (IMP::container)   
  T  
BrownianDynamicsTAMD (IMP::atom)   EM2DScore (IMP::em2d)   MarginalHBondRestraint (IMP::isd)   QuasiNewton (IMP::gsl)   
BuildModel (IMP.pmi.macros)   Embedding (IMP::statistics)   MarginalNOERestraint (IMP::isd)   
  R  
TableRefiner (IMP::core)   
BuildModel1 (IMP.pmi.macros)   EMReaderWriter (IMP::em)   MasksManager (IMP::em2d)   TALOSReader (IMP.isd.TALOSReader)   
  C  
Ensemble (IMP::multifit)   Mass (IMP::atom)   RadialDistributionFunction (IMP::saxs)   TALOSRestraint (IMP::isd)   
EnsembleGenerator (IMP::multi_state)   MasterCommunicator (IMP.parallel.master_communicator)   RadiusDependentDistanceMask (IMP::em)   TAMDCentroid (IMP::atom)   
CAAngleRestraint (IMP::atom)   Entry (IMP.isd.Entry)   MatchTemplateResult (IMP::em2d)   RadiusDependentKernelParameters (IMP::em)   TAMDParticle (IMP::atom)   
CADihedralRestraint (IMP::atom)   EnvelopeFitRestraint (IMP::em)   MaxVectorKDMetric (IMP::algebra)   RadiusOfGyrationRestraint (IMP::multifit)   TempDir (IMP.test)   
CAlphaPDBSelector (IMP::atom)   EnvelopePenetrationRestraint (IMP::em)   MCCGSampler (IMP::core)   RadiusOfGyrationRestraint (IMP::saxs)   TestCase (IMP.test)   
CappedAssignmentContainer (IMP::domino)   EnvelopeScore (IMP::em)   MeanAbsoluteDifference (IMP::em2d)   RAII (IMP)   TextInput (IMP)   
CBetaPDBSelector (IMP::atom)   EqualitySubsetFilterTable (IMP::domino)   Memoizer (IMP)   RangeViewAssignmentContainer (IMP::domino)   TextOutput (IMP)   
CenteredMat (IMP::em2d)   EquivalenceAndExclusionSubsetFilterTable (IMP::domino)   MergeTreeBuilder (IMP::multifit)   RatioVolatilityScore (IMP::saxs)   TextWriter (IMP::display)   
CenterOfMass (IMP::atom)   EquivalenceSubsetFilterTable (IMP::domino)   Metric (IMP::statistics)   ReadAssignmentContainer (IMP::domino)   TIFFImageReaderWriter (IMP::em2d)   
Centroid (IMP::core)   Error (IMP.parallel)   MetricClosePairsFinder (IMP::misc)   ReadHDF5AssignmentContainer (IMP::domino)   Timer (IMP)   
CentroidOfRefined (IMP::core)   EuclideanMetric (IMP::statistics)   MinimumPairRestraint (IMP::container)   RecursiveAssignmentsTable (IMP::domino)   TopologyPlot (IMP.pmi.plotting.topology)   
Chain (IMP::atom)   EuclideanVectorKDMetric (IMP::algebra)   MinimumPairScore (IMP::container)   RecursivePartitionalClusteringEmbedding (IMP::statistics)   TopologyReader (IMP.pmi.topology)   
ChainPDBSelector (IMP::atom)   EvaluationState (IMP)   MinimumQuadRestraint (IMP::container)   RecursivePartitionalClusteringMetric (IMP::statistics)   Transform (IMP::core)   
Charged (IMP::atom)   EventException (IMP)   MinimumQuadScore (IMP::container)   RecursiveStates (IMP::domino)   Transformation2D (IMP::algebra)   
CHARMMAtom (IMP::atom)   EventPairsOptimizerState (IMP::container)   MinimumRestraint (IMP::core)   RefCountChecker (IMP.test)   Transformation3D (IMP::algebra)   
CHARMMAtomTopology (IMP::atom)   EventQuadsOptimizerState (IMP::container)   MinimumRestraintScoreSubsetFilterTable (IMP::domino)   Reference (IMP::core)   Transformation3DToText (IMP.EMageFit.imp_general.io)   
