IMP  2.4.0
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  
CysteineCrossLinkRestraint (IMP::isd)   
  I  
ParticleIndexPairsAdaptor (IMP::kernel)   SettingsData (IMP::multifit)   
  D  
ParticleInputs (IMP::kernel)   SGEPESlaveArray (IMP.parallel)   
AddBoolFlag (IMP::base)   Image (IMP::em2d)   ParticleOutputs (IMP::kernel)   SGEQsubSlaveArray (IMP.parallel)   
AddFloatFlag (IMP::base)   Database2 (IMP.EMageFit.database)   ImageHeader (IMP::em)   ParticlesAdaptor (IMP::domino)   Shift (IMP::score_functor)   
AddIntFlag (IMP::base)   DataObject (IMP::core)   ImageReaderWriter (IMP::em2d)   ParticlesDummyRestraint (IMP::em2d)   Showable (IMP::base)   
AddScores (IMP::score_functor)   DataPointsAssignment (IMP::multifit)   IMPRestraints (IMP.modeller)   ParticleStates (IMP::domino)   SigmoidRestraintSphere (IMP::pmi)   
AddStringFlag (IMP::base)   DecayPairContainerOptimizerState (IMP::misc)   ImproperSingletonScore (IMP::atom)   ParticleStatesTable (IMP::domino)   SimpleAssignmentsTable (IMP::domino)   
AdvancedFlag (IMP::base)   Decorator (IMP::kernel)   InBoundingBox3DSingletonPredicate (IMP::core)   PartitionalClustering (IMP::statistics)   SimpleLoadLink (IMP::rmf)   
Alignment (IMP.pmi.analysis)   DefaultEmbeddingD (IMP::algebra)   InContainerPairFilter (IMP::container)   PartitionalClusteringWithCenter (IMP::statistics)   SimpleSaveLink (IMP::rmf)   
AlignmentClustering (IMP.multifit.cluster)   DeltaDistributionFunction (IMP::saxs)   InContainerQuadFilter (IMP::container)   PathLocalPlanner (IMP::kinematics)   Simplex (IMP::gsl)   
AlignSymmetric (IMP::cnmultifit)   Demuxer (IMP.isd.demux_trajs)   InContainerSingletonFilter (IMP::container)   PCAAligner (IMP::em)   Simulator (IMP::atom)   
AllBipartitePairContainer (IMP::container)   DenseFloatLogGridKD (IMP::algebra)   InContainerTripletFilter (IMP::container)   PCAFitRestraint (IMP::em)   SingleLinkage (IMP::em2d)   
AllMol2Selector (IMP::atom)   DenseGrid3D (IMP::algebra)   IncrementalScoringFunction (IMP::core)   PCAFitRestraint (IMP::em2d)   SingletonConstraint (IMP::core)   
AllPairContainer (IMP::container)   DenseGridStorageD (IMP::algebra)   Index (IMP::base)   PDBSelector (IMP::atom)   SingletonContainer (IMP::kernel)   
AllPDBSelector (IMP::atom)   DenseIntLogGrid3D (IMP::algebra)   IndexException (IMP::base)   PermutationStates (IMP::domino)   SingletonContainerAdaptor (IMP::kernel)   
AllSamePairPredicate (IMP::core)   DensityDataPoints (IMP::multifit)   IndexStates (IMP::domino)   Pipe (IMP.isd.utils)   SingletonContainerSet (IMP::container)   
AllSameQuadPredicate (IMP::core)   DensityFillingRestraint (IMP::em)   IndexVector (IMP::base)   PivyWriter (IMP::display)   SingletonContainerStatistics (IMP::container)   
AllSameSingletonPredicate (IMP::core)   DensityHeader (IMP::em)   InitialDockingFromXlinks (IMP.EMageFit.buildxlinks)   Plane3D (IMP::algebra)   SingletonGeometry (IMP::display)   
AllSameTripletPredicate (IMP::core)   DensityMap (IMP::em)   InputAdaptor (IMP::base)   PlaneGeometry (IMP::display)   SingletonModifier (IMP::kernel)   
