IMP logo
IMP Reference Guide  develop.031dafb4d2,2024/05/21
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  
DensityFillingRestraint (IMP::em)   InitialDockingFromXlinks (IMP.EMageFit.buildxlinks)   PoreRadiusSingletonScore (IMP::npctransport)   SlabWithCylindricalPoreWireGeometry (IMP::npctransport)   
DensityHeader (IMP::em)   InputAdaptor (IMP)   PoreSideVolumeLocationRestraint (IMP::npc)   SlabWithPore (IMP::npc)   
AddBoolFlag (IMP)   DensityMap (IMP::em)   InternalCoordinatesConstraint (IMP::pmi1)   PPDBSelector (IMP::atom)   SlabWithPore (IMP::npctransport)   
AddFloatFlag (IMP)   DependencyScoreState (IMP::domino)   InternalException (IMP)   Precision (IMP.pmi.analysis)   SlabWithSphericalIndent (IMP::npc)   
AddIntFlag (IMP)   DerivativeAccumulator (IMP)   IntsOrder (IMP::em2d)   Precision (IMP.pmi1.analysis)   SlabWithSphericalIndentGeometry (IMP::npc)   
AddScores (IMP::score_functor)   DerivativeCalculator (IMP::saxs)   IOException (IMP)   PredicatePairsRestraint (IMP::container)   SlabWithSphericalIndentMBMScore (IMP::npc)   
AddStringFlag (IMP)   DerivativesFromRefined (IMP::core)   IsCollisionPairPredicate (IMP::core)   PredicateQuadsRestraint (IMP::container)   SlabWithToroidalPore (IMP::npctransport)   
AdvancedFlag (IMP)   DerivativesToRefined (IMP::core)   ISDRestraint (IMP::spb)   PredicateSingletonScore (IMP::core)   SlabWithToroidalPore (IMP::npc)   
Alignment (IMP.pmi.analysis)   DiameterRestraint (IMP::core)   ISDRestraint (IMP::isd)   PredicateSingletonsRestraint (IMP::container)   SlabWithToroidalPoreGoPairScore (IMP::npc)   
Alignment (IMP.pmi1.analysis)   DiameterRgyrRestraint (IMP::spb)   IsosurfaceGeometry (IMP::display)   PredicateTripletsRestraint (IMP::container)   SlabWithToroidalPoreMBMScore (IMP::npc)   
AlignmentClustering (IMP.multifit.cluster)   Diffusion (IMP::atom)   
  J  
PrincipalComponentAnalysisD (IMP::algebra)   SlabWithToroidalPorePairScore (IMP::npctransport)   
AlignSymmetric (IMP::cnmultifit)   Dihedral (IMP::atom)   PrismaticJoint (IMP::kinematics)   SlabWithToroidalPoreWireGeometry (IMP::npc)   
AllBipartitePairContainer (IMP::container)   DihedralAngleRevoluteJoint (IMP::kinematics)   JaccardDistanceMatrix (IMP.pmi.io.crosslink)   ProbabilisticAnchorGraph (IMP::multifit)   SlabWithToroidalPoreWireGeometry (IMP::npctransport)   
AllMol2Selector (IMP::atom)   DihedralMover (IMP::kinematics)   JaccardDistanceMatrix (IMP.pmi1.io.crosslink)   ProbabilisticSubsetFilterTable (IMP::domino)   Slice (IMP::domino)   
AllPairContainer (IMP::container)   DihedralRestraint (IMP::core)   JeffreysPrior (IMP.pmi.restraints.parameters)   ProcessOutput (IMP.pmi.output)   SmoothingFunction (IMP::atom)   
AllPDBSelector (IMP::atom)   DihedralSingletonScore (IMP::atom)   JeffreysPrior (IMP.pmi1.restraints.parameters)   ProcessOutput (IMP.pmi1.output)   Soap (IMP::score_functor)   
AllSamePairPredicate (IMP::core)   Direction (IMP::core)   JeffreysRestraint (IMP::isd)   Profile (IMP::saxs)   SoapPairFilter (IMP::atom)   
AllSameQuadPredicate (IMP::core)   DirectionalDOF (IMP::kinematics)   Joint (IMP::kinematics)   ProfileClustering (IMP::saxs)   SoftCylinderPairScore (IMP::misc)   
AllSameSingletonPredicate (IMP::core)   DirectionAngle (IMP::core)   JPGImageReaderWriter (IMP::em2d)   ProfileFitter (IMP::saxs)   SoftSpherePairScore (IMP::core)   
AllSameTripletPredicate (IMP::core)   DirectionMover (IMP::core)   
  K  
Profiler (IMP::benchmark)   SoftSubSurfacePairScore (IMP::core)   
AmbiguousCompositeRestraint (IMP.pmi.restraints.proteomics)   DirectorObjectChecker (IMP.test)   ProjectingOptions (IMP::em2d)   SoftSuperSurfacePairScore (IMP::core)   
AmbiguousCompositeRestraint (IMP.pmi1.restraints.proteomics)   DiscreteSampler (IMP::domino)   KClosePairsPairScore (IMP::core)   ProjectingParameters (IMP::em2d)   SoftwareProvenance (IMP::core)   
AmbiguousNOERestraint (IMP::isd)   DisjointSetsSubsetFilterTable (IMP::domino)   KernelParameters (IMP::em)   ProjectionFinder (IMP::em2d)   SolventAccessibleSurface (IMP::saxs)   
AmbiguousRestraint (IMP::isd)   DistanceFilter (IMP::em2d)   Key (IMP)   ProjectionMask (IMP::em2d)   SparseGrid3D (IMP::algebra)   
Analysis (IMP.isd.Analysis)   DistanceFilterTable (IMP::em2d)   KinematicForest (IMP::kinematics)   ProjectionParameters (IMP::em2d)   SparseGridStorageD (IMP::algebra)   
AnalysisReplicaExchange (IMP.pmi.macros)   DistanceMask (IMP::em)   KinematicForestScoreState (IMP::kinematics)   ProjectionParametersScoreState (IMP::em2d)   SparseSymmetricPairMemoizer (IMP)   
AnalysisReplicaExchange (IMP.pmi1.macros)   DistancePairScore (IMP::score_functor)   KinematicNode (IMP::kinematics)   ProjectionStates (IMP::em2d)   SparseUnboundedGrid3D (IMP::algebra)   
AnalysisReplicaExchange0 (IMP.pmi.macros)   DistancePairScore (IMP::core)   KinkPairScore (IMP::spb)   ProteinChainRestraint (IMP::npc)   SparseUnboundedGridD (IMP::algebra)   
AnalysisReplicaExchange0 (IMP.pmi1.macros)   DistancePairScoreWithCache (IMP::score_functor)   KMeans (IMP::kmeans)   ProteinContactRestraint (IMP::npc)   SphereD (IMP::algebra)   
AnchorsData (IMP::multifit)   DistanceRestraint (IMP.pmi.restraints.basic)   
  L  
ProteinKinematics (IMP::kinematics)   SphereDistance (IMP::score_functor)   
AnchorToCylidnricalPorePairScore (IMP::npctransport)   DistanceRestraint (IMP.pmi1.restraints.basic)   ProteinLigandAtomPairScore (IMP::atom)   SphereDistancePairScore (IMP::core)   
AndPDBSelector (IMP::atom)   DistanceRestraint (IMP::core)   LabelGeometry (IMP::display)   ProteinLigandRestraint (IMP::atom)   SphereDistanceToSingletonScore (IMP::core)   