CHARMMBondEndpoint (IMP::atom)   EventSingletonsOptimizerState (IMP::container)   MinimumSingletonRestraint (IMP::container)   ReferenceFrame3D (IMP::algebra)   TransformationAndReflectionSymmetry (IMP::core)   
CHARMMBondParameters (IMP::atom)   EventTripletsOptimizerState (IMP::container)   MinimumSingletonScore (IMP::container)   ReferenceFrameGeometry (IMP::display)   TransformationJoint (IMP::kinematics)   
CHARMMConnection (IMP::atom)   ExampleComplexRestraint (IMP::example)   MinimumTripletRestraint (IMP::container)   ReferenceFrameToText (IMP.EMageFit.imp_general.io)   TransformationSymmetry (IMP::core)   
CHARMMDihedralParameters (IMP::atom)   ExampleConstraint (IMP::example)   MinimumTripletScore (IMP::container)   RefinedPairsPairScore (IMP::core)   TransformedDistancePairScore (IMP::core)   
CharmmForceFieldRestraint (IMP.pmi.restraints.stereochemistry)   ExampleDecorator (IMP::example)   Model (IMP)   Refiner (IMP)   TransformMover (IMP::pmi)   
CharmmForceFieldRestraint (IMP.pmi.restraints_new.stereochemistry)   ExampleObject (IMP::example)   ModelException (IMP)   Reflection3D (IMP::algebra)   Triangle3D (IMP::algebra)   
CHARMMIdealResidueTopology (IMP::atom)   ExamplePairScore (IMP::example)   ModellerRestraints (IMP.modeller)   RegistrationResult (IMP::em2d)   TriangleGeometry (IMP::display)   
CHARMMInternalCoordinate (IMP::atom)   ExampleRestraint (IMP::example)   ModelLoader (IMP.modeller)   RelativePositionMover (IMP::em2d)   TripletConstraint (IMP::core)   
CHARMMParameters (IMP::atom)   ExampleSingletonModifier (IMP::example)   ModelObject (IMP)   RemoteError (IMP.parallel)   TripletContainer (IMP)   
CHARMMPatch (IMP::atom)   ExampleSubsetFilterTable (IMP::example)   ModifierVisitor (IMP::core)   RemoveRigidMotionOptimizerState (IMP::atom)   TripletContainerAdaptor (IMP)   
CHARMMResidueTopology (IMP::atom)   ExampleTemplateClassD (IMP::example)   Mol2Selector (IMP::atom)   RemoveTranslationOptimizerState (IMP::atom)   TripletContainerSet (IMP::container)   
CHARMMResidueTopologyBase (IMP::atom)   ExampleUnaryFunction (IMP::example)   MolCnSymmAxisDetector (IMP::cnmultifit)   ReplicaExchange (IMP.pmi.samplers)   TripletContainerStatistics (IMP::container)   
CHARMMSegmentTopology (IMP::atom)   Exception (IMP)   MolecularDynamics (IMP::atom)   ReplicaExchange (IMP::mpi)   TripletModifier (IMP)   
CHARMMStereochemistryRestraint (IMP::atom)   ExcludedVolumeRestraint (IMP::core)   MolecularDynamics (IMP.pmi.samplers)   ReplicaExchange0 (IMP.pmi.macros)   TripletPredicate (IMP)   
CHARMMTopology (IMP::atom)   ExcludedVolumeSphere (IMP.pmi.restraints.stereochemistry)   MolecularDynamics (IMP::isd)   Representation (IMP.pmi.representation)   TripletRestraint (IMP::core)   
ChecksScoreState (IMP::core)   ExclusionSubsetFilterTable (IMP::domino)   MolecularDynamicsMover (IMP::isd)   Representation (IMP::atom)   TripletsConstraint (IMP::container)   
ChiFreeScore (IMP::saxs)   ExclusiveConsecutivePairContainer (IMP::container)   Molecule (IMP::atom)   RepulsiveDistancePairScore (IMP::isd)   TripletScore (IMP)   
ChildrenRefiner (IMP::core)   ExclusiveConsecutivePairFilter (IMP::container)   Molecule (IMP.pmi.topology)   Residue (IMP::atom)   TripletsOptimizerState (IMP::container)   