AmbiguousCompositeRestraint (IMP.pmi.restraints.proteomics)   DependencyScoreState (IMP::domino)   InternalException (IMP::base)   Pointer (IMP::base)   SingletonPredicate (IMP::kernel)   
AmbiguousNOERestraint (IMP::isd)   DerivativeAccumulator (IMP::kernel)   IntsOrder (IMP::em2d)   PointerMember (IMP::base)   SingletonRestraint (IMP::core)   
AmbiguousRestraint (IMP::isd)   DerivativeCalculator (IMP::saxs)   IOException (IMP::base)   PointGeometry (IMP::display)   SingletonsConstraint (IMP::container)   
Analysis (IMP.isd.Analysis)   DerivativesFromRefined (IMP::core)   IsCollisionPairPredicate (IMP::core)   PolarResamplingParameters (IMP::em2d)   SingletonScore (IMP::kernel)   
AnalysisReplicaExchange0 (IMP.pmi.macros)   DerivativesToRefined (IMP::core)   IsosurfaceGeometry (IMP::display)   PolygonGeometry (IMP::display)   SingletonsGeometry (IMP::display)   
AnchorsData (IMP::multifit)   DiameterRestraint (IMP::core)   
  J  
PPDBSelector (IMP::atom)   SingletonsOptimizerState (IMP::container)   
AndPDBSelector (IMP::atom)   Diffusion (IMP::atom)   Precision (IMP.pmi.analysis)   SingletonsRestraint (IMP::container)   
Angle (IMP::atom)   Dihedral (IMP::atom)   JeffreysRestraint (IMP::isd)   PredicatePairsRestraint (IMP::container)   SingletonStatistical (IMP::score_functor)   
AngleRestraint (IMP::core)   DihedralAngleRevoluteJoint (IMP::kinematics)   Joint (IMP::kinematics)   PredicateQuadsRestraint (IMP::container)   SkinSurfaceGeometry (IMP::display)   
AngleSingletonScore (IMP::atom)   DihedralRestraint (IMP::core)   JPGImageReaderWriter (IMP::em2d)   PredicateSingletonScore (IMP::core)   Slave (IMP.parallel)   
AngleTripletScore (IMP::core)   DihedralSingletonScore (IMP::atom)   
  K  
PredicateSingletonsRestraint (IMP::container)   SlaveArray (IMP.parallel)   
AngularVelocity (IMP::atom)   DirectorObjectChecker (IMP.test)   PredicateTripletsRestraint (IMP::container)   Slice (IMP::domino)   
ApplicationTestCase (IMP.test)   DiscreteSampler (IMP::domino)   KClosePairsPairScore (IMP::core)   PrincipalComponentAnalysisD (IMP::algebra)   SmoothingFunction (IMP::atom)   
Array (IMP::base)   DisjointSetsSubsetFilterTable (IMP::domino)   KernelParameters (IMP::em)   PrismaticJoint (IMP::kinematics)   Soap (IMP::score_functor)   
AssemblyHeader (IMP::multifit)   DistanceFilter (IMP::em2d)   Key (IMP::kernel)   ProbabilisticAnchorGraph (IMP::multifit)   SoapPairFilter (IMP::atom)   
Assignment (IMP::domino)   DistanceFilterTable (IMP::em2d)   KinematicForest (IMP::kinematics)   ProbabilisticSubsetFilterTable (IMP::domino)   SoftCylinderPairScore (IMP::misc)   
AssignmentContainer (IMP::domino)   DistanceMask (IMP::em)   KinematicForestScoreState (IMP::kinematics)   ProcessOutput (IMP.pmi.output)   SoftSpherePairScore (IMP::core)   
AssignmentsTable (IMP::domino)   DistancePairScore (IMP::core)   KinematicNode (IMP::kinematics)   Profile (IMP::saxs)   SolventAccessibleSurface (IMP::saxs)   
Atom (IMP::atom)   DistancePairScore (IMP::score_functor)   KMeans (IMP::kmeans)   ProfileClustering (IMP::saxs)   SparseGrid3D (IMP::algebra)   
AtomicCrossLinkMSRestraint (IMP::isd)   DistanceRestraint (IMP::core)   
  L  
ProfileFitter (IMP::saxs)   SparseGridStorageD (IMP::algebra)   
