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IMP Reference Guide  develop.548de65454,2020/12/02
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 | Y | Z
  A  
Demuxer (IMP.isd.demux_trajs)   ImproperSingletonScore (IMP::atom)   Plane3D (IMP::algebra)   SingletonPredicate (IMP)   
DenseFloatLogGridKD (IMP::algebra)   InBoundingBox3DSingletonPredicate (IMP::core)   PlaneDihedralRestraint (IMP.pmi.restraints.stereochemistry)   SingletonRestraint (IMP::core)   
AddBoolFlag (IMP)   DenseGrid3D (IMP::algebra)   InContainerPairFilter (IMP::container)   PlaneDihedralRestraint (IMP.pmi1.restraints.stereochemistry)   SingletonsConstraint (IMP::container)   
AddFloatFlag (IMP)   DenseGridStorageD (IMP::algebra)   InContainerQuadFilter (IMP::container)   PlaneGeometry (IMP::display)   SingletonScore (IMP)   
AddIntFlag (IMP)   DenseIntLogGrid3D (IMP::algebra)   InContainerSingletonFilter (IMP::container)   PMIMoleculeHierarchy (IMP.pmi.topology)   SingletonsGeometry (IMP::display)   
AddScores (IMP::score_functor)   DensityDataPoints (IMP::multifit)   InContainerTripletFilter (IMP::container)   PMIMoleculeHierarchy (IMP.pmi1.topology)   SingletonsOptimizerState (IMP::container)   
AddStringFlag (IMP)   DensityFillingRestraint (IMP::em)   IncrementalScoringFunction (IMP::core)   Pointer (IMP)   SingletonsRestraint (IMP::container)   
AdvancedFlag (IMP)   DensityHeader (IMP::em)   Index (IMP)   PointerMember (IMP)   SingletonStatistical (IMP::score_functor)   
Alignment (IMP.pmi.analysis)   DensityMap (IMP::em)   IndexException (IMP)   PointGeometry (IMP::display)   SitesGeometry (IMP::npctransport)   
Alignment (IMP.pmi1.analysis)   DependencyScoreState (IMP::domino)   IndexStates (IMP::domino)   PointToSphereDistance (IMP::score_functor)   SitesPairScore (IMP::npctransport)   
AlignmentClustering (IMP.multifit.cluster)   DerivativeAccumulator (IMP)   IndexVector (IMP)   PolarResamplingParameters (IMP::em2d)   SitesPairScoreParameters (IMP::npctransport)   
AlignSymmetric (IMP::cnmultifit)   DerivativeCalculator (IMP::saxs)   InitialDockingFromXlinks (IMP.EMageFit.buildxlinks)   PolygonGeometry (IMP::display)   SkinSurfaceGeometry (IMP::display)   
AllBipartitePairContainer (IMP::container)   DerivativesFromRefined (IMP::core)   InputAdaptor (IMP)   PoreRadiusSingletonScore (IMP::npctransport)   SlabWithCylindricalPore (IMP::npctransport)   
AllMol2Selector (IMP::atom)   DerivativesToRefined (IMP::core)   InternalCoordinatesConstraint (IMP::pmi)   PoreSideVolumeLocationRestraint (IMP::npc)   SlabWithCylindricalPorePairScore (IMP::npctransport)   
AllPairContainer (IMP::container)   DiameterRestraint (IMP::core)   InternalCoordinatesConstraint (IMP::pmi1)   PPDBSelector (IMP::atom)   SlabWithCylindricalPoreWireGeometry (IMP::npctransport)   
AllPDBSelector (IMP::atom)   DiameterRgyrRestraint (IMP::spb)   InternalException (IMP)   Precision (IMP.pmi.analysis)   SlabWithPore (IMP::npctransport)   
AllSamePairPredicate (IMP::core)   Diffusion (IMP::atom)   IntsOrder (IMP::em2d)   Precision (IMP.pmi1.analysis)   SlabWithToroidalPore (IMP::npctransport)   
AllSameQuadPredicate (IMP::core)   Dihedral (IMP::atom)   IOException (IMP)   PredicatePairsRestraint (IMP::container)   SlabWithToroidalPorePairScore (IMP::npctransport)   
AllSameSingletonPredicate (IMP::core)   DihedralAngleRevoluteJoint (IMP::kinematics)   IsCollisionPairPredicate (IMP::core)   PredicateQuadsRestraint (IMP::container)   SlabWithToroidalPoreWireGeometry (IMP::npctransport)   
AllSameTripletPredicate (IMP::core)   DihedralMover (IMP::kinematics)   ISDRestraint (IMP::spb)   PredicateSingletonScore (IMP::core)   Slice (IMP::domino)   
AmbiguousCompositeRestraint (IMP.pmi.restraints.proteomics)   DihedralRestraint (IMP::core)   ISDRestraint (IMP::isd)   PredicateSingletonsRestraint (IMP::container)   SmoothingFunction (IMP::atom)   
AmbiguousCompositeRestraint (IMP.pmi1.restraints.proteomics)   DihedralSingletonScore (IMP::atom)   IsosurfaceGeometry (IMP::display)   PredicateTripletsRestraint (IMP::container)   Soap (IMP::score_functor)   
AmbiguousNOERestraint (IMP::isd)   Direction (IMP::core)   
  J  
PrincipalComponentAnalysisD (IMP::algebra)   SoapPairFilter (IMP::atom)   
AmbiguousRestraint (IMP::isd)   DirectionalDOF (IMP::kinematics)   PrismaticJoint (IMP::kinematics)   SoftCylinderPairScore (IMP::misc)   
Analysis (IMP.isd.Analysis)   DirectionAngle (IMP::core)   JaccardDistanceMatrix (IMP.pmi.io.crosslink)   ProbabilisticAnchorGraph (IMP::multifit)   SoftSpherePairScore (IMP::core)   
AnalysisReplicaExchange (IMP.pmi.macros)   DirectionMover (IMP::core)   JaccardDistanceMatrix (IMP.pmi1.io.crosslink)   ProbabilisticSubsetFilterTable (IMP::domino)   SoftSubSurfacePairScore (IMP::core)   
AnalysisReplicaExchange (IMP.pmi1.macros)   DirectorObjectChecker (IMP.test)   JeffreysPrior (IMP.pmi.restraints.parameters)   ProcessOutput (IMP.pmi1.output)   SoftSuperSurfacePairScore (IMP::core)   
AnalysisReplicaExchange0 (IMP.pmi.macros)   DiscreteSampler (IMP::domino)   JeffreysPrior (IMP.pmi1.restraints.parameters)   ProcessOutput (IMP.pmi.output)   SoftwareProvenance (IMP::core)   
AnalysisReplicaExchange0 (IMP.pmi1.macros)   DisjointSetsSubsetFilterTable (IMP::domino)   JeffreysRestraint (IMP::isd)   Profile (IMP::saxs)   SolventAccessibleSurface (IMP::saxs)   