ChimeraWriter (IMP::display)   ExtendedGridIndexD (IMP::algebra)   MonteCarlo (IMP.pmi.samplers)   ResidueAngleRestraint (IMP.pmi.restraints.stereochemistry)   TripletsRestraint (IMP::container)   
ChiScore (IMP::saxs)   EzRestraint (IMP::atom)   MonteCarlo (IMP::core)   ResidueBondRestraint (IMP.pmi.restraints.stereochemistry)   TruncatedHarmonic (IMP::core)   
ChiScoreLog (IMP::saxs)   
  F  
MonteCarloMover (IMP::core)   ResidueDihedralRestraint (IMP.pmi.restraints.stereochemistry)   Typed (IMP::core)   
ChiSquaredScore (IMP::em2d)   MonteCarloMoverResult (IMP::core)   ResidueRotamer (IMP::rotamer)   TypedPairScore (IMP::core)   
ChiSquareMetric (IMP::statistics)   FFTFitting (IMP::multifit)   MonteCarloRelativeMoves (IMP.EMageFit.monte_carlo)   ResidueType (IMP::atom)   TypeException (IMP)   
CloseBipartitePairContainer (IMP::container)   FFTFittingOutput (IMP::multifit)   MonteCarloWithBasinHopping (IMP::core)   Resolution (IMP::pmi)   
  U  
ClosedCubicSpline (IMP::core)   FilterGeometry (IMP::display)   MonteCarloWithLocalOptimization (IMP::core)   Restraint (IMP::saxs)   
ClosePairContainer (IMP::container)   FilterOperator (IMP.pmi.io.crosslink)   MoveStatisticsScoreState (IMP::core)   Restraint (IMP)   UnaryFunction (IMP)   
ClosePairsFinder (IMP::core)   Fine2DRegistrationRestraint (IMP::em2d)   MRCReaderWriter (IMP::em)   RestraintCache (IMP::domino)   UnaryFunctionEvaluate (IMP::score_functor)   
ClosePairsPairScore (IMP::core)   FitParameters (IMP::saxs)   MSConnectivityRestraint (IMP::core)   RestraintGeometry (IMP::display)   UnboundedGridRangeD (IMP::algebra)   
Clustering (IMP.pmi.analysis)   FitRestraint (IMP::em)   MultipleBinormalRestraint (IMP::modeller)   RestraintsAdaptor (IMP)   Uncertainty (IMP::pmi)   
ClusterSet (IMP::em2d)   FittingSolutionRecord (IMP::multifit)   MultiStateModel (IMP::multi_state)   RestraintScoreSubsetFilterTable (IMP::domino)   UncheckedWeakPointer (IMP)   
CnSymmAxisDetector (IMP::cnmultifit)   FittingSolutions (IMP::em)   MultiStateModelScore (IMP::multi_state)   RestraintSet (IMP)   Undecorator (IMP)   
CoarseCARestraint (IMP.pmi.restraints_new.stereochemistry)   FittingStates (IMP::multifit)   MultivariateFNormalSufficient (IMP::isd)   RestraintSetGeometry (IMP::display)   UniformBackboneSampler (IMP::kinematics)   
CoarseCC (IMP::em)   FixedRefiner (IMP::core)   MyMetric (write_a_metric)   RestraintsScoringFunction (IMP::core)   UniformPrior (IMP::isd)   
CoarseCCatIntervals (IMP::em)   FixedXYZ (IMP::algebra)   
  N  
ResultsDB (IMP.EMageFit.solutions_io)   UnivariateFunction (IMP::isd)   
CoarseConvolution (IMP::em)   Flag (IMP)   RevoluteJoint (IMP::kinematics)   UnorderedTypePairPredicate (IMP::core)   
CoinFlipPairPredicate (IMP::core)   FloatIndex (IMP)   NearestNeighborD (IMP::algebra)   RevoluteJointMover (IMP::kinematics)   UnorderedTypeQuadPredicate (IMP::core)   
CoinFlipQuadPredicate (IMP::core)   FNormal (IMP::isd)   NearestNeighborsClosePairsFinder (IMP::core)   RigidBodiesImageFitRestraint (IMP::em2d)   UnorderedTypeSingletonPredicate (IMP::core)   