ATOMPDBSelector (IMP::atom)   DistributePairsScoreState (IMP::container)   Profiler (IMP::benchmark)   SparseSymmetricPairMemoizer (IMP::base)   
AtomType (IMP::atom)   DistributeQuadsScoreState (IMP::container)   LabelGeometry (IMP::display)   ProjectingOptions (IMP::em2d)   SparseUnboundedGrid3D (IMP::algebra)   
AttributeOptimizer (IMP::kernel)   DistributeSingletonsScoreState (IMP::container)   LangevinThermostatOptimizerState (IMP::atom)   ProjectingParameters (IMP::em2d)   SparseUnboundedGridD (IMP::algebra)   
AttributeSingletonPredicate (IMP::core)   DistributeTripletsScoreState (IMP::container)   LeavesRefiner (IMP::core)   ProjectionFinder (IMP::em2d)   SphereD (IMP::algebra)   
AverageDistanceLinkage (IMP::em2d)   Distribution (IMP::saxs)   LennardJones (IMP::atom)   ProjectionMask (IMP::em2d)   SphereDistance (IMP::score_functor)   
  B  
DockOrder (IMP.EMageFit.buildxlinks)   LennardJonesPairScore (IMP::atom)   ProjectionParameters (IMP::em2d)   SphereDistancePairScore (IMP::core)   
DOF (IMP::kinematics)   LessPairBySecond (IMP::em2d)   ProjectionParametersScoreState (IMP::em2d)   SphereDistanceToSingletonScore (IMP::core)   
BackbonePDBSelector (IMP::atom)   DOFsSampler (IMP::kinematics)   Linear (IMP::core)   ProjectionStates (IMP::em2d)   SphereGeometry (IMP::display)   
BallMover (IMP::core)   Domain (IMP::atom)   Linear1DFunction (IMP::isd)   ProteinKinematics (IMP::kinematics)   SpherePatch3D (IMP::algebra)   
BallMover (IMP::symmetry)   DominoModel (IMP.EMageFit.domino_model)   LinearFit2D (IMP::algebra)   ProteinLigandAtomPairScore (IMP::atom)   SphericalVector3D (IMP::algebra)   
BerendsenThermostatOptimizerState (IMP::atom)   DominoSampler (IMP::domino)   LinearLowerBound (IMP::score_functor)   ProteinLigandRestraint (IMP::atom)   SpiderHeader (IMP::em)   
BinormalTerm (IMP::modeller)   Dope (IMP::score_functor)   LinearVelocity (IMP::atom)   ProteinsAnchorsSamplingSpace (IMP::multifit)   SpiderImageReaderWriter (IMP::em2d)   
BivariateFunction (IMP::isd)   DopePairScore (IMP::atom)   ListAssignmentContainer (IMP::domino)   ProteomicsData (IMP::multifit)   SpiderMapReaderWriter (IMP::em)   
Bond (IMP::atom)   DummyRestraint (IMP::em2d)   ListAssignmentsTable (IMP::domino)   ProteomicsEMAlignmentAtomic (IMP::multifit)   State (IMP::atom)   
ForceFieldParameters::Bond (IMP::atom)   DummyRestraint (IMP::multifit)   ListPairContainer (IMP::container)   PseudoAtomicRestraint (IMP.pmi.restraints.stereochemistry)   StateAdaptor (IMP::misc)   
BondAngleRevoluteJoint (IMP::kinematics)   DynamicListPairContainer (IMP::container)   ListQuadContainer (IMP::container)   PymolWriter (IMP::display)   Statistical (IMP::score_functor)   
Bonded (IMP::atom)   DynamicListQuadContainer (IMP::container)   ListSingletonContainer (IMP::container)   PythonDirectedGraph (IMP::kernel)   StatisticalPairScore (IMP::core)   
BondedPairFilter (IMP::atom)   DynamicListSingletonContainer (IMP::container)   ListSubsetFilterTable (IMP::domino)   
  Q  
Statistics (IMP.isd.Statistics)   
BondEndpointsRefiner (IMP::atom)   DynamicListTripletContainer (IMP::container)   ListTripletContainer (IMP::container)   SteepestDescent (IMP::core)   