AnchorsData (IMP::multifit)   DistanceFilter (IMP::em2d)   Joint (IMP::kinematics)   ProfileClustering (IMP::saxs)   SparseGrid3D (IMP::algebra)   
AnchorToCylidnricalPorePairScore (IMP::npctransport)   DistanceFilterTable (IMP::em2d)   JPGImageReaderWriter (IMP::em2d)   ProfileFitter (IMP::saxs)   SparseGridStorageD (IMP::algebra)   
AndPDBSelector (IMP::atom)   DistanceMask (IMP::em)   
  K  
Profiler (IMP::benchmark)   SparseSymmetricPairMemoizer (IMP)   
Angle (IMP::atom)   DistancePairScore (IMP::score_functor)   ProjectingOptions (IMP::em2d)   SparseUnboundedGrid3D (IMP::algebra)   
AngleRestraint (IMP::core)   DistancePairScore (IMP::core)   KClosePairsPairScore (IMP::core)   ProjectingParameters (IMP::em2d)   SparseUnboundedGridD (IMP::algebra)   
AngleSingletonScore (IMP::atom)   DistanceRestraint (IMP.pmi.restraints.basic)   KernelParameters (IMP::em)   ProjectionFinder (IMP::em2d)   SphereD (IMP::algebra)   
AngleTripletScore (IMP::core)   DistanceRestraint (IMP.pmi1.restraints.basic)   Key (IMP)   ProjectionMask (IMP::em2d)   SphereDistance (IMP::score_functor)   
AngularVelocity (IMP::atom)   DistanceRestraint (IMP::core)   KinematicForest (IMP::kinematics)   ProjectionParameters (IMP::em2d)   SphereDistancePairScore (IMP::core)   
ApplicationTestCase (IMP.test)   DistanceRMSDMetric (IMP::spb)   KinematicForestScoreState (IMP::kinematics)   ProjectionParametersScoreState (IMP::em2d)   SphereDistanceToSingletonScore (IMP::core)   
ArgumentParser (IMP)   DistanceTerminiRestraint (IMP::spb)   KinematicNode (IMP::kinematics)   ProjectionStates (IMP::em2d)   SphereGeometry (IMP::display)   
Array (IMP)   DistanceToPointRestraint (IMP.pmi.restraints.basic)   KinkPairScore (IMP::spb)   ProteinChainRestraint (IMP::npc)   SpherePatch3D (IMP::algebra)   
AssemblyHeader (IMP::multifit)   DistanceToPointRestraint (IMP.pmi1.restraints.basic)   KMeans (IMP::kmeans)   ProteinContactRestraint (IMP::npc)   SphericalVector3D (IMP::algebra)   
AssemblySymmetryByDihedralRestraint (IMP::npc)   DistributePairsScoreState (IMP::container)   
  L  
ProteinKinematics (IMP::kinematics)   SpiderHeader (IMP::em)   
AssemblySymmetryByDistanceRestraint (IMP::npc)   DistributeQuadsScoreState (IMP::container)   ProteinLigandAtomPairScore (IMP::atom)   SpiderImageReaderWriter (IMP::em2d)   
Assignment (IMP::domino)   DistributeSingletonsScoreState (IMP::container)   LabelGeometry (IMP::display)   ProteinLigandRestraint (IMP::atom)   SpiderMapReaderWriter (IMP::em)   
AssignmentContainer (IMP::domino)   DistributeTripletsScoreState (IMP::container)   LangevinThermostatOptimizerState (IMP::atom)   ProteinProximityRestraint (IMP::npc)   State (IMP::atom)   
AssignmentsTable (IMP::domino)   Distribution (IMP::saxs)   LateralSurfaceConstraint (IMP::core)   ProteinsAnchorsSamplingSpace (IMP::multifit)   State (IMP.pmi.topology)   
AsymUnit (IMP.pmi.mmcif)   Distribution (IMP::isd)   LeavesRefiner (IMP::core)   ProteomicsData (IMP::multifit)   State (IMP.mmcif.util)   
AsymUnit (IMP.pmi1.mmcif)   DockOrder (IMP.EMageFit.buildxlinks)   LennardJones (IMP::atom)   ProteomicsEMAlignmentAtomic (IMP::multifit)   StateAdaptor (IMP::misc)   
Atom (IMP::atom)   DOF (IMP::kinematics)   LennardJonesPairScore (IMP::atom)   ProtocolOutput (IMP.pmi1.mmcif)   StatHierarchyHandler (IMP.pmi1.output)   
AtomicCrossLinkMSRestraint (IMP.pmi.restraints.crosslinking)   DOFsSampler (IMP::kinematics)   LessPairBySecond (IMP::em2d)   ProtocolOutput (IMP.pmi.mmcif)   StatHierarchyHandler (IMP.pmi.output)   
AtomicCrossLinkMSRestraint (IMP.pmi1.restraints.crosslinking)   DOFValues (IMP::kinematics)   Line3D (IMP::algebra)   ProtocolOutput (IMP.pmi.output)   Statistical (IMP::score_functor)   
AtomicCrossLinkMSRestraint (IMP::isd)   Domain (IMP::atom)   Linear (IMP::core)   ProtocolOutput (IMP.pmi1.output)   StatisticalPairScore (IMP::core)   
ATOMPDBSelector (IMP::atom)   DominoModel (IMP.EMageFit.domino_model)   Linear1DFunction (IMP::isd)   Provenance (IMP::core)   Statistics (IMP.isd.Statistics)   
AtomType (IMP::atom)   DominoSampler (IMP::domino)   LinearFit2D (IMP::algebra)   Provenanced (IMP::core)   Statistics (IMP::npctransport)   
AtomTypePDBSelector (IMP::atom)   Dope (IMP::score_functor)   LinearInteraction (IMP::npctransport)   PseudoAtomicRestraint (IMP.pmi.restraints.stereochemistry)   SteepestDescent (IMP::core)   
AttributeDistancePairScore (IMP::spb)   DopePairScore (IMP::atom)   LinearInteractionPairScore (IMP::npctransport)   PseudoAtomicRestraint (IMP.pmi1.restraints.stereochemistry)   StereochemistryPairFilter (IMP::atom)   
AttributeOptimizer (IMP)   DummyRestraint (IMP::em2d)   LinearLowerBound (IMP::score_functor)   PymolWriter (IMP::display)   Stopwatch (IMP.pmi1.tools)   
AttributeSingletonPredicate (IMP::core)   DummyRestraint (IMP::multifit)   LinearSoftSpherePairScore (IMP::npctransport)   PythonDirectedGraph (IMP)   Stopwatch (IMP.pmi.tools)   
AverageDistanceLinkage (IMP::em2d)   DynamicListPairContainer (IMP::container)   LinearVelocity (IMP::atom)   PythonExampleConstraint (IMP.example)   StructureProvenance (IMP::core)   
  B  
DynamicListQuadContainer (IMP::container)   LinearWellPairScore (IMP::npctransport)   PythonExamplePairScore (IMP.example)   StructureSource (IMP::atom)   
DynamicListSingletonContainer (IMP::container)   ListAssignmentContainer (IMP::domino)   PythonExampleRestraint (IMP.example)   StructureWarning (IMP.pmi)   