Angle (IMP::atom)   DistanceRMSDMetric (IMP::spb)   LangevinThermostatOptimizerState (IMP::atom)   ProteinProximityRestraint (IMP::npc)   SphereGeometry (IMP::display)   
AngleRestraint (IMP::core)   DistanceTerminiRestraint (IMP::spb)   LateralSurfaceConstraint (IMP::core)   ProteinsAnchorsSamplingSpace (IMP::multifit)   SpherePatch3D (IMP::algebra)   
AngleSingletonScore (IMP::atom)   DistanceToPointRestraint (IMP.pmi.restraints.basic)   LeavesRefiner (IMP::core)   ProteomicsData (IMP::multifit)   SphericalIndentSurfaceDepthPairScore (IMP::npc)   
AngleTripletScore (IMP::core)   DistanceToPointRestraint (IMP.pmi1.restraints.basic)   LennardJones (IMP::atom)   ProteomicsEMAlignmentAtomic (IMP::multifit)   SphericalVector3D (IMP::algebra)   
AngularVelocity (IMP::atom)   DistributePairsScoreState (IMP::container)   LennardJonesPairScore (IMP::atom)   ProtocolOutput (IMP.pmi.mmcif)   SpiderHeader (IMP::em)   
ApplicationTestCase (IMP.test)   DistributeQuadsScoreState (IMP::container)   LessPairBySecond (IMP::em2d)   ProtocolOutput (IMP.pmi1.mmcif)   SpiderImageReaderWriter (IMP::em2d)   
ArgumentParser (IMP)   DistributeSingletonsScoreState (IMP::container)   Line3D (IMP::algebra)   ProtocolOutput (IMP.pmi.output)   SpiderMapReaderWriter (IMP::em)   
Array (IMP)   DistributeTripletsScoreState (IMP::container)   Linear (IMP::core)   ProtocolOutput (IMP.pmi1.output)   State (IMP::atom)   
AssemblyHeader (IMP::multifit)   Distribution (IMP::saxs)   Linear1DFunction (IMP::isd)   Provenance (IMP::core)   State (IMP.pmi.topology)   
AssemblySymmetryByDihedralRestraint (IMP::npc)   Distribution (IMP::isd)   LinearFit2D (IMP::algebra)   Provenanced (IMP::core)   StateAdaptor (IMP::misc)   
AssemblySymmetryByDistanceRestraint (IMP::npc)   DockOrder (IMP.EMageFit.buildxlinks)   LinearInteraction (IMP::npctransport)   PseudoAtomicRestraint (IMP.pmi.restraints.stereochemistry)   StatHierarchyHandler (IMP.pmi1.output)   
Assignment (IMP::domino)   DockRefFormatter (IMP.multifit.transforms)   LinearInteractionPairScore (IMP::npctransport)   PseudoAtomicRestraint (IMP.pmi1.restraints.stereochemistry)   StatHierarchyHandler (IMP.pmi.output)   
AssignmentContainer (IMP::domino)   DOF (IMP::kinematics)   LinearLowerBound (IMP::score_functor)   PymolWriter (IMP::display)   Statistical (IMP::score_functor)   
AssignmentsTable (IMP::domino)   DOFsSampler (IMP::kinematics)   LinearSoftSpherePairScore (IMP::npctransport)   PythonDirectedGraph (IMP)   StatisticalPairScore (IMP::core)   
AsymUnit (IMP.pmi.mmcif)   DOFValues (IMP::kinematics)   LinearVelocity (IMP::atom)   PythonExampleConstraint (IMP.example)   Statistics (IMP.isd.Statistics)   
AsymUnit (IMP.pmi1.mmcif)   Domain (IMP::atom)   LinearWellPairScore (IMP::npctransport)   PythonExamplePairScore (IMP.example)   Statistics (IMP::npctransport)   
Atom (IMP::atom)   DominoModel (IMP.EMageFit.domino_model)   ListAssignmentContainer (IMP::domino)   PythonExampleRestraint (IMP.example)   SteepestDescent (IMP::core)   
AtomicCrossLinkMSRestraint (IMP.pmi.restraints.crosslinking)   DominoSampler (IMP::domino)   ListAssignmentsTable (IMP::domino)   PythonExampleSingletonModifier (IMP.example)   StereochemistryPairFilter (IMP::atom)   
AtomicCrossLinkMSRestraint (IMP.pmi1.restraints.crosslinking)   Dope (IMP::score_functor)   ListPairContainer (IMP::container)   PythonExampleUnaryFunction (IMP.example)   Stopwatch (IMP.pmi.tools)   
AtomicCrossLinkMSRestraint (IMP::isd)   DopePairScore (IMP::atom)   ListQuadContainer (IMP::container)   
  Q  
Stopwatch (IMP.pmi1.tools)   
ATOMPDBSelector (IMP::atom)   DummyRestraint (IMP::em2d)   ListSingletonContainer (IMP::container)   StructureProvenance (IMP::core)   
AtomType (IMP::atom)   DummyRestraint (IMP::multifit)   ListSubsetFilterTable (IMP::domino)   QuadConstraint (IMP::core)   StructureSource (IMP::atom)   
AtomTypePDBSelector (IMP::atom)   DynamicListPairContainer (IMP::container)   ListTripletContainer (IMP::container)   QuadContainer (IMP)   StructureWarning (IMP.pmi)   
AttributeDistancePairScore (IMP::spb)   DynamicListQuadContainer (IMP::container)   LoadLink (IMP::rmf)   QuadContainerAdaptor (IMP)   StudentTRestraint (IMP::isd)   
AttributeOptimizer (IMP)   DynamicListSingletonContainer (IMP::container)   LocalPlanner (IMP::kinematics)   QuadContainerSet (IMP::container)   Subset (IMP::domino)   
AttributeSingletonPredicate (IMP::core)   DynamicListTripletContainer (IMP::container)   LocalWorker (IMP.parallel)   QuadContainerStatistics (IMP::container)   SubsetFilter (IMP::domino)   
AverageDistanceLinkage (IMP::em2d)   DynamicNearestNeighbor3D (IMP::algebra)   LogEmbeddingD (IMP::algebra)   QuadModifier (IMP)   SubsetFilterTable (IMP::domino)   
  B  
  E  
LogHolder (IMP.isd.demux_trajs)   QuadPredicate (IMP)   SubsetMover (IMP::core)   
LognormalAmbiguousRestraint (IMP::isd)   QuadraticClosePairsFinder (IMP::core)   Surface (IMP::core)   
BackbonePDBSelector (IMP::atom)   EdgePairGeometry (IMP::core)   LogNormalMover (IMP::core)   QuadRestraint (IMP::core)   SurfaceDepthPairScore (IMP::score_functor)   
BallMover (IMP::symmetry)   EdgePairsGeometry (IMP::core)   LognormalRestraint (IMP::isd)   QuadsConstraint (IMP::container)   SurfaceDepthPairScore (IMP::core)   
BallMover (IMP::core)   ElasticNetworkRestraint (IMP.pmi.restraints.stereochemistry)   LogPairScore (IMP::misc)   QuadScore (IMP)   SurfaceDistancePairScore (IMP::core)   