CoinFlipSingletonPredicate (IMP::core)   ForceFieldParameters (IMP::atom)   NeighborsTable (IMP::core)   RigidBodiesProfileHandler (IMP::saxs)   UnorderedTypeTripletPredicate (IMP::core)   
CoinFlipTripletPredicate (IMP::core)   ForceSwitch (IMP::atom)   NestedRigidBodyStates (IMP::domino)   RigidBody (IMP::core)   UsageException (IMP)   
CollisionCrossSection (IMP::em2d)   FormFactorTable (IMP::saxs)   NetworkError (IMP.parallel)   RigidBodyAnglePairScore (IMP::core)   
  V  
Color (IMP::display)   Fragment (IMP::atom)   NOERestraint (IMP::isd)   RigidBodyDerivativeGeometry (IMP::core)   
ColorChange (IMP.pmi.tools)   FretData (IMP::isd)   NoMoreSlavesError (IMP.parallel)   RigidBodyDerivativesGeometry (IMP::core)   Value (IMP)   
Colored (IMP::display)   FretRestraint (IMP::isd)   NonAlternativePDBSelector (IMP::atom)   RigidBodyDiffusion (IMP::atom)   ValueException (IMP)   
CommandDispatcher (IMP)   
  G  
NonCopyable (IMP)   RigidBodyDistancePairScore (IMP::core)   Vector (IMP)   
CommonEndpointPairFilter (IMP::misc)   NonHydrogenMol2Selector (IMP::atom)   RigidBodyFrameGeometry (IMP::core)   VectorBaseD (IMP::algebra)   
CompareMultiStateModels (IMP::multi_state)   Gaussian (IMP::core)   NonRigidMember (IMP::core)   RigidBodyFramesGeometry (IMP::core)   VectorD (IMP::algebra)   
ComplementarityRestraint (IMP::multifit)   Gaussian3D (IMP::algebra)   NonWaterNonHydrogenPDBSelector (IMP::atom)   RigidBodyHierarchyGeometry (IMP::core)   VectorDEmbedding (IMP::statistics)   
CompleteLinkage (IMP::em2d)   GaussianEMRestraint (IMP::isd)   NonWaterPDBSelector (IMP::atom)   RigidBodyMember (IMP::core)   VectorKDMetric (IMP::algebra)   
ComponentHeader (IMP::multifit)   GaussianProcessInterpolation (IMP::isd)   NormalizedSphereDistancePairScore (IMP::core)   RigidBodyMover (IMP::symmetry)   VelocityScalingOptimizerState (IMP::atom)   
ComponentTopology (IMP.pmi.topology)   GaussianProcessInterpolationRestraint (IMP::isd)   NormalMover (IMP::core)   RigidBodyMover (IMP::core)   VersionInfo (IMP)   
CompositeJoint (IMP::kinematics)   GaussianRestraint (IMP::isd)   NotPDBSelector (IMP::atom)   RigidBodyStates (IMP::domino)   VolumeRestraint (IMP::core)   
CompositeRestraint (IMP.pmi.restraints.proteomics)   GeneralizedGuinierPorodFunction (IMP::isd)   NPDBSelector (IMP::atom)   RigidBodyTorque (IMP::core)   Voxel (IMP::em)   
CompositeRestraint (IMP::pmi)   GenericAttributeSingletonScore (IMP::core)   Nuisance (IMP::isd)   RigidBodyTunneler (IMP::core)   
  W  
CompoundStates (IMP::domino)   GenericBoundingBox3DSingletonScore (IMP::core)   
  O  
RigidBodyUmbrella (IMP::core)   
Cone3D (IMP::algebra)   GenericDistanceToSingletonScore (IMP::core)   RigidClosePairsFinder (IMP::core)   WarningContext (IMP)   
Configuration (IMP)   GeometricHash (IMP::multifit)   Object (IMP)   RigidMember (IMP::core)   WaterPDBSelector (IMP::atom)   
ConfigurationSet (IMP)   GeometricPrimitiveD (IMP::algebra)   OpenCubicSpline (IMP::core)   RotamerAngleTuple (IMP::rotamer)   WeakPointer (IMP)   
ConfigurationSetRMSDMetric (IMP::statistics)   Geometry (IMP::display)   OpenCubicSpline (IMP::score_functor)   RotamerCalculator (IMP::rotamer)   Weight (IMP::isd)   