BackbonePDBSelector (IMP::atom)   DynamicListTripletContainer (IMP::container)   ListAssignmentsTable (IMP::domino)   PythonExampleSingletonModifier (IMP.example)   StudentTRestraint (IMP::isd)   
BallMover (IMP::symmetry)   DynamicNearestNeighbor3D (IMP::algebra)   ListPairContainer (IMP::container)   PythonExampleUnaryFunction (IMP.example)   Subset (IMP::domino)   
BallMover (IMP::core)   
  E  
ListQuadContainer (IMP::container)   
  Q  
SubsetFilter (IMP::domino)   
BerendsenThermostatOptimizerState (IMP::atom)   ListSingletonContainer (IMP::container)   SubsetFilterTable (IMP::domino)   
BinormalTerm (IMP::core)   EdgePairGeometry (IMP::core)   ListSubsetFilterTable (IMP::domino)   QuadConstraint (IMP::core)   SubsetMover (IMP::core)   
BipartitePairsStatisticsOptimizerState (IMP::npctransport)   EdgePairsGeometry (IMP::core)   ListTripletContainer (IMP::container)   QuadContainer (IMP)   Surface (IMP::core)   
BiStableDistanceRestraint (IMP.pmi.restraints.basic)   ElasticNetworkRestraint (IMP.pmi.restraints.stereochemistry)   LoadLink (IMP::rmf)   QuadContainerAdaptor (IMP)   SurfaceDepthPairScore (IMP::core)   
BiStableDistanceRestraint (IMP.pmi1.restraints.basic)   ElasticNetworkRestraint (IMP.pmi1.restraints.stereochemistry)   LocalPlanner (IMP::kinematics)   QuadContainerSet (IMP::container)   SurfaceDepthPairScore (IMP::score_functor)   
BivariateFunction (IMP::isd)   ElectronMicroscopy2D (IMP.pmi.restraints.em2d)   LocalWorker (IMP.parallel)   QuadContainerStatistics (IMP::container)   SurfaceDistancePairScore (IMP::core)   
BodyStatisticsOptimizerState (IMP::npctransport)   ElectronMicroscopy2D (IMP.pmi1.restraints.em2d)   LogEmbeddingD (IMP::algebra)   QuadModifier (IMP)   SurfaceDistancePairScore (IMP::score_functor)   
Bond (IMP::atom)   ElectronMicroscopy2D_FFT (IMP.pmi.restraints.em2d)   LogHolder (IMP.isd.demux_trajs)   QuadPredicate (IMP)   SurfaceGeometry (IMP::core)   
ForceFieldParameters::Bond (IMP::atom)   ElectronMicroscopy2D_FFT (IMP.pmi1.restraints.em2d)   LognormalAmbiguousRestraint (IMP::isd)   QuadraticClosePairsFinder (IMP::core)   SurfaceGeometryConstraint (IMP::core)   
BondAngleRevoluteJoint (IMP::kinematics)   ElementTable (IMP::atom)   LogNormalMover (IMP::core)   QuadRestraint (IMP::core)   SurfaceHeightPairScore (IMP::score_functor)   
Bonded (IMP::atom)   Ellipsoid3D (IMP::algebra)   LognormalRestraint (IMP::isd)   QuadsConstraint (IMP::container)   SurfaceHeightPairScore (IMP::core)   
BondedPairFilter (IMP::atom)   EllipsoidGeometry (IMP::display)   LogPairScore (IMP::misc)   QuadScore (IMP)   SurfaceMeshGeometry (IMP::display)   
BondEndpointsRefiner (IMP::atom)   EM2DRestraint (IMP::spb)   LogWrapper (IMP::isd)   QuadsOptimizerState (IMP::container)   SurfaceMover (IMP::core)   
BondGeometry (IMP::atom)   Em2DRestraint (IMP::em2d)   LoopStatistical (IMP::score_functor)   QuadsRestraint (IMP::container)   SurfacesGeometry   
BondGraph (IMP::atom)   Em2DRestraintParameters (IMP::em2d)   LoopStatisticalPairScore (IMP::atom)   QuasiNewton (IMP::gsl)   SurfaceShellDensityMap (IMP::em)   
BondPairContainer (IMP::atom)   EM2DScore (IMP::em2d)   LowestRefinedPairScore (IMP::misc)   
  R  
SurfaceSymmetryConstraint (IMP::core)   
BondsGeometry (IMP::atom)   Embedding (IMP::statistics)   LRUCache (IMP)   SurfaceTetheredChain (IMP::core)   
BondSingletonScore (IMP::atom)   EMReaderWriter (IMP::em)   
  M  
RadialDistributionFunction (IMP::saxs)   Switching (IMP::isd)   
BoundedGridRangeD (IMP::algebra)   Ensemble (IMP.mmcif.util)   RadiusDependentDistanceMask (IMP::em)   Symmetric (IMP::pmi)   
BoundingBoxD (IMP::algebra)   Ensemble (IMP::multifit)   Manager (IMP.parallel)   RadiusOfGyrationRestraint (IMP::saxs)   Symmetric (IMP::pmi1)   
BoundingBoxGeometry (IMP::display)   EnsembleGenerator (IMP::multi_state)   ManagerCommunicator (IMP.parallel.manager_communicator)   RadiusOfGyrationRestraint (IMP::multifit)   SymmetryRestraint (IMP.pmi.restraints.stereochemistry)   
BoxedMover (IMP::spb)   Entity (IMP.pmi.mmcif)   MapCrossLinkDataBaseOnStructure (IMP.pmi.io.crosslink)   RAII (IMP)   SymmetryRestraint (IMP.pmi1.restraints.stereochemistry)   
BoxSweepClosePairsFinder (IMP::core)   Entity (IMP.pmi1.mmcif)   MapCrossLinkDataBaseOnStructure (IMP.pmi1.io.crosslink)   RangeViewAssignmentContainer (IMP::domino)   System (IMP.pmi.topology)   
BranchAndBoundAssignmentsTable (IMP::domino)   Entry (IMP.isd.Entry)   MapDistanceTransform (IMP::em)   RatioVolatilityScore (IMP::saxs)   
  T  
BranchAndBoundSampler (IMP::domino)   EnvelopeFitRestraint (IMP::em)   MapReaderWriter (IMP::em)   ReadAssignmentContainer (IMP::domino)   
BrownianDynamics (IMP::atom)   EnvelopePenetrationRestraint (IMP::em)   MarginalHBondRestraint (IMP::isd)   ReadHDF5AssignmentContainer (IMP::domino)   TableRefiner (IMP::core)   
BrownianDynamicsTAMD (IMP::atom)   EnvelopeScore (IMP::em)   MarginalNOERestraint (IMP::isd)   RecursiveAssignmentsTable (IMP::domino)   TALOSReader (IMP.isd.TALOSReader)   
BrownianDynamicsTAMDWithSlabSupport (IMP::npctransport)   EqualitySubsetFilterTable (IMP::domino)   MasksManager (IMP::em2d)   RecursivePartitionalClusteringEmbedding (IMP::statistics)   TALOSRestraint (IMP::isd)   
BuildModel (IMP.pmi1.macros)   EquivalenceAndExclusionSubsetFilterTable (IMP::domino)   Mass (IMP::atom)   RecursivePartitionalClusteringMetric (IMP::statistics)   TAMDCentroid (IMP::atom)   