BerendsenThermostatOptimizerState (IMP::atom)   ElasticNetworkRestraint (IMP.pmi1.restraints.stereochemistry)   LogWrapper (IMP::isd)   QuadsOptimizerState (IMP::container)   SurfaceDistancePairScore (IMP::score_functor)   
BinormalTerm (IMP::core)   ElectronMicroscopy2D (IMP.pmi.restraints.em2d)   LoopStatistical (IMP::score_functor)   QuadsRestraint (IMP::container)   SurfaceGeometry (IMP::core)   
BipartitePairsStatisticsOptimizerState (IMP::npctransport)   ElectronMicroscopy2D (IMP.pmi1.restraints.em2d)   LoopStatisticalPairScore (IMP::atom)   QuasiNewton (IMP::gsl)   SurfaceGeometryConstraint (IMP::core)   
BiStableDistanceRestraint (IMP.pmi.restraints.basic)   ElectronMicroscopy2D_FFT (IMP.pmi.restraints.em2d)   LowestRefinedPairScore (IMP::misc)   
  R  
SurfaceHeightPairScore (IMP::core)   
BiStableDistanceRestraint (IMP.pmi1.restraints.basic)   ElectronMicroscopy2D_FFT (IMP.pmi1.restraints.em2d)   LRUCache (IMP)   SurfaceHeightPairScore (IMP::score_functor)   
BivariateFunction (IMP::isd)   ElementTable (IMP::atom)   
  M  
RadialDistributionFunction (IMP::saxs)   SurfaceMeshGeometry (IMP::display)   
BodyStatisticsOptimizerState (IMP::npctransport)   Ellipsoid3D (IMP::algebra)   RadiusDependentDistanceMask (IMP::em)   SurfaceMover (IMP::core)   
Bond (IMP::atom)   EllipsoidGeometry (IMP::display)   Manager (IMP.parallel)   RadiusOfGyrationRestraint (IMP::saxs)   SurfacesGeometry   
ForceFieldParameters::Bond (IMP::atom)   EM2DRestraint (IMP::spb)   ManagerCommunicator (IMP.parallel.manager_communicator)   RadiusOfGyrationRestraint (IMP::multifit)   SurfaceShellDensityMap (IMP::em)   
BondAngleRevoluteJoint (IMP::kinematics)   Em2DRestraint (IMP::em2d)   MapCrossLinkDataBaseOnStructure (IMP.pmi.io.crosslink)   RAII (IMP)   SurfaceSymmetryConstraint (IMP::core)   
Bonded (IMP::atom)   Em2DRestraintParameters (IMP::em2d)   MapCrossLinkDataBaseOnStructure (IMP.pmi1.io.crosslink)   RangeViewAssignmentContainer (IMP::domino)   SurfaceTetheredChain (IMP::core)   
BondedPairFilter (IMP::atom)   EM2DScore (IMP::em2d)   MapDistanceTransform (IMP::em)   RatioVolatilityScore (IMP::saxs)   Switching (IMP::isd)   
BondEndpointsRefiner (IMP::atom)   Embedding (IMP::statistics)   MapReaderWriter (IMP::em)   ReadAssignmentContainer (IMP::domino)   Symmetric (IMP::pmi1)   
BondGeometry (IMP::atom)   EMReaderWriter (IMP::em)   MarginalHBondRestraint (IMP::isd)   ReadHDF5AssignmentContainer (IMP::domino)   Symmetric (IMP::pmi)   
BondGraph (IMP::atom)   Ensemble (IMP::multifit)   MarginalNOERestraint (IMP::isd)   RecursiveAssignmentsTable (IMP::domino)   SymmetryRestraint (IMP.pmi1.restraints.stereochemistry)   
BondPairContainer (IMP::atom)   EnsembleGenerator (IMP::multi_state)   MasksManager (IMP::em2d)   RecursivePartitionalClusteringEmbedding (IMP::statistics)   SymmetryRestraint (IMP.pmi.restraints.stereochemistry)   
BondsGeometry (IMP::atom)   Entity (IMP.pmi.mmcif)   Mass (IMP::atom)   RecursivePartitionalClusteringMetric (IMP::statistics)   System (IMP.pmi.topology)   
BondSingletonScore (IMP::atom)   Entity (IMP.pmi1.mmcif)   MatchTemplateResult (IMP::em2d)   RecursiveStates (IMP::domino)   
  T  
BoundedGridRangeD (IMP::algebra)   Entry (IMP.isd.Entry)   MaxVectorKDMetric (IMP::algebra)   RefCountChecker (IMP.test)   
BoundingBoxD (IMP::algebra)   EnvelopeFitRestraint (IMP::em)   MCCGSampler (IMP::core)   Reference (IMP::core)   TableRefiner (IMP::core)   
BoundingBoxGeometry (IMP::display)   EnvelopePenetrationRestraint (IMP::em)   MeanAbsoluteDifference (IMP::em2d)   ReferenceFrame3D (IMP::algebra)   TALOSReader (IMP.isd.TALOSReader)   
BoxedMover (IMP::spb)   EnvelopeScore (IMP::em)   MembraneExclusionRestraint (IMP.pmi.restraints.npc)   ReferenceFrameGeometry (IMP::display)   TALOSRestraint (IMP::isd)   
BoxSweepClosePairsFinder (IMP::core)   EqualitySubsetFilterTable (IMP::domino)   MembraneExclusionRestraint (IMP.pmi1.restraints.npc)   ReferenceFrameToText (IMP.EMageFit.imp_general.io)   TAMDCentroid (IMP::atom)   
BranchAndBoundAssignmentsTable (IMP::domino)   EquivalenceAndExclusionSubsetFilterTable (IMP::domino)   MembraneExclusionRestraint (IMP::npc)   RefinedPairsPairScore (IMP::core)   TAMDParticle (IMP::atom)   
BranchAndBoundSampler (IMP::domino)   EquivalenceSubsetFilterTable (IMP::domino)   MembraneRestraint (IMP.pmi.restraints.basic)   Refiner (IMP)   TempResidue (IMP.pmi.topology)   
BrownianDynamics (IMP::atom)   Error (IMP.parallel)   MembraneRestraint (IMP::pmi)   Reflection3D (IMP::algebra)   TestCase (IMP.test)   
BrownianDynamicsTAMD (IMP::atom)   EuclideanMetric (IMP::statistics)   MembraneRestraint (IMP::pmi1)   RegistrationResult (IMP::em2d)   TextInput (IMP)   
BrownianDynamicsTAMDWithSlabSupport (IMP::npctransport)   EuclideanVectorKDMetric (IMP::algebra)   MembraneSurfaceLocationConditionalRestraint (IMP.pmi.restraints.npc)   RelativePositionMover (IMP::em2d)   TextOutput (IMP)   
BuildModel (IMP.pmi1.macros)   LinearInteractionPairScore::EvaluationCache (IMP::npctransport)   MembraneSurfaceLocationConditionalRestraint (IMP.pmi1.restraints.npc)   RelaxingSpring (IMP::npctransport)   TextWriter (IMP::display)   
BuildModel1 (IMP.pmi1.macros)   EvaluationState (IMP)   MembraneSurfaceLocationConditionalRestraint (IMP::npc)   RemoteError (IMP.parallel)   ThreeToOneConverter (IMP.pmi1.tools)   
BuildSystem (IMP.pmi.macros)   EventException (IMP)   MembraneSurfaceLocationRestraint (IMP.pmi.restraints.npc)   RemoveRigidMotionOptimizerState (IMP::atom)   TIFFImageReaderWriter (IMP::em2d)   
  C  