BondGeometry (IMP::atom)   DynamicNearestNeighbor3D (IMP::algebra)   LoadLink (IMP::rmf)   QuadConstraint (IMP::core)   StereochemistryPairFilter (IMP::atom)   
BondGraph (IMP::atom)   
  E  
LocalPlanner (IMP::kinematics)   QuadContainer (IMP::kernel)   Subsequence (IMP.pmi.io)   
BondPairContainer (IMP::atom)   LocalSlave (IMP.parallel)   QuadContainerAdaptor (IMP::kernel)   SubsequenceData (IMP.pmi.io)   
BondsGeometry (IMP::atom)   EdgePairGeometry (IMP::core)   LogEmbeddingD (IMP::algebra)   QuadContainerSet (IMP::container)   Subset (IMP::domino)   
BondSingletonScore (IMP::atom)   EdgePairsGeometry (IMP::core)   LogHolder (IMP.isd.demux_trajs)   QuadContainerStatistics (IMP::container)   SubsetFilter (IMP::domino)   
BoundedGridRangeD (IMP::algebra)   ElasticNetworkRestraint (IMP.pmi.restraints.stereochemistry)   LognormalRestraint (IMP::isd)   QuadModifier (IMP::kernel)   SubsetFilterTable (IMP::domino)   
BoundingBoxD (IMP::algebra)   ElementTable (IMP::atom)   LogPairScore (IMP::misc)   QuadPredicate (IMP::kernel)   SurfaceMeshGeometry (IMP::display)   
BoundingBoxGeometry (IMP::display)   Ellipsoid3D (IMP::algebra)   LogWrapper (IMP::isd)   QuadraticClosePairsFinder (IMP::core)   SurfaceShellDensityMap (IMP::em)   
BoxSweepClosePairsFinder (IMP::core)   EllipsoidGeometry (IMP::display)   LowestRefinedPairScore (IMP::misc)   QuadRestraint (IMP::core)   Switching (IMP::isd)   
BranchAndBoundAssignmentsTable (IMP::domino)   Em2DRestraint (IMP::em2d)   LRUCache (IMP::base)   QuadsConstraint (IMP::container)   Symmetric (IMP::pmi)   
BranchAndBoundSampler (IMP::domino)   Em2DRestraintParameters (IMP::em2d)   
  M  
QuadScore (IMP::kernel)   System (IMP.pmi.topology)   
BrownianDynamics (IMP::atom)   EM2DScore (IMP::em2d)   QuadsOptimizerState (IMP::container)   SystemBase (IMP.pmi.topology)   
BuildModel (IMP.pmi.macros)   Embedding (IMP::statistics)   Manager (IMP.parallel)   QuadsRestraint (IMP::container)   
  T  
BuildModel1 (IMP.pmi.macros)   EMReaderWriter (IMP::em)   MapDistanceTransform (IMP::em)   QuasiNewton (IMP::gsl)   
  C  
Ensemble (IMP::multifit)   MapReaderWriter (IMP::em)   
  R  
TableRefiner (IMP::core)   
Entry (IMP.isd.Entry)   MarginalHBondRestraint (IMP::isd)   TALOSReader (IMP.isd.TALOSReader)   
CAlphaPDBSelector (IMP::atom)   EnvelopeFitRestraint (IMP::em)   MarginalNOERestraint (IMP::isd)   RadialDistributionFunction (IMP::saxs)   TALOSRestraint (IMP::isd)   
CappedAssignmentContainer (IMP::domino)   EnvelopePenetrationRestraint (IMP::em)   MasksManager (IMP::em2d)   RadiusDependentDistanceMask (IMP::em)   TempDir (IMP.test)   
CBetaPDBSelector (IMP::atom)   EnvelopeScore (IMP::em)   Mass (IMP::atom)   RadiusDependentKernelParameters (IMP::em)   TestCase (IMP.test)   
CenteredMat (IMP::em2d)   EqualitySubsetFilterTable (IMP::domino)   MasterCommunicator (IMP.parallel.master_communicator)   RadiusOfGyrationRestraint (IMP::multifit)   TextInput (IMP::base)   
CenterOfMass (IMP::atom)   EquivalenceAndExclusionSubsetFilterTable (IMP::domino)   MatchTemplateResult (IMP::em2d)   RadiusOfGyrationRestraint (IMP::saxs)   TextOutput (IMP::base)   