BuildModel1 (IMP.pmi1.macros)   EquivalenceSubsetFilterTable (IMP::domino)   MatchTemplateResult (IMP::em2d)   RecursiveStates (IMP::domino)   TAMDParticle (IMP::atom)   
BuildSystem (IMP.pmi.macros)   Error (IMP.parallel)   MaxVectorKDMetric (IMP::algebra)   RefCountChecker (IMP.test)   TempResidue (IMP.pmi.topology)   
  C  
EuclideanMetric (IMP::statistics)   MCCGSampler (IMP::core)   Reference (IMP::core)   TestCase (IMP.test)   
EuclideanVectorKDMetric (IMP::algebra)   MeanAbsoluteDifference (IMP::em2d)   ReferenceFrame3D (IMP::algebra)   TextInput (IMP)   
CAAngleRestraint (IMP::atom)   LinearInteractionPairScore::EvaluationCache (IMP::npctransport)   MembraneExclusionRestraint (IMP.npc.npc_restraints)   ReferenceFrameGeometry (IMP::display)   TextOutput (IMP)   
CADihedralRestraint (IMP::atom)   EvaluationState (IMP)   MembraneExclusionRestraint (IMP::npc)   ReferenceFrameToText (IMP.EMageFit.imp_general.io)   TextWriter (IMP::display)   
CAlphaPDBSelector (IMP::atom)   EventException (IMP)   MembraneRestraint (IMP::pmi)   RefinedPairsPairScore (IMP::core)   ThreeToOneConverter (IMP.pmi.tools)   
CappedAssignmentContainer (IMP::domino)   EventPairsOptimizerState (IMP::container)   MembraneRestraint (IMP::pmi1)   Refiner (IMP)   ThreeToOneConverter (IMP.pmi1.tools)   
CBetaPDBSelector (IMP::atom)   EventQuadsOptimizerState (IMP::container)   MembraneSurfaceLocationConditionalRestraint (IMP.npc.npc_restraints)   Reflection3D (IMP::algebra)   TIFFImageReaderWriter (IMP::em2d)   
CCDLoopClosure (IMP::kinematics)   EventSingletonsOptimizerState (IMP::container)   MembraneSurfaceLocationConditionalRestraint (IMP::npc)   RegistrationResult (IMP::em2d)   TiltSingletonScore (IMP::spb)   
CellMover (IMP::spb)   EventTripletsOptimizerState (IMP::container)   MembraneSurfaceLocationRestraint (IMP.npc.npc_restraints)   RelativePositionMover (IMP::em2d)   TopologyPlot (IMP.pmi1.plotting.topology)   
CenteredMat (IMP::em2d)   ExampleComplexRestraint (IMP::example)   MembraneSurfaceLocationRestraint (IMP::npc)   RelaxingSpring (IMP::npctransport)   TopologyPlot (IMP.pmi.plotting.topology)   
CenterOfMass (IMP::atom)   ExampleConstraint (IMP::example)   Memoizer (IMP)   RemoteError (IMP.parallel)   TopologyReader (IMP.pmi1.topology)   
Centroid (IMP::core)   ExampleDecorator (IMP::example)   MergeTreeBuilder (IMP::multifit)   RemoveRigidMotionOptimizerState (IMP::atom)   TopologyReader (IMP.pmi.topology)   
CentroidOfRefined (IMP::core)   ExampleObject (IMP::example)   Metric (IMP::statistics)   RemoveTranslationOptimizerState (IMP::atom)   Torus3D (IMP::algebra)   
Chain (IMP::atom)   ExamplePairScore (IMP::example)   MetricClosePairsFinder (IMP::misc)   ReplicaExchange (IMP.pmi1.samplers)   TotalScoreOutput (IMP.pmi.io)   
ChainPDBSelector (IMP::atom)   ExampleRestraint (IMP::example)   MinimumPairRestraint (IMP::container)   ReplicaExchange (IMP.pmi.samplers)   TotalScoreOutput (IMP.pmi1.io)   
ChainStatisticsOptimizerState (IMP::npctransport)   ExampleSingletonModifier (IMP::example)   MinimumPairScore (IMP::container)   ReplicaExchange (IMP::mpi)   Transform (IMP::core)   
ChainType (IMP::atom)   ExampleSubsetFilterTable (IMP::example)   MinimumQuadRestraint (IMP::container)   ReplicaExchange0 (IMP.pmi.macros)   Transformation2D (IMP::algebra)   
Charged (IMP::atom)   ExampleTemplateClassD (IMP::example)   MinimumQuadScore (IMP::container)   ReplicaExchange0 (IMP.pmi1.macros)   Transformation3D (IMP::algebra)   
CHARMMAtom (IMP::atom)   ExampleUnaryFunction (IMP::example)   MinimumRestraint (IMP::core)   Representation (IMP::atom)   Transformation3DToText (IMP.EMageFit.imp_general.io)   
CHARMMAtomTopology (IMP::atom)   Exception (IMP)   MinimumRestraintScoreSubsetFilterTable (IMP::domino)   Representation (IMP.pmi1.representation)   TransformationAndReflectionSymmetry (IMP::core)   
CHARMMBondEndpoint (IMP::atom)   ExcludedVolumeRestraint (IMP::core)   MinimumSingletonRestraint (IMP::container)   RepulsiveDistancePairScore (IMP::isd)   TransformationJoint (IMP::kinematics)   
CHARMMBondParameters (IMP::atom)   ExcludedVolumeSphere (IMP.pmi.restraints.stereochemistry)   MinimumSingletonScore (IMP::container)   Residue (IMP::atom)   TransformationSymmetry (IMP::core)   
CHARMMConnection (IMP::atom)   ExcludedVolumeSphere (IMP.pmi1.restraints.stereochemistry)   MinimumSphereDistancePairScore (IMP::npc)   ResidueAlphabet (IMP.pmi.alphabets)   TransformationSymmetry (IMP::spb)   
CHARMMDihedralParameters (IMP::atom)   ExcludeZRangeSingletonScore (IMP::npctransport)   MinimumTripletRestraint (IMP::container)   ResidueAngleRestraint (IMP.pmi1.restraints.stereochemistry)   TransformationSymmetryMover (IMP::core)   
CharmmForceFieldRestraint (IMP.pmi.restraints.stereochemistry)   ExclusionSubsetFilterTable (IMP::domino)   MinimumTripletScore (IMP::container)   ResidueAngleRestraint (IMP.pmi.restraints.stereochemistry)   TransformedDistancePairScore (IMP::core)   
CharmmForceFieldRestraint (IMP.pmi1.restraints.stereochemistry)   ExclusiveConsecutivePairContainer (IMP::container)   MissingFileWarning (IMP.pmi)   ResidueBondRestraint (IMP.pmi.restraints.stereochemistry)   TransformMover (IMP::pmi)   
CHARMMIdealResidueTopology (IMP::atom)   ExclusiveConsecutivePairFilter (IMP::container)   Model (IMP)   ResidueBondRestraint (IMP.pmi1.restraints.stereochemistry)   TransformMover (IMP::pmi1)   