EventPairsOptimizerState (IMP::container)   MembraneSurfaceLocationRestraint (IMP.pmi1.restraints.npc)   RemoveTranslationOptimizerState (IMP::atom)   TiltSingletonScore (IMP::spb)   
EventQuadsOptimizerState (IMP::container)   MembraneSurfaceLocationRestraint (IMP::npc)   ReplicaExchange (IMP.pmi.samplers)   TopologyPlot (IMP.pmi.plotting.topology)   
CAAngleRestraint (IMP::atom)   EventSingletonsOptimizerState (IMP::container)   Memoizer (IMP)   ReplicaExchange (IMP.pmi1.samplers)   TopologyPlot (IMP.pmi1.plotting.topology)   
CADihedralRestraint (IMP::atom)   EventTripletsOptimizerState (IMP::container)   MergeTreeBuilder (IMP::multifit)   ReplicaExchange (IMP::mpi)   TopologyReader (IMP.pmi1.topology)   
CAlphaPDBSelector (IMP::atom)   ExampleComplexRestraint (IMP::example)   Metric (IMP::statistics)   ReplicaExchange (IMP.pmi.macros)   TopologyReader (IMP.pmi.topology)   
CappedAssignmentContainer (IMP::domino)   ExampleConstraint (IMP::example)   MetricClosePairsFinder (IMP::misc)   ReplicaExchange0 (IMP.pmi1.macros)   ToroidalPoreSurfaceDepthPairScore (IMP::npc)   
CBetaPDBSelector (IMP::atom)   ExampleDecorator (IMP::example)   MinimumPairRestraint (IMP::container)   Representation (IMP.pmi1.representation)   Torus3D (IMP::algebra)   
CCDLoopClosure (IMP::kinematics)   ExampleObject (IMP::example)   MinimumPairScore (IMP::container)   Representation (IMP::atom)   TotalScoreOutput (IMP.pmi.io)   
CellMover (IMP::spb)   ExamplePairScore (IMP::example)   MinimumQuadRestraint (IMP::container)   RepulsiveDistancePairScore (IMP::isd)   TotalScoreOutput (IMP.pmi1.io)   
CenterOfMass (IMP::atom)   ExampleRestraint (IMP::example)   MinimumQuadScore (IMP::container)   Residue (IMP::atom)   Transform (IMP::core)   
Centroid (IMP::core)   ExampleSingletonModifier (IMP::example)   MinimumRestraint (IMP::core)   ResidueAlphabet (IMP.pmi.alphabets)   Transformation2D (IMP::algebra)   
CentroidOfRefined (IMP::core)   ExampleSubsetFilterTable (IMP::example)   MinimumRestraintScoreSubsetFilterTable (IMP::domino)   ResidueAngleRestraint (IMP.pmi.restraints.stereochemistry)   Transformation3D (IMP::algebra)   
Chain (IMP::atom)   ExampleTemplateClassD (IMP::example)   MinimumSingletonRestraint (IMP::container)   ResidueAngleRestraint (IMP.pmi1.restraints.stereochemistry)   Transformation3DToText (IMP.EMageFit.imp_general.io)   
ChainPDBSelector (IMP::atom)   ExampleUnaryFunction (IMP::example)   MinimumSingletonScore (IMP::container)   ResidueBondRestraint (IMP.pmi.restraints.stereochemistry)   TransformationAndReflectionSymmetry (IMP::core)   
ChainStatisticsOptimizerState (IMP::npctransport)   Exception (IMP)   MinimumSphereDistancePairScore (IMP::npc)   ResidueBondRestraint (IMP.pmi1.restraints.stereochemistry)   TransformationJoint (IMP::kinematics)   
ChainType (IMP::atom)   ExcludedVolumeRestraint (IMP::core)   MinimumTripletRestraint (IMP::container)   ResidueDihedralRestraint (IMP.pmi.restraints.stereochemistry)   TransformationSymmetry (IMP::spb)   
Charged (IMP::atom)   ExcludedVolumeSphere (IMP.pmi.restraints.stereochemistry)   MinimumTripletScore (IMP::container)   ResidueDihedralRestraint (IMP.pmi1.restraints.stereochemistry)   TransformationSymmetry (IMP::core)   
CHARMMAtom (IMP::atom)   ExcludedVolumeSphere (IMP.pmi1.restraints.stereochemistry)   MissingFileWarning (IMP.pmi)   ResiduePairListParser (IMP.pmi.io.crosslink)   TransformationSymmetryMover (IMP::core)   
CHARMMAtomTopology (IMP::atom)   ExcludeZRangeSingletonScore (IMP::npctransport)   Model (IMP)   ResiduePairListParser (IMP.pmi1.io.crosslink)   TransformedDistancePairScore (IMP::core)   
CHARMMBondEndpoint (IMP::atom)   ExclusionSubsetFilterTable (IMP::domino)   ModelException (IMP)   ResidueProteinProximityRestraint (IMP.pmi.restraints.basic)   TransformMover (IMP::pmi)   
CHARMMBondParameters (IMP::atom)   ExclusiveConsecutivePairContainer (IMP::container)   ModellerRestraints (IMP.modeller)   ResidueProteinProximityRestraint (IMP::isd)   TransformMover (IMP::pmi1)   
CHARMMConnection (IMP::atom)   ExclusiveConsecutivePairFilter (IMP::container)   ModelLoader (IMP.modeller)   ResidueRotamer (IMP::rotamer)   Transporting (IMP::npctransport)   
CHARMMDihedralParameters (IMP::atom)   ExtendedGridIndexD (IMP::algebra)   ModelObject (IMP)   ResidueType (IMP::atom)   Triangle3D (IMP::algebra)   
CharmmForceFieldRestraint (IMP.pmi.restraints.stereochemistry)   ExternalBarrier (IMP.pmi.restraints.basic)   ModifierVisitor (IMP::core)   ResidueTypePDBSelector (IMP::atom)   TriangleGeometry (IMP::display)   
CharmmForceFieldRestraint (IMP.pmi1.restraints.stereochemistry)   ExternalBarrier (IMP.pmi1.restraints.basic)   Mol2Selector (IMP::atom)   Resolution (IMP::pmi)   TripletConstraint (IMP::core)   
CHARMMIdealResidueTopology (IMP::atom)   EzRestraint (IMP::atom)   MolCnSymmAxisDetector (IMP::cnmultifit)   Resolution (IMP::pmi1)   TripletContainer (IMP)   
CHARMMInternalCoordinate (IMP::atom)   
  F  
MolecularDynamics (IMP::atom)   Restraint (IMP)   TripletContainerAdaptor (IMP)   
CHARMMParameters (IMP::atom)   MolecularDynamics (IMP.pmi.samplers)   Restraint (IMP::saxs)   TripletContainerSet (IMP::container)   
CHARMMPatch (IMP::atom)   FFTFitting (IMP::multifit)   MolecularDynamics (IMP.pmi1.samplers)   RestraintBase (IMP.pmi1.restraints)   TripletContainerStatistics (IMP::container)   
CHARMMResidueTopology (IMP::atom)   FFTFittingOutput (IMP::multifit)   MolecularDynamics (IMP::isd)   RestraintCache (IMP::domino)   TripletModifier (IMP)   