ConfigurationSetXYZEmbedding (IMP::statistics)   GeometryProcessor (IMP::display)   Optimizer (IMP)   RotamerLibrary (IMP::rotamer)   WeightedDerivativesToRefined (IMP::core)   
ConjugateGradients (IMP.pmi.samplers)   GeometrySet (IMP::display)   OptimizerState (IMP)   Rotation2D (IMP::algebra)   WeightedExcludedVolumeRestraint (IMP::multifit)   
ConjugateGradients (IMP::gsl)   GetModelDensity (IMP.pmi.analysis)   OptionParser (IMP)   Rotation3D (IMP::algebra)   WeightedFitParameters (IMP::saxs)   
ConjugateGradients (IMP::core)   GridClosePairsFinder (IMP::core)   Order (IMP::domino)   RRT (IMP::kinematics)   WeightedProfileFitter (IMP::saxs)   
ConnectingPairContainer (IMP::container)   GridD (IMP::algebra)   OrderedTypePairPredicate (IMP::core)   RunInTempDir (IMP.test)   WeightedSphereDistancePairScore (IMP::core)   
ConnectivityCrossLinkMS (IMP.pmi.restraints.crosslinking)   GridIndexD (IMP::algebra)   OrderedTypeQuadPredicate (IMP::core)   
  S  
WeightMover (IMP::isd)   
ConnectivityNetworkRestraint (IMP.pmi.restraints.proteomics)   GridStates (IMP::em2d)   OrderedTypeSingletonPredicate (IMP::core)   WeightRestraint (IMP::isd)   
ConnectivityRestraint (IMP.pmi.restraints.proteomics)   GSLOptimizer (IMP::gsl)   OrderedTypeTripletPredicate (IMP::core)   SameResiduePairFilter (IMP::atom)   WeightScore (IMP::score_functor)   
ConnectivityRestraint (IMP::core)   
  H  
OrientedSoap (IMP::score_functor)   SampleAssignmentContainer (IMP::domino)   WormLikeChain (IMP::misc)   
ConnollySurfacePoint (IMP::algebra)   OrientedSoapPairScore (IMP::atom)   SampledDensityMap (IMP::em)   WriteAssignmentContainer (IMP::domino)   
ConsecutivePairContainer (IMP::container)   Harmonic (IMP::core)   OrPDBSelector (IMP::atom)   SampleObjects (IMP.pmi.sampling_tools)   WriteHDF5AssignmentContainer (IMP::domino)   
ConsecutivePairFilter (IMP::container)   Harmonic (IMP::score_functor)   Output (IMP.pmi.output)   Sampler (IMP)   WriteOptimizerState (IMP::display)   
ConstantPairPredicate (IMP::core)   HarmonicDistancePairScore (IMP::core)   
  P  
SaveLink (IMP::rmf)   WritePDBOptimizerState (IMP::atom)   
ConstantQuadPredicate (IMP::core)   HarmonicLowerBound (IMP::core)   SaveOptimizerState (IMP::rmf)   Writer (IMP::display)   
ConstantRestraint (IMP::core)   HarmonicLowerBound (IMP::score_functor)   PackedAssignmentContainer (IMP::domino)   SaveToConfigurationSetOptimizerState (IMP)   WriterAdaptor (IMP::display)   
ConstantSingletonPredicate (IMP::core)   HarmonicSphereDistancePairScore (IMP::core)   PairConstraint (IMP::core)   SAXSMultiStateModelScore (IMP::multi_state)   WriteRestraintScoresOptimizerState (IMP::core)   
ConstantTripletPredicate (IMP::core)   HarmonicUpperBound (IMP::core)   PairContainer (IMP)   Scale (IMP::isd)   
  X  
Constraint (IMP)   HarmonicUpperBound (IMP::score_functor)   PairContainerAdaptor (IMP)   ScopedAddCacheAttribute (IMP)   
ConstVector (IMP)   HarmonicUpperBoundSphereDiameterPairScore (IMP::core)   PairContainerSet (IMP::container)   ScopedSetAttribute (IMP)   Xlink (IMP.EMageFit.buildxlinks)   