CHARMMInternalCoordinate (IMP::atom)   ExtendedGridIndexD (IMP::algebra)   ModelException (IMP)   ResidueDihedralRestraint (IMP.pmi.restraints.stereochemistry)   Transporting (IMP::npctransport)   
CHARMMParameters (IMP::atom)   ExternalBarrier (IMP.pmi.restraints.basic)   ModellerRestraints (IMP.modeller)   ResidueDihedralRestraint (IMP.pmi1.restraints.stereochemistry)   Triangle3D (IMP::algebra)   
CHARMMPatch (IMP::atom)   ExternalBarrier (IMP.pmi1.restraints.basic)   ModelLoader (IMP.modeller)   ResiduePairListParser (IMP.pmi1.io.crosslink)   TriangleGeometry (IMP::display)   
CHARMMResidueTopology (IMP::atom)   EzRestraint (IMP::atom)   ModelObject (IMP)   ResiduePairListParser (IMP.pmi.io.crosslink)   TripletConstraint (IMP::core)   
CHARMMResidueTopologyBase (IMP::atom)   
  F  
ModifierVisitor (IMP::core)   ResidueRotamer (IMP::rotamer)   TripletContainer (IMP)   
CHARMMSegmentTopology (IMP::atom)   Mol2Selector (IMP::atom)   ResidueType (IMP::atom)   TripletContainerAdaptor (IMP)   
CHARMMStereochemistryRestraint (IMP::atom)   FFTFitting (IMP::multifit)   MolCnSymmAxisDetector (IMP::cnmultifit)   ResidueTypePDBSelector (IMP::atom)   TripletContainerSet (IMP::container)   
CHARMMTopology (IMP::atom)   FFTFittingOutput (IMP::multifit)   MolecularDynamics (IMP::atom)   Resolution (IMP::pmi)   TripletContainerStatistics (IMP::container)   
ChecksScoreState (IMP::core)   FGChain (IMP::npctransport)   MolecularDynamics (IMP.pmi.samplers)   Resolution (IMP::pmi1)   TripletModifier (IMP)   
ChiFreeScore (IMP::saxs)   FibrilSampler (IMP::kinematics)   MolecularDynamics (IMP.pmi1.samplers)   Restraint (IMP)   TripletPredicate (IMP)   
ChildrenRefiner (IMP::core)   FilterGeometry (IMP::display)   MolecularDynamics (IMP::isd)   Restraint (IMP::saxs)   TripletRestraint (IMP::core)   
ChiScore (IMP::saxs)   FilterOperator (IMP.pmi.io.crosslink)   MolecularDynamicsMover (IMP::isd)   RestraintBase (IMP.pmi1.restraints)   TripletsConstraint (IMP::container)   
ChiScoreLog (IMP::saxs)   FilterOperator (IMP.pmi1.io.crosslink)   MolecularDynamicsWithWte (IMP::spb)   RestraintCache (IMP::domino)   TripletScore (IMP)   
ChiSquaredScore (IMP::em2d)   FilterProvenance (IMP::core)   Molecule (IMP::atom)   RestraintGeometry (IMP::display)   TripletsOptimizerState (IMP::container)   
ChiSquareMetric (IMP::spb)   Fine2DRegistrationRestraint (IMP::em2d)   Molecule (IMP.pmi.topology)   RestraintInfo (IMP)   TripletsRestraint (IMP::container)   
ChiSquareMetric (IMP::statistics)   FitParameters (IMP::saxs)   MonteCarlo (IMP.pmi.samplers)   RestraintsAdaptor (IMP)   TruncatedHarmonic (IMP::core)   
CloseBipartitePairContainer (IMP::container)   FitRestraint (IMP::em)   MonteCarlo (IMP.pmi1.samplers)   RestraintScoreSubsetFilterTable (IMP::domino)   TwoStateGoModelRestraint (IMP::spb)   
ClosedCubicSpline (IMP::core)   FittingSolutionRecord (IMP::multifit)   MonteCarlo (IMP::core)   RestraintSet (IMP)   Typed (IMP::core)   
ClosePairContainer (IMP::container)   FittingSolutions (IMP::em)   MonteCarloMover (IMP::core)   RestraintSetGeometry (IMP::display)   TypedPairScore (IMP::core)   
ClosePairsFinder (IMP::core)   FittingStates (IMP::multifit)   MonteCarloMoverResult (IMP::core)   RestraintsScoringFunction (IMP::core)   TypedSitesGeometry (IMP::npctransport)   
ClosePairsPairScore (IMP::core)   FixedFormatParser (IMP.pmi.io.crosslink)   MonteCarloRelativeMoves (IMP.EMageFit.monte_carlo)   ResultsDB (IMP.EMageFit.solutions_io)   TypeException (IMP)   
Cluster (IMP.pmi.output)   FixedFormatParser (IMP.pmi1.io.crosslink)   MonteCarloWithBasinHopping (IMP::core)   RevoluteJoint (IMP::kinematics)   
  U  
Cluster (IMP.pmi1.output)   FixedRefiner (IMP::core)   MonteCarloWithLocalOptimization (IMP::core)   RevoluteJointMover (IMP::kinematics)   
Clustering (IMP.pmi.analysis)   FixedXYZ (IMP::algebra)   MonteCarloWithWte (IMP::spb)   RigidBodiesImageFitRestraint (IMP::em2d)   UnaryFunction (IMP)   
Clustering (IMP.pmi1.analysis)   Flag (IMP)   MoveStatisticsScoreState (IMP::core)   RigidBodiesProfileHandler (IMP::saxs)   UnaryFunctionEvaluate (IMP::score_functor)   
ClusterProvenance (IMP::core)   FloatIndex (IMP)   MRCReaderWriter (IMP::em)   RigidBody (IMP::core)   UnboundedGridRangeD (IMP::algebra)   
ClusterSet (IMP::em2d)   FNormal (IMP::isd)   MSConnectivityRestraint (IMP::core)   RigidBodyAnglePairScore (IMP::core)   Uncertainty (IMP::pmi)   
CnSymmAxisDetector (IMP::cnmultifit)   ForceFieldParameters (IMP::atom)   MultipleBinormalRestraint (IMP::core)   RigidBodyDerivativeGeometry (IMP::core)   Uncertainty (IMP::pmi1)   
CoarseCC (IMP::em)   ForceSwitch (IMP::atom)   MultiStateModel (IMP::multi_state)   RigidBodyDerivativesGeometry (IMP::core)   UncheckedWeakPointer (IMP)   
CoarseCCatIntervals (IMP::em)   FormFactorTable (IMP::saxs)   MultiStateModelScore (IMP::multi_state)   RigidBodyDiffusion (IMP::atom)   Undecorator (IMP)   
CoarseConvolution (IMP::em)   Fragment (IMP::atom)   MultivariateFNormalSufficient (IMP::isd)   RigidBodyDistancePairScore (IMP::core)   UniformBackboneSampler (IMP::kinematics)   
CoinFlipPairPredicate (IMP::core)   FreelyJointedChain (IMP::misc)   MyMetric (write_a_metric)   RigidBodyFrameGeometry (IMP::core)   UniformBoundedRestraint (IMP::spb)   
CoinFlipQuadPredicate (IMP::core)   FretData (IMP::isd)   MyOptimizerState (write_an_optimizer_state)   RigidBodyFramesGeometry (IMP::core)   UniformPrior (IMP::isd)   