CHARMMResidueTopologyBase (IMP::atom)   FGChain (IMP::npctransport)   MolecularDynamicsMover (IMP::isd)   RestraintGeometry (IMP::display)   TripletPredicate (IMP)   
CHARMMSegmentTopology (IMP::atom)   FibrilSampler (IMP::kinematics)   MolecularDynamicsWithWte (IMP::spb)   RestraintInfo (IMP)   TripletRestraint (IMP::core)   
CHARMMStereochemistryRestraint (IMP::atom)   FilterGeometry (IMP::display)   Molecule (IMP::atom)   RestraintsAdaptor (IMP)   TripletsConstraint (IMP::container)   
CHARMMTopology (IMP::atom)   FilterOperator (IMP.pmi.io.crosslink)   Molecule (IMP.pmi.topology)   RestraintScoreSubsetFilterTable (IMP::domino)   TripletScore (IMP)   
ChecksScoreState (IMP::core)   FilterOperator (IMP.pmi1.io.crosslink)   MonteCarlo (IMP.pmi.samplers)   RestraintSet (IMP)   TripletsOptimizerState (IMP::container)   
ChiFreeScore (IMP::saxs)   FilterProvenance (IMP::core)   MonteCarlo (IMP.pmi1.samplers)   RestraintSetGeometry (IMP::display)   TripletsRestraint (IMP::container)   
ChildrenRefiner (IMP::core)   FitParameters (IMP::saxs)   MonteCarlo (IMP::core)   RestraintsScoringFunction (IMP::core)   TruncatedHarmonic (IMP::core)   
ChimeraFormatter (IMP.multifit.transforms)   FitRestraint (IMP::em)   MonteCarloMover (IMP::core)   ResultsDB (IMP.EMageFit.solutions_io)   TwoStateGoModelRestraint (IMP::spb)   
ChiScore (IMP::saxs)   FitRestraintBayesEM3D (IMP::em)   MonteCarloMoverResult (IMP::core)   RevoluteJoint (IMP::kinematics)   Typed (IMP::core)   
ChiScoreLog (IMP::saxs)   FittingSolutionRecord (IMP::multifit)   MonteCarloRelativeMoves (IMP.EMageFit.monte_carlo)   RevoluteJointMover (IMP::kinematics)   TypedPairScore (IMP::core)   
ChiSquaredScore (IMP::em2d)   FittingSolutions (IMP::em)   MonteCarloWithBasinHopping (IMP::core)   RigidBodiesImageFitRestraint (IMP::em2d)   TypedSitesGeometry (IMP::npctransport)   
ChiSquareMetric (IMP::spb)   FittingStates (IMP::multifit)   MonteCarloWithLocalOptimization (IMP::core)   RigidBodiesProfileHandler (IMP::saxs)   TypeException (IMP)   
ChiSquareMetric (IMP::statistics)   FixedFormatParser (IMP.pmi.io.crosslink)   MonteCarloWithWte (IMP::spb)   RigidBody (IMP::core)   
  U  
CloseBipartitePairContainer (IMP::container)   FixedFormatParser (IMP.pmi1.io.crosslink)   MoveStatisticsScoreState (IMP::core)   RigidBodyAnglePairScore (IMP::core)   
ClosedCubicSpline (IMP::core)   FixedRefiner (IMP::core)   MRCReaderWriter (IMP::em)   RigidBodyDerivativeGeometry (IMP::core)   UnaryFunction (IMP)   
ClosePairContainer (IMP::container)   FixedXYZ (IMP::algebra)   MSConnectivityRestraint (IMP::core)   RigidBodyDerivativesGeometry (IMP::core)   UnaryFunctionEvaluate (IMP::score_functor)   
ClosePairsFinder (IMP::core)   Flag (IMP)   MultipleBinormalRestraint (IMP::core)   RigidBodyDiffusion (IMP::atom)   UnboundedGridRangeD (IMP::algebra)   
ClosePairsPairScore (IMP::core)   FloatIndex (IMP)   MultiStateModel (IMP::multi_state)   RigidBodyDistancePairScore (IMP::core)   Uncertainty (IMP::pmi1)   
Cluster (IMP.pmi.output)   FNormal (IMP::isd)   MultiStateModelScore (IMP::multi_state)   RigidBodyFrameGeometry (IMP::core)   Uncertainty (IMP::pmi)   
Cluster (IMP.pmi1.output)   ForceFieldParameters (IMP::atom)   MultivariateFNormalSufficient (IMP::isd)   RigidBodyFramesGeometry (IMP::core)   UncheckedWeakPointer (IMP)   
Clustering (IMP.pmi.analysis)   ForceSwitch (IMP::atom)   MyMetric (write_a_metric)   RigidBodyHierarchyGeometry (IMP::core)   Undecorator (IMP)   
Clustering (IMP.pmi1.analysis)   FormFactorTable (IMP::saxs)   
  N  
RigidBodyMember (IMP::core)   UniformBackboneSampler (IMP::kinematics)   
ClusterProvenance (IMP::core)   Fragment (IMP::atom)   RigidBodyMover (IMP::symmetry)   UniformBoundedRestraint (IMP::spb)   
ClusterSet (IMP::em2d)   FreelyJointedChain (IMP::misc)   NearestNeighborD (IMP::algebra)   RigidBodyMover (IMP::core)   UniformPrior (IMP::isd)   
CnSymmAxisDetector (IMP::cnmultifit)   FretData (IMP::isd)   NearestNeighborsClosePairsFinder (IMP::core)   RigidBodyNewMover (IMP::spb)   UnitSimplexBaseD (IMP::algebra)   
CoarseCCatIntervals (IMP::em)   FretRestraint (IMP::isd)   NeighborsTable (IMP::core)   RigidBodyPackingScore (IMP::spb)   UnitSimplexD (IMP::algebra)   
CoarseConvolution (IMP::em)   FStudentT (IMP::isd)   NestedRigidBodyStates (IMP::domino)   RigidBodyStates (IMP::domino)   UnitSimplexD<-1 > (IMP::algebra)   
CoinFlipPairPredicate (IMP::core)   FunctorLinearInteractionPairScore (IMP::npctransport)   NetworkError (IMP.parallel)   RigidBodyTorque (IMP::core)   UnivariateFunction (IMP::isd)   
CoinFlipQuadPredicate (IMP::core)   FunctorLinearSoftSpherePairScore (IMP::npctransport)   NOERestraint (IMP::isd)   RigidBodyTunneler (IMP::core)   UnorderedTypePairPredicate (IMP::core)   
CoinFlipSingletonPredicate (IMP::core)   FusionRestraint (IMP.pmi.restraints.stereochemistry)   NoMoreWorkersError (IMP.parallel)   RigidBodyUmbrella (IMP::core)   UnorderedTypeQuadPredicate (IMP::core)   
CoinFlipTripletPredicate (IMP::core)   FusionRestraint (IMP.pmi1.restraints.stereochemistry)   NonAlternativePDBSelector (IMP::atom)   RigidClosePairsFinder (IMP::core)   UnorderedTypeSingletonPredicate (IMP::core)   
CollisionCrossSection (IMP::em2d)   FuzzyBoolean (IMP.pmi.restraints.proteomics)   NonCopyable (IMP)   RigidLeavesRefiner (IMP::multifit)   UnorderedTypeTripletPredicate (IMP::core)   
Color (IMP::display)   FuzzyBoolean (IMP.pmi1.restraints.proteomics)   NonHydrogenMol2Selector (IMP::atom)   RigidMember (IMP::core)   UsageException (IMP)   
ColorChange (IMP.pmi.tools)   FuzzyRestraint (IMP.pmi.restraints.proteomics)   NonHydrogenPDBSelector (IMP::atom)   RMFHierarchyHandler (IMP.pmi1.output)   