Centroid (IMP::core)   EquivalenceSubsetFilterTable (IMP::domino)   MaxVectorKDMetric (IMP::algebra)   RAII (IMP::base)   TextWriter (IMP::display)   
CentroidOfRefined (IMP::core)   Error (IMP.parallel)   MCCGSampler (IMP::core)   RangeViewAssignmentContainer (IMP::domino)   TIFFImageReaderWriter (IMP::em2d)   
Chain (IMP::atom)   EuclideanMetric (IMP::statistics)   MeanAbsoluteDifference (IMP::em2d)   ReadAssignmentContainer (IMP::domino)   Timer (IMP::base)   
ChainPDBSelector (IMP::atom)   EuclideanVectorKDMetric (IMP::algebra)   Memoizer (IMP::base)   ReadHDF5AssignmentContainer (IMP::domino)   TopologyPlot (IMP.pmi.plotting.topology)   
Charged (IMP::atom)   EvaluationState (IMP::kernel)   MergeTreeBuilder (IMP::multifit)   RecursiveAssignmentsTable (IMP::domino)   TopologyReader (IMP.pmi.topology)   
CHARMMAtom (IMP::atom)   EventException (IMP::base)   Metric (IMP::statistics)   RecursivePartitionalClusteringEmbedding (IMP::statistics)   Transform (IMP::core)   
CHARMMAtomTopology (IMP::atom)   EventPairsOptimizerState (IMP::container)   MetricClosePairsFinder (IMP::misc)   RecursivePartitionalClusteringMetric (IMP::statistics)   Transformation2D (IMP::algebra)   
CHARMMBondEndpoint (IMP::atom)   EventQuadsOptimizerState (IMP::container)   MinimumPairRestraint (IMP::container)   RecursiveStates (IMP::domino)   Transformation3D (IMP::algebra)   
CHARMMBondParameters (IMP::atom)   EventSingletonsOptimizerState (IMP::container)   MinimumPairScore (IMP::container)   RefCountChecker (IMP.test)   Transformation3DToText (IMP.EMageFit.imp_general.io)   
CHARMMConnection (IMP::atom)   EventTripletsOptimizerState (IMP::container)   MinimumQuadRestraint (IMP::container)   Reference (IMP::core)   TransformationAndReflectionSymmetry (IMP::core)   
CHARMMDihedralParameters (IMP::atom)   ExampleComplexRestraint (IMP::example)   MinimumQuadScore (IMP::container)   ReferenceFrame3D (IMP::algebra)   TransformationJoint (IMP::kinematics)   
CharmmForceFieldRestraint (IMP.pmi.restraints.stereochemistry)   ExampleConstraint (IMP::example)   MinimumRestraint (IMP::core)   ReferenceFrameGeometry (IMP::display)   TransformationSymmetry (IMP::core)   
CharmmForceFieldRestraint (IMP.pmi.restraints_new.stereochemistry)   ExampleDecorator (IMP::example)   MinimumRestraintScoreSubsetFilterTable (IMP::domino)   ReferenceFrameToText (IMP.EMageFit.imp_general.io)   TransformedDistancePairScore (IMP::core)   
CHARMMIdealResidueTopology (IMP::atom)   ExampleObject (IMP::example)   MinimumSingletonRestraint (IMP::container)   RefinedPairsPairScore (IMP::core)   TransformMover (IMP::pmi)   
CHARMMInternalCoordinate (IMP::atom)   ExamplePairScore (IMP::example)   MinimumSingletonScore (IMP::container)   Refiner (IMP::kernel)   Triangle3D (IMP::algebra)   
CHARMMParameters (IMP::atom)   ExampleRestraint (IMP::example)   MinimumTripletRestraint (IMP::container)   Reflection3D (IMP::algebra)   TriangleGeometry (IMP::display)   
CHARMMPatch (IMP::atom)   ExampleSingletonModifier (IMP::example)   MinimumTripletScore (IMP::container)   RegistrationResult (