CoinFlipSingletonPredicate (IMP::core)   FretRestraint (IMP::isd)   
  N  
RigidBodyHierarchyGeometry (IMP::core)   UnitSimplexBaseD (IMP::algebra)   
CoinFlipTripletPredicate (IMP::core)   FStudentT (IMP::isd)   RigidBodyMember (IMP::core)   UnitSimplexD (IMP::algebra)   
CollisionCrossSection (IMP::em2d)   FunctorLinearInteractionPairScore (IMP::npctransport)   NearestNeighborD (IMP::algebra)   RigidBodyMover (IMP::symmetry)   UnitSimplexD<-1 > (IMP::algebra)   
Color (IMP::display)   FunctorLinearSoftSpherePairScore (IMP::npctransport)   NearestNeighborsClosePairsFinder (IMP::core)   RigidBodyMover (IMP::core)   UnivariateFunction (IMP::isd)   
ColorChange (IMP.pmi.tools)   FusionRestraint (IMP.pmi.restraints.stereochemistry)   NeighborsTable (IMP::core)   RigidBodyNewMover (IMP::spb)   UnorderedTypePairPredicate (IMP::core)   
ColorChange (IMP.pmi1.tools)   FusionRestraint (IMP.pmi1.restraints.stereochemistry)   NestedRigidBodyStates (IMP::domino)   RigidBodyPackingScore (IMP::spb)   UnorderedTypeQuadPredicate (IMP::core)   
Colored (IMP::display)   FuzzyBoolean (IMP.pmi.restraints.proteomics)   NetworkError (IMP.parallel)   RigidBodyStates (IMP::domino)   UnorderedTypeSingletonPredicate (IMP::core)   
CombineProvenance (IMP::core)   FuzzyBoolean (IMP.pmi1.restraints.proteomics)   NOERestraint (IMP::isd)   RigidBodyTorque (IMP::core)   UnorderedTypeTripletPredicate (IMP::core)   
CommandDispatcher (IMP)   FuzzyRestraint (IMP.pmi.restraints.proteomics)   NoMoreWorkersError (IMP.parallel)   RigidBodyTunneler (IMP::core)   UsageException (IMP)   
CommonEndpointPairFilter (IMP::misc)   FuzzyRestraint (IMP.pmi1.restraints.proteomics)   NonAlternativePDBSelector (IMP::atom)   RigidBodyUmbrella (IMP::core)   
  V  
CompareMultiStateModels (IMP::multi_state)   
  G  
NonCopyable (IMP)   RigidClosePairsFinder (IMP::core)   
ComplementarityRestraint (IMP::multifit)   NonHydrogenMol2Selector (IMP::atom)   RigidLeavesRefiner (IMP::multifit)   Value (IMP)   
CompleteLinkage (IMP::em2d)   GammaPrior (IMP::isd)   NonHydrogenPDBSelector (IMP::atom)   RigidMember (IMP::core)   ValueException (IMP)   
ComponentHeader (IMP::multifit)   Gaussian (IMP::spb)   NonRigidMember (IMP::core)   RMFFrame (IMP.mmcif.util)   Vector (IMP)   
CompositeJoint (IMP::kinematics)   Gaussian (IMP::core)   NonWaterNonHydrogenPDBSelector (IMP::atom)   RMFHierarchyHandler (IMP.pmi1.output)   VectorBaseD (IMP::algebra)   
CompositeRestraint (IMP.pmi.restraints.proteomics)   Gaussian3D (IMP::algebra)   NonWaterPDBSelector (IMP::atom)   RMFHierarchyHandler (IMP.pmi.output)   VectorD (IMP::algebra)   
CompositeRestraint (IMP.pmi1.restraints.proteomics)   GaussianAnchorEMRestraint (IMP::isd)   NormalizedSphereDistancePairScore (IMP::core)   RMSD (IMP.pmi.analysis)   VectorDEmbedding (IMP::statistics)   
CompositeRestraint (IMP::npc)   GaussianEMRestraint (IMP::bayesianem)   NormalMover (IMP::core)   RMSD (IMP.pmi1.analysis)   VectorKDMetric (IMP::algebra)   
CompositeRestraint (IMP::pmi)   GaussianEMRestraint (IMP.pmi.restraints.em)   NormalSigmaPCRestraint (IMP::isd)   RMSDMetric (IMP::spb)   VelocityScalingOptimizerState (IMP::atom)   
CompositeRestraint (IMP::pmi1)   GaussianEMRestraint (IMP.pmi1.restraints.em)   NotPDBSelector (IMP::atom)   RMSDOutput (IMP.pmi1.io)   VersionInfo (IMP)   
CompoundStates (IMP::domino)   GaussianEMRestraint (IMP::isd)   NPDBSelector (IMP::atom)   RotamerAngleTuple (IMP::rotamer)   VolumeRestraint (IMP::core)   
Cone3D (IMP::algebra)   GaussianEMRestraintWrapper (IMP.bayesianem.restraint)   Nuisance (IMP::isd)   RotamerCalculator (IMP::rotamer)   Voxel (IMP::em)   
Configuration (IMP)   GaussianProcessInterpolation (IMP::isd)   NuisanceRangeModifier (IMP::spb)   RotamerLibrary (IMP::rotamer)   
  W  
ConfigurationSet (IMP)   GaussianProcessInterpolationRestraint (IMP::isd)   
  O  
Rotation2D (IMP::algebra)   
ConfigurationSetRMSDMetric (IMP::statistics)   GaussianRestraint (IMP::isd)   Rotation3D (IMP::algebra)   WarningContext (IMP)   
ConfigurationSetXYZEmbedding (IMP::statistics)   GeneralizedGuinierPorodFunction (IMP::isd)   Object (IMP)   RRT (IMP::kinematics)   WaterPDBSelector (IMP::atom)   
ConjugateGradients (IMP.pmi.samplers)   GenericAttributeSingletonScore (IMP::core)   OneDimensionalDistribution (IMP::isd)   RRT::RRTNode (IMP::kinematics)   WeakPointer (IMP)   
ConjugateGradients (IMP.pmi1.samplers)   GenericBoundingBox3DSingletonScore (IMP::core)   OneDimensionalSufficientDistribution (IMP::isd)   
  S  
Weight (IMP::isd)   
ConjugateGradients (IMP::gsl)   GenericBoundingSphere3DSingletonScore (IMP::core)   OpenCubicSpline (IMP::score_functor)   WeightedDerivativesToRefined (IMP::core)   
ConjugateGradients (IMP::core)   GenericDistanceToSingletonScore (IMP::core)   OpenCubicSpline (IMP::core)   SameParticlePairFilter (IMP::spb)   WeightedExcludedVolumeRestraint (IMP::multifit)   
ConnectingPairContainer (IMP::container)   GeometricHash (IMP::multifit)   Optimizer (IMP)   SameResiduePairFilter (IMP::atom)   WeightedFitParameters (IMP::saxs)   
ConnectivityCrossLinkMS (IMP.pmi1.restraints.crosslinking)   GeometricPrimitiveD (IMP::algebra)   OptimizerState (IMP)   SameRigidBodyPairFilter (IMP::spb)   WeightedProfileFitter (IMP::saxs)   