  V  
ColorChange (IMP.pmi1.tools)   FuzzyRestraint (IMP.pmi1.restraints.proteomics)   NonRigidMember (IMP::core)   RMFHierarchyHandler (IMP.pmi.output)   
Colored (IMP::display)   
  G  
NonWaterNonHydrogenPDBSelector (IMP::atom)   RMSD (IMP.pmi1.analysis)   Value (IMP)   
CombineProvenance (IMP::core)   NonWaterPDBSelector (IMP::atom)   RMSD (IMP.pmi.analysis)   ValueException (IMP)   
CommandDispatcher (IMP)   GammaPrior (IMP::isd)   NormalizedSphereDistancePairScore (IMP::core)   RMSDMetric (IMP::spb)   Vector (IMP)   
CommonEndpointPairFilter (IMP::misc)   Gaussian (IMP::spb)   NormalMover (IMP::core)   RMSDOutput (IMP.pmi1.io)   VectorBaseD (IMP::algebra)   
CompareMultiStateModels (IMP::multi_state)   Gaussian (IMP::core)   NormalSigmaPCRestraint (IMP::isd)   RotamerAngleTuple (IMP::rotamer)   VectorD (IMP::algebra)   
ComplementarityRestraint (IMP::multifit)   Gaussian3D (IMP::algebra)   NotPDBSelector (IMP::atom)   RotamerCalculator (IMP::rotamer)   VectorDEmbedding (IMP::statistics)   
CompleteLinkage (IMP::em2d)   GaussianAnchorEMRestraint (IMP::isd)   NPDBSelector (IMP::atom)   RotamerLibrary (IMP::rotamer)   VectorKDMetric (IMP::algebra)   
ComponentHeader (IMP::multifit)   GaussianEMRestraint (IMP::bayesianem)   Nuisance (IMP::isd)   Rotation2D (IMP::algebra)   VelocityScalingOptimizerState (IMP::atom)   
CompositeJoint (IMP::kinematics)   GaussianEMRestraint (IMP.pmi.restraints.em)   NuisanceRangeModifier (IMP::spb)   Rotation3D (IMP::algebra)   VersionInfo (IMP)   
CompositeRestraint (IMP.pmi.restraints.proteomics)   GaussianEMRestraint (IMP.pmi1.restraints.em)   
  O  
RRT (IMP::kinematics)   VolumeRestraint (IMP::core)   
CompositeRestraint (IMP.pmi1.restraints.proteomics)   GaussianEMRestraint (IMP::isd)   RRT::RRTNode (IMP::kinematics)   Voxel (IMP::em)   
CompositeRestraint (IMP::npc)   GaussianEMRestraintWrapper (IMP.bayesianem.restraint)   Object (IMP)   
  S  
  W  
CompositeRestraint (IMP::pmi)   GaussianProcessInterpolation (IMP::isd)   OneDimensionalDistribution (IMP::isd)   
CompositeRestraint (IMP::pmi1)   GaussianProcessInterpolationRestraint (IMP::isd)   OneDimensionalSufficientDistribution (IMP::isd)   SameParticlePairFilter (IMP::spb)   WarningContext (IMP)   
CompoundStates (IMP::domino)   GaussianRestraint (IMP::isd)   OpenCubicSpline (IMP::score_functor)   SameResiduePairFilter (IMP::atom)   WaterPDBSelector (IMP::atom)   
Cone3D (IMP::algebra)   GeneralizedGuinierPorodFunction (IMP::isd)   OpenCubicSpline (IMP::core)   SameRigidBodyPairFilter (IMP::spb)   WeakPointer (IMP)   
Configuration (IMP)   GenericAttributeSingletonScore (IMP::core)   Optimizer (IMP)   SampleAssignmentContainer (IMP::domino)   Weight (IMP::isd)   
ConfigurationSet (IMP)   GenericBoundingBox3DSingletonScore (IMP::core)   OptimizerState (IMP)   SampledDensityMap (IMP::em)   WeightedDerivativesToRefined (IMP::core)   
ConfigurationSetRMSDMetric (IMP::statistics)   GenericBoundingSphere3DSingletonScore (IMP::core)   Order (IMP::domino)   SampleProvenance (IMP::core)   WeightedExcludedVolumeRestraint (IMP::multifit)   
ConfigurationSetXYZEmbedding (IMP::statistics)   GenericDistanceToSingletonScore (IMP::core)   OrderedDefaultDict (IMP.pmi.tools)   Sampler (IMP)   WeightedFitParameters (IMP::saxs)   
ConjugateGradients (IMP.pmi.samplers)   GeometricHash (IMP::multifit)   OrderedDefaultDict (IMP.pmi1.tools)   SaveLink (IMP::rmf)   WeightedProfileFitter (IMP::saxs)   
ConjugateGradients (IMP.pmi1.samplers)   GeometricPrimitiveD (IMP::algebra)   OrderedTypePairPredicate (IMP::core)   SaveOptimizerState (IMP::rmf)   WeightedSphereDistancePairScore (IMP::core)   
ConjugateGradients (IMP::gsl)   Geometry (IMP::display)   OrderedTypeQuadPredicate (IMP::core)   SaveToConfigurationSetOptimizerState (IMP)   WeightedSum (IMP::core)   
ConjugateGradients (IMP::core)   GeometryProcessor (IMP::display)   OrderedTypeSingletonPredicate (IMP::core)   SAXSISDRestraint (IMP.pmi.restraints.saxs)   WeightedSumOfExponential (IMP::core)   
ConnectingPairContainer (IMP::container)   GeometrySet (IMP::display)   OrderedTypeTripletPredicate (IMP::core)   SAXSISDRestraint (IMP.pmi1.restraints.saxs)   WeightMover (IMP::isd)   
ConnectivityCrossLinkMS (IMP.pmi1.restraints.crosslinking)   GetModelDensity (IMP.pmi.analysis)   OrientedSoap (IMP::score_functor)   SAXSMultiCombinationScore (IMP::multi_state)   WeightRestraint (IMP.pmi.restraints.parameters)   
ConnectivityNetworkRestraint (IMP.pmi.restraints.proteomics)   GetModelDensity (IMP.pmi1.analysis)   OrientedSoapPairScore (IMP::atom)   SAXSMultiStateModelScore (IMP::multi_state)   WeightRestraint (IMP.pmi1.restraints.parameters)   
ConnectivityNetworkRestraint (IMP.pmi1.restraints.proteomics)   GetModelDensity (IMP.sampcon.precision_rmsd)   OrPDBSelector (IMP::atom)   SAXSRestraint (IMP.pmi.restraints.saxs)   WeightRestraint (IMP::isd)   
ConnectivityRestraint (IMP.pmi.restraints.proteomics)   GlobalStatisticsOptimizerState (IMP::npctransport)   Output (IMP.pmi.output)   SAXSRestraint (IMP.pmi1.restraints.saxs)   WeightScore (IMP::score_functor)   
ConnectivityRestraint (IMP.pmi.restraints.stereochemistry)   GMMParser (IMP.pmi.mmcif)   Output (IMP.pmi1.output)   Scale (IMP::isd)   Worker (IMP.parallel)   
ConnectivityRestraint (IMP.pmi1.restraints.proteomics)   GoodScoringModelSelector (IMP.sampcon.good_scoring_model_selector)   OutputStatistics (IMP.pmi.output)   ScopedAddCacheAttribute (IMP)   WorkerArray (IMP.parallel)   