Container (IMP)   HarmonicUpperBoundSphereDistancePairScore (IMP::core)   PairContainerStatistics (IMP::container)   Score (IMP::score_functor)   XlinksDict (IMP.EMageFit.buildxlinks)   
Context (IMP.parallel)   HarmonicWell (IMP::core)   PairGeometry (IMP::display)   ScoreAccumulator (IMP)   XLTable (IMP.pmi.io.xltable)   
Copy (IMP::atom)   HasHigherCCC (IMP::em2d)   PairListSubsetFilterTable (IMP::domino)   ScoreFunction (IMP::em2d)   XplorReaderWriter (IMP::em)   
Cosine (IMP::core)   HasLowerScore (IMP::em2d)   PairModifier (IMP)   ScoreState (IMP)   XYZ (IMP::core)   
CoulombPairScore (IMP::atom)   HeapAssignmentContainer (IMP::domino)   PairPredicate (IMP)   ScoreUnaryFunction (IMP::score_functor)   XYZDerivativeGeometry (IMP::core)   
Covariance1DFunction (IMP::isd)   HeapRecord (IMP.EMageFit.solutions_io)   PairRestraint (IMP::core)   ScoringFunction (IMP)   XYZDerivativesGeometry (IMP::core)   
Cover (IMP::core)   HierarchiesGeometry (IMP::atom)   PairsConstraint (IMP::container)   ScoringFunctionAdaptor (IMP)   XYZR (IMP::core)   
CoverBond (IMP::atom)   Hierarchy (IMP::core)   PairScore (IMP)   SecondaryStructureResidue (IMP::atom)   XYZRGeometry (IMP::core)   
CoverRefined (IMP::core)   Hierarchy (IMP::atom)   PairsGeometry (IMP::display)   Segment3D (IMP::algebra)   XYZRsGeometry (IMP::core)   
CPDBSelector (IMP::atom)   HierarchyCounter (IMP::core)   PairsOptimizerState (IMP::container)   SegmentationParameters (IMP::em2d)   XYZStates (IMP::domino)   
CreateLogContext (IMP)   HierarchyDatabase (IMP.pmi.tools)   PairsRestraint (IMP::container)   SegmentGeometry (IMP::display)   
  d  
CrossLink (IMP.pmi.io)   HierarchyGeometry (IMP::atom)   ParabolicFit2D (IMP::algebra)   Selection (IMP::atom)   
CrossLinkData (IMP.pmi.io)   HierarchyLoadLink (IMP::rmf)   Particle (IMP)   SelectionGeometry (IMP::atom)   dof (IMP.pmi.dof)   
CrossLinkData (IMP::isd)   HierarchySaveLink (IMP::rmf)   ParticleAdaptor (IMP)   Sequences (IMP.pmi.topology)   
  p  
CrossLinkDataBaseKeywordsConverter (IMP.pmi.io.crosslink)   HierarchyTraits (IMP::core)   ParticleEmbedding (IMP::statistics)   SerialMover (IMP::core)   
CrossLinkMS (IMP.pmi.nonmantained)   HierarchyVisitor (IMP::core)   ParticleIndexAdaptor (IMP)   SetCheckState (IMP)   piecewise_linear_distribution (IMP)   
CrossLinkMSRestraint (IMP::isd)   HighDensityEmbedding (IMP::em)   ParticleIndexesAdaptor (IMP)   SetLogState (IMP)   
  s  
CrossLinkTable (IMP.pmi.analysis)   HistogramD (IMP::statistics)   ParticleIndexPairsAdaptor (IMP)   SetLogTarget (IMP)   
CustomXYZR (IMP::misc)   History (IMP.isd.History)   ParticleInputs (IMP)   SetNumberOfThreads (IMP)   sfo_common (IMP.isd.shared_functions)   
CvEstimator (IMP.isd.TuneRex)   HybridMonteCarlo (IMP::isd)   ParticleOutputs (IMP)   SettingsData (IMP::multifit)   
  v  
Cylinder3D (IMP::algebra)   HydrogenPDBSelector (IMP::atom)   ParticlesAdaptor (IMP::domino)   SetupRigidBody (IMP.pmi.dof)   
CylinderGeometry (IMP::display)   
  I  
ParticlesDummyRestraint (IMP::em2d)   SGEPESlaveArray (IMP.parallel)   vonMises (IMP::isd)   
Image (IMP::em2d)   
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