ConnectivityNetworkRestraint (IMP.pmi.restraints.proteomics)   Geometry (IMP::display)   Order (IMP::domino)   SampleAssignmentContainer (IMP::domino)   WeightedSphereDistancePairScore (IMP::core)   
ConnectivityNetworkRestraint (IMP.pmi1.restraints.proteomics)   GeometryProcessor (IMP::display)   OrderedDefaultDict (IMP.pmi.tools)   SampledDensityMap (IMP::em)   WeightedSum (IMP::core)   
ConnectivityRestraint (IMP.pmi.restraints.proteomics)   GeometrySet (IMP::display)   OrderedDefaultDict (IMP.pmi1.tools)   SampleProvenance (IMP::core)   WeightedSumOfExponential (IMP::core)   
ConnectivityRestraint (IMP.pmi.restraints.stereochemistry)   GetModelDensity (IMP.pmi.analysis)   OrderedTypePairPredicate (IMP::core)   Sampler (IMP)   WeightMover (IMP::isd)   
ConnectivityRestraint (IMP.pmi1.restraints.proteomics)   GetModelDensity (IMP.pmi1.analysis)   OrderedTypeQuadPredicate (IMP::core)   SaveLink (IMP::rmf)   WeightRestraint (IMP.pmi1.restraints.parameters)   
ConnectivityRestraint (IMP.pmi1.restraints.stereochemistry)   GetModelDensity (IMP.sampcon.precision_rmsd)   OrderedTypeSingletonPredicate (IMP::core)   SaveOptimizerState (IMP::rmf)   WeightRestraint (IMP::isd)   
ConnectivityRestraint (IMP::core)   GlobalStatisticsOptimizerState (IMP::npctransport)   OrderedTypeTripletPredicate (IMP::core)   SaveToConfigurationSetOptimizerState (IMP)   WeightRestraint (IMP.pmi.restraints.parameters)   
ConnollySurfacePoint (IMP::algebra)   GMMParser (IMP.pmi.mmcif)   OrientedSoap (IMP::score_functor)   SAXSISDRestraint (IMP.pmi1.restraints.saxs)   WeightScore (IMP::score_functor)   
ConsecutivePairContainer (IMP::container)   GoodScoringModelSelector (IMP.sampcon.good_scoring_model_selector)   OrientedSoapPairScore (IMP::atom)   SAXSISDRestraint (IMP.pmi.restraints.saxs)   Worker (IMP.parallel)   
ConsecutivePairFilter (IMP::container)   GridClosePairsFinder (IMP::core)   OrPDBSelector (IMP::atom)   SAXSMultiStateModelScore (IMP::multi_state)   WorkerArray (IMP.parallel)   
ConstantPairPredicate (IMP::core)   GridD (IMP::algebra)   Output (IMP.pmi.output)   SAXSRestraint (IMP.pmi1.restraints.saxs)   WormLikeChain (IMP::misc)   
ConstantQuadPredicate (IMP::core)   GridIndexD (IMP::algebra)   Output (IMP.pmi1.output)   Scale (IMP::isd)   WriteAssignmentContainer (IMP::domino)   
ConstantRestraint (IMP::core)   GridStates (IMP::em2d)   OutputStatistics (IMP.pmi.output)   ScopedAddCacheAttribute (IMP)   WriteHDF5AssignmentContainer (IMP::domino)   
ConstantSingletonPredicate (IMP::core)   GSLOptimizer (IMP::gsl)   OutputStatistics (IMP.pmi1.output)   ScopedSetAttribute (IMP)   WriteOptimizerState (IMP::display)   
ConstantTripletPredicate (IMP::core)   
  H  
  P  
Score (IMP::score_functor)   WritePDBOptimizerState (IMP::atom)   
Constraint (IMP)   ScoreAccumulator (IMP)   Writer (IMP::display)   
ConstVector (IMP)   Harmonic (IMP::score_functor)   PackedAssignmentContainer (IMP::domino)   ScoreFunction (IMP::em2d)   WriterAdaptor (IMP::display)   
ContactMapMetric (IMP::spb)   Harmonic (IMP::core)   PairConstraint (IMP::core)   ScoreState (IMP)   WriteRestraintScoresOptimizerState (IMP::core)   
Container (IMP)   HarmonicDistancePairScore (IMP::core)   PairContainer (IMP)   ScoreUnaryFunction (IMP::score_functor)   
  X  
Context (IMP.parallel)   HarmonicLowerBound (IMP::score_functor)   PairContainerAdaptor (IMP)   Scoring (IMP::npctransport)   
Copy (IMP::atom)   HarmonicLowerBound (IMP::core)   PairContainerSet (IMP::container)   ScoringFunction (IMP)   Xlink (IMP.EMageFit.buildxlinks)   
Cosine (IMP::core)   HarmonicSphereDistancePairScore (IMP::core)   PairContainerStatistics (IMP::container)   ScoringFunctionAdaptor (IMP)   XlinksDict (IMP.EMageFit.buildxlinks)   
CoulombPairScore (IMP::atom)   HarmonicSpringSingletonScore (IMP::npctransport)   PairGeometry (IMP::display)   ScriptProvenance (IMP::core)   XLTable (IMP.pmi1.io.xltable)   
Covariance1DFunction (IMP::isd)   HarmonicSurfaceDepthPairScore (IMP::core)   PairListSubsetFilterTable (IMP::domino)   SecondaryStructure (IMP.pmi1.restraints.stereochemistry)   XorPDBSelector (IMP::atom)   
Cover (IMP::core)   HarmonicSurfaceDistancePairScore (IMP::core)   PairModifier (IMP)   SecondaryStructure (IMP.pmi.restraints.stereochemistry)   XplorReaderWriter (IMP::em)   
CoverBond (IMP::atom)   HarmonicSurfaceHeightPairScore (IMP::core)   PairPredicate (IMP)   SecondaryStructureResidue (IMP::atom)   XYRadialPositionLowerRestraint (IMP::npc)   
CoverRefined (IMP::core)   HarmonicUpperBound (IMP::score_functor)   PairRestraint (IMP::core)   Segment3D (IMP::algebra)   XYRadialPositionLowerRestraint (IMP.npc.npc_restraints)   
CPDBSelector (IMP::atom)   HarmonicUpperBound (IMP::core)   PairsConstraint (IMP::container)   SegmentationParameters (IMP::em2d)   XYRadialPositionRestraint (IMP.npc.npc_restraints)   
CreateLogContext (IMP)   HarmonicUpperBoundSphereDiameterPairScore (IMP::core)   PairScore (IMP)   SegmentGeometry (IMP::display)   XYRadialPositionRestraint (IMP::npc)   
CrossCorrelationRestraint (IMP.pmi.restraints.em)   HarmonicUpperBoundSphereDistancePairScore (IMP::core)   PairsGeometry (IMP::display)   Segments (IMP.pmi.tools)   XYRadialPositionUpperRestraint (IMP.npc.npc_restraints)   
CrossCorrelationRestraint (IMP.pmi1.restraints.em)   HarmonicWell (IMP::core)   PairsOptimizerState (IMP::container)   Segments (IMP.pmi1.tools)   XYRadialPositionUpperRestraint (IMP::npc)   