ConnectivityRestraint (IMP.pmi1.restraints.stereochemistry)   GridClosePairsFinder (IMP::core)   OutputStatistics (IMP.pmi1.output)   ScopedSetAttribute (IMP)   WormLikeChain (IMP::misc)   
ConnectivityRestraint (IMP::core)   GridD (IMP::algebra)   OverallPositionRestraint (IMP::npc)   Score (IMP::score_functor)   WriteAssignmentContainer (IMP::domino)   
ConnollySurfacePoint (IMP::algebra)   GridIndexD (IMP::algebra)   
  P  
ScoreAccumulator (IMP)   WriteHDF5AssignmentContainer (IMP::domino)   
ConsecutivePairContainer (IMP::container)   GridStates (IMP::em2d)   ScoreFunction (IMP::em2d)   WriteOptimizerState (IMP::display)   
ConsecutivePairFilter (IMP::container)   GSLOptimizer (IMP::gsl)   PackedAssignmentContainer (IMP::domino)   ScoreState (IMP)   WritePDBOptimizerState (IMP::atom)   
ConstantPairPredicate (IMP::core)   
  H  
PairConstraint (IMP::core)   ScoreUnaryFunction (IMP::score_functor)   Writer (IMP.mmcif.util)   
ConstantQuadPredicate (IMP::core)   PairContainer (IMP)   ScoreWithCache (IMP::score_functor)   Writer (IMP::display)   
ConstantRestraint (IMP::core)   Harmonic (IMP::score_functor)   PairContainerAdaptor (IMP)   Scoring (IMP::npctransport)   WriterAdaptor (IMP::display)   
ConstantSingletonPredicate (IMP::core)   Harmonic (IMP::core)   PairContainerSet (IMP::container)   ScoringFunction (IMP)   WriteRestraintScoresOptimizerState (IMP::core)   
ConstantTripletPredicate (IMP::core)   HarmonicDistancePairScore (IMP::core)   PairContainerStatistics (IMP::container)   ScoringFunctionAdaptor (IMP)   
  X  
Constraint (IMP)   HarmonicLowerBound (IMP::score_functor)   PairGeometry (IMP::display)   ScriptProvenance (IMP::core)   
ConstVector (IMP)   HarmonicLowerBound (IMP::core)   PairListSubsetFilterTable (IMP::domino)   SecondaryStructure (IMP.pmi1.restraints.stereochemistry)   XAxialPositionLowerRestraint (IMP::npc)   
ContactMapMetric (IMP::spb)   HarmonicSphereDistancePairScore (IMP::core)   PairModifier (IMP)   SecondaryStructureResidue (IMP::atom)   XAxialPositionRestraint (IMP::npc)   
Container (IMP)   HarmonicSpringSingletonScore (IMP::npctransport)   PairPredicate (IMP)   Segment3D (IMP::algebra)   XAxialPositionUpperRestraint (IMP::npc)   
Context (IMP.parallel)   HarmonicSurfaceDepthPairScore (IMP::core)   PairRestraint (IMP::core)   SegmentationParameters (IMP::em2d)   Xlink (IMP.EMageFit.buildxlinks)   
Copy (IMP::atom)   HarmonicSurfaceDistancePairScore (IMP::core)   PairsConstraint (IMP::container)   SegmentGeometry (IMP::display)   XlinksDict (IMP.EMageFit.buildxlinks)   
Cosine (IMP::core)   HarmonicSurfaceHeightPairScore (IMP::core)   PairScore (IMP)   Segments (IMP.pmi.tools)   XLTable (IMP.pmi1.io.xltable)   
CoulombPairScore (IMP::atom)   HarmonicUpperBound (IMP::score_functor)   PairsGeometry (IMP::display)   Segments (IMP.pmi1.tools)   XorPDBSelector (IMP::atom)   
Covariance1DFunction (IMP::isd)   HarmonicUpperBound (IMP::core)   PairsOptimizerState (IMP::container)   Selection (IMP::atom)   XplorReaderWriter (IMP::em)   
Cover (IMP::core)   HarmonicUpperBoundSphereDiameterPairScore (IMP::core)   PairsRestraint (IMP::container)   SelectionGeometry (IMP::atom)   XYRadialPositionLowerRestraint (IMP.pmi1.restraints.npc)   
CoverBond (IMP::atom)   HarmonicUpperBoundSphereDistancePairScore (IMP::core)   ParabolicFit2D (IMP::algebra)   Sequences (IMP.pmi1.topology)   XYRadialPositionLowerRestraint (IMP.pmi.restraints.npc)   
CoverRefined (IMP::core)   HarmonicWell (IMP::core)   ParameterWarning (IMP.pmi)   Sequences (IMP.pmi.topology)   XYRadialPositionLowerRestraint (IMP::npc)   
CPDBSelector (IMP::atom)   HarmonicWellPairScore (IMP::npctransport)   Particle (IMP)   SerialMover (IMP::core)   XYRadialPositionRestraint (IMP.pmi1.restraints.npc)   
CreateLogContext (IMP)   HasHigherCCC (IMP::em2d)   ParticleAdaptor (IMP)   SetCheckState (IMP)   XYRadialPositionRestraint (IMP.pmi.restraints.npc)   
CrossCorrelationRestraint (IMP.pmi1.restraints.em)   HasLowerScore (IMP::em2d)   ParticleEmbedding (IMP::statistics)   SetLogState (IMP)   XYRadialPositionRestraint (IMP::npc)   
CrossLinkData (IMP::isd)   HeapAssignmentContainer (IMP::domino)   ParticleFactory (IMP::npctransport)   SetLogTarget (IMP)   XYRadialPositionUpperRestraint (IMP.pmi1.restraints.npc)   
CrossLinkDataBase (IMP.pmi.io.crosslink)   HeapRecord (IMP.EMageFit.solutions_io)   ParticleIndexAdaptor (IMP)   SetNumberOfThreads (IMP)   XYRadialPositionUpperRestraint (IMP::npc)   
CrossLinkDataBaseFromStructure (IMP.pmi.io.crosslink)   HelixDecorator (IMP::spb)   ParticleIndexesAdaptor (IMP)   SettingsData (IMP::multifit)   XYRadialPositionUpperRestraint (IMP.pmi.restraints.npc)   
CrossLinkDataBaseFromStructure (IMP.pmi1.io.crosslink)   HelixRestraint (IMP.pmi.restraints.stereochemistry)   ParticleIndexPairsAdaptor (IMP)   SetupConnectivityNetworkRestraint (IMP.pmi.restraints.proteomics)   XYZ (IMP::core)   
CrossLinkDataBaseKeywordsConverter (IMP.pmi.io.crosslink)   HelixRestraint (IMP.pmi1.restraints.stereochemistry)   ParticleInputs (IMP)   SetupConnectivityNetworkRestraint (IMP.pmi1.restraints.proteomics)   XYZDerivativeGeometry (IMP::core)   
CrossLinkDataBaseKeywordsConverter (IMP.pmi1.io.crosslink)   HelixRestraint (IMP::atom)   ParticleOutputs (IMP)   SetupMembraneRestraint (IMP.pmi1.restraints.proteomics)   XYZDerivativesGeometry (IMP::core)   
CrossLinkingMassSpectrometryRestraint (IMP.pmi.restraints.crosslinking)   HierarchiesGeometry (IMP::atom)   ParticlesAdaptor (IMP::domino)   SGEPEWorkerArray (IMP.parallel)   XYZR (IMP::core)   
CrossLinkingMassSpectrometryRestraint (IMP.pmi1.restraints.crosslinking)   Hierarchy (IMP::core)   ParticlesDummyRestraint (IMP::em2d)   SGEQsubWorkerArray (IMP.parallel)   XYZRGeometry (IMP::core)   
CrossLinkMS (IMP.pmi1.nonmantained)   Hierarchy (IMP::atom)   ParticleStates (IMP::domino)   Shift (IMP::score_functor)   XYZRsGeometry (IMP::core)   
CrossLinkMSRestraint (IMP::isd)   HierarchyCounter (IMP::core)   ParticleStatesTable (IMP::domino)   Showable (IMP)   XYZStates (IMP::domino)   
CrossLinkRestraintSet (IMP::pmi)   HierarchyDatabase (IMP.pmi1.tools)   ParticleTransportStatisticsOptimizerState (IMP::npctransport)   SigmoidRestraintSphere (IMP::pmi1)   
  Y  
CrossLinkTable (IMP.pmi.analysis)   HierarchyGeometry (IMP::atom)   PartitionalClustering (IMP::statistics)   SimpleAssignmentsTable (IMP::domino)   
CrossLinkTable (IMP.pmi1.analysis)   HierarchyLoadLink (IMP::rmf)   PartitionalClusteringWithCenter (IMP::statistics)   SimpleLoadLink (IMP::rmf)   YAxialPositionLowerRestraint (IMP::npc)   
CustomXYZR (IMP::misc)   HierarchySaveLink (IMP::rmf)   PathLocalPlanner (IMP::kinematics)   SimpleSaveLink (IMP::rmf)   YAxialPositionLowerRestraint (IMP.pmi.restraints.npc)   
CvEstimator (IMP.isd.TuneRex)   HierarchyTraits (IMP::core)   PbcBoxedMover (IMP::spb)   Simplex (IMP::gsl)   YAxialPositionLowerRestraint (IMP.pmi1.restraints.npc)   
Cylinder3D (IMP::algebra)   HierarchyVisitor (IMP::core)   PbcBoxedRigidBodyMover (IMP::spb)   SimulationData (IMP::npctransport)   YAxialPositionRestraint (IMP.pmi.restraints.npc)   
CylinderGeometry (IMP::display)   HierarchyWithSitesLoadLink (IMP::npctransport)   PCAAligner (IMP::em)   Simulator (IMP::atom)   YAxialPositionRestraint (IMP::npc)   
CylinderRestraint (IMP.pmi.restraints.basic)   HierarchyWithSitesSaveLink (IMP::npctransport)   PCAFitRestraint (IMP::em)   SingleLinkage (IMP::em2d)   YAxialPositionRestraint (IMP.pmi1.restraints.npc)   
CylinderRestraint (IMP.pmi1.restraints.basic)   HighDensityEmbedding (IMP::em)   PCAFitRestraint (IMP::em2d)   SingletonConstraint (IMP::core)   YAxialPositionUpperRestraint (IMP::npc)   
CysteineCrossLinkData (IMP::isd)   HistogramD (IMP::statistics)   PDBRecord (IMP::atom)   SingletonContainer (IMP)   YAxialPositionUpperRestraint (IMP.pmi.restraints.npc)   
CysteineCrossLinkRestraint (IMP::isd)   History (IMP.isd.History)   PDBSelector (IMP::atom)   SingletonContainerAdaptor (IMP)   YAxialPositionUpperRestraint (IMP.pmi1.restraints.npc)   
  D  
HybridMonteCarlo (IMP::isd)   PDBSequences (IMP.pmi.topology)   SingletonContainerSet (IMP::container)   
  Z  
HydrogenPDBSelector (IMP::atom)   PenalizedComplexityPrior (IMP::isd)   SingletonContainerStatistics (IMP::container)   
Database2 (IMP.EMageFit.database)   
  I  
PerinuclearVolumeLocationRestraint (IMP::npc)   SingletonGeometry (IMP::display)   ZAxialPositionLowerRestraint (IMP.pmi.restraints.npc)   
DataEntry (IMP.pmi.output)   PermutationStates (IMP::domino)   SingletonModifier (IMP)   ZAxialPositionLowerRestraint (IMP::npc)   
DataEntry (IMP.pmi1.output)   Image (IMP::em2d)   Pipe (IMP.isd.utils)   SingletonPredicate (IMP)   ZAxialPositionLowerRestraint (IMP.pmi1.restraints.npc)   
DataObject (IMP::core)   ImageHeader (IMP::em)   PivyWriter (IMP::display)   SingletonRestraint (IMP::core)   ZAxialPositionRestraint (IMP.pmi.restraints.npc)   
DataPointsAssignment (IMP::multifit)   ImageReaderWriter (IMP::em2d)   Plane3D (IMP::algebra)   SingletonsConstraint (IMP::container)   ZAxialPositionRestraint (IMP::npc)   
DecayPairContainerOptimizerState (IMP::misc)   IMPRestraints (IMP.modeller)   PlaneDihedralRestraint (IMP.pmi.restraints.stereochemistry)   SingletonScore (IMP)   ZAxialPositionRestraint (IMP.pmi1.restraints.npc)   
Decorator (IMP)   ImproperSingletonScore (IMP::atom)   PlaneDihedralRestraint (IMP.pmi1.restraints.stereochemistry)   SingletonsGeometry (IMP::display)   ZAxialPositionUpperRestraint (IMP::npc)   
DefaultEmbeddingD (IMP::algebra)   InBoundingBox3DSingletonPredicate (IMP::core)   PlaneGeometry (IMP::display)   SingletonsOptimizerState (IMP::container)   ZAxialPositionUpperRestraint (IMP.pmi1.restraints.npc)   
DegreesOfFreedom (IMP.pmi.dof)   InContainerPairFilter (IMP::container)   PMIMoleculeHierarchy (IMP.pmi.topology)   SingletonsRestraint (IMP::container)   ZAxialPositionUpperRestraint (IMP.pmi.restraints.npc)   
DeltaDistributionFunction (IMP::saxs)   InContainerQuadFilter (IMP::container)   PMIMoleculeHierarchy (IMP.pmi1.topology)   SingletonStatistical (IMP::score_functor)   ZBiasSingletonScore (IMP::npctransport)   
Demuxer (IMP.isd.demux_trajs)   InContainerSingletonFilter (IMP::container)   Pointer (IMP)   SitesGeometry (IMP::npctransport)   
  g  
DenseFloatLogGridKD (IMP::algebra)   InContainerTripletFilter (IMP::container)   PointerMember (IMP)   SitesPairScore (IMP::npctransport)   
DenseGrid3D (IMP::algebra)   Index (IMP)   PointGeometry (IMP::display)   SitesPairScoreParameters (IMP::npctransport)   graphNode (IMP.spatiotemporal.graphNode)   
DenseGridStorageD (IMP::algebra)   IndexException (IMP)   PointToSphereDistance (IMP::score_functor)   SkinSurfaceGeometry (IMP::display)   
  s  
DenseIntLogGrid3D (IMP::algebra)   IndexStates (IMP::domino)   PolarResamplingParameters (IMP::em2d)   SlabWithCylindricalPore (IMP::npctransport)   
DensityDataPoints (IMP::multifit)   IndexVector (IMP)   PolygonGeometry (IMP::display)   SlabWithCylindricalPorePairScore (IMP::npctransport)   sfo_common (IMP.isd.shared_functions)   
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