CrossLinkData (IMP::isd)   HarmonicWellPairScore (IMP::npctransport)   PairsRestraint (IMP::container)   Selection (IMP::atom)   XYZ (IMP::core)   
CrossLinkDataBase (IMP.pmi.io.crosslink)   HasHigherCCC (IMP::em2d)   ParabolicFit2D (IMP::algebra)   SelectionGeometry (IMP::atom)   XYZDerivativeGeometry (IMP::core)   
CrossLinkDataBaseFromStructure (IMP.pmi.io.crosslink)   HasLowerScore (IMP::em2d)   ParameterWarning (IMP.pmi)   Sequences (IMP.pmi.topology)   XYZDerivativesGeometry (IMP::core)   
CrossLinkDataBaseFromStructure (IMP.pmi1.io.crosslink)   HeapAssignmentContainer (IMP::domino)   Particle (IMP)   Sequences (IMP.pmi1.topology)   XYZR (IMP::core)   
CrossLinkDataBaseKeywordsConverter (IMP.pmi.io.crosslink)   HeapRecord (IMP.EMageFit.solutions_io)   ParticleAdaptor (IMP)   SerialMover (IMP::core)   XYZRGeometry (IMP::core)   
CrossLinkDataBaseKeywordsConverter (IMP.pmi1.io.crosslink)   HelixDecorator (IMP::spb)   ParticleEmbedding (IMP::statistics)   SetCheckState (IMP)   XYZRsGeometry (IMP::core)   
CrossLinkingMassSpectrometryRestraint (IMP.pmi.restraints.crosslinking)   HelixRestraint (IMP.pmi.restraints.stereochemistry)   ParticleFactory (IMP::npctransport)   SetLogState (IMP)   XYZStates (IMP::domino)   
CrossLinkingMassSpectrometryRestraint (IMP.pmi1.restraints.crosslinking)   HelixRestraint (IMP.pmi1.restraints.stereochemistry)   ParticleIndexAdaptor (IMP)   SetLogTarget (IMP)   
  Y  
CrossLinkMS (IMP.pmi1.nonmantained)   HelixRestraint (IMP::atom)   ParticleIndexesAdaptor (IMP)   SetNumberOfThreads (IMP)   
CrossLinkMSRestraint (IMP::isd)   HierarchiesGeometry (IMP::atom)   ParticleIndexPairsAdaptor (IMP)   SettingsData (IMP::multifit)   YAxialPositionLowerRestraint (IMP.npc.npc_restraints)   
CrossLinkTable (IMP.pmi.analysis)   Hierarchy (IMP::core)   ParticleInputs (IMP)   SetupConnectivityNetworkRestraint (IMP.pmi1.restraints.proteomics)   YAxialPositionLowerRestraint (IMP::npc)   
CrossLinkTable (IMP.pmi1.analysis)   Hierarchy (IMP::atom)   ParticleOutputs (IMP)   SetupConnectivityNetworkRestraint (IMP.pmi.restraints.proteomics)   YAxialPositionRestraint (IMP.npc.npc_restraints)   
CustomXYZR (IMP::misc)   HierarchyCounter (IMP::core)   ParticlesAdaptor (IMP::domino)   SetupMembraneRestraint (IMP.pmi1.restraints.proteomics)   YAxialPositionRestraint (IMP::npc)   
CvEstimator (IMP.isd.TuneRex)   HierarchyDatabase (IMP.pmi1.tools)   ParticlesDummyRestraint (IMP::em2d)   SGEPEWorkerArray (IMP.parallel)   YAxialPositionUpperRestraint (IMP::npc)   
Cylinder3D (IMP::algebra)   HierarchyGeometry (IMP::atom)   ParticleStates (IMP::domino)   SGEQsubWorkerArray (IMP.parallel)   YAxialPositionUpperRestraint (IMP.npc.npc_restraints)   
CylinderGeometry (IMP::display)   HierarchyLoadLink (IMP::rmf)   ParticleStatesTable (IMP::domino)   Shift (IMP::score_functor)   
  Z  
CylinderRestraint (IMP.pmi.restraints.basic)   HierarchySaveLink (IMP::rmf)   ParticleTransportStatisticsOptimizerState (IMP::npctransport)   Showable (IMP)   
CylinderRestraint (IMP.pmi1.restraints.basic)   HierarchyTraits (IMP::core)   PartitionalClustering (IMP::statistics)   SigmoidRestraintSphere (IMP::pmi1)   ZAxialPositionLowerRestraint (IMP.npc.npc_restraints)   
CysteineCrossLinkData (IMP::isd)   HierarchyVisitor (IMP::core)   PartitionalClusteringWithCenter (IMP::statistics)   SimpleAssignmentsTable (IMP::domino)   ZAxialPositionLowerRestraint (IMP::npc)   
CysteineCrossLinkRestraint (IMP::isd)   HierarchyWithSitesLoadLink (IMP::npctransport)   PathLocalPlanner (IMP::kinematics)   SimpleLoadLink (IMP::rmf)   ZAxialPositionRestraint (IMP.npc.npc_restraints)   
  D  
HierarchyWithSitesSaveLink (IMP::npctransport)   PbcBoxedMover (IMP::spb)   SimpleSaveLink (IMP::rmf)   ZAxialPositionRestraint (IMP::npc)   
HighDensityEmbedding (IMP::em)   PbcBoxedRigidBodyMover (IMP::spb)   Simplex (IMP::gsl)   ZAxialPositionUpperRestraint (IMP::npc)   
Database2 (IMP.EMageFit.database)   HistogramD (IMP::statistics)   PCAAligner (IMP::em)   SimulationData (IMP::npctransport)   ZAxialPositionUpperRestraint (IMP.npc.npc_restraints)   
DataEntry (IMP.pmi.output)   History (IMP.isd.History)   PCAFitRestraint (IMP::em)   Simulator (IMP::atom)   ZBiasSingletonScore (IMP::npctransport)   
DataEntry (IMP.pmi1.output)   HybridMonteCarlo (IMP::isd)   PCAFitRestraint (IMP::em2d)   SingleLinkage (IMP::em2d)   
  p  
DataObject (IMP::core)   HydrogenPDBSelector (IMP::atom)   PDBSelector (IMP::atom)   SingletonConstraint (IMP::core)   
DataPointsAssignment (IMP::multifit)   
  I  
PDBSequences (IMP.pmi.topology)   SingletonContainer (IMP)   piecewise_linear_distribution (IMP)   
DecayPairContainerOptimizerState (IMP::misc)   PenalizedComplexityPrior (IMP::isd)   SingletonContainerAdaptor (IMP)   
  s  
Decorator (IMP)   Image (IMP::em2d)   PerinuclearVolumeLocationRestraint (IMP::npc)   SingletonContainerSet (IMP::container)   
DefaultEmbeddingD (IMP::algebra)   ImageHeader (IMP::em)   PermutationStates (IMP::domino)   SingletonContainerStatistics (IMP::container)   sfo_common (IMP.isd.shared_functions)   
DegreesOfFreedom (IMP.pmi.dof)   ImageReaderWriter (IMP::em2d)   Pipe (IMP.isd.utils)   SingletonGeometry (IMP::display)   
  v  
DeltaDistributionFunction (IMP::saxs)   IMPRestraints (IMP.modeller)   PivyWriter (IMP::display)   SingletonModifier (IMP)   
vonMises (IMP::isd)   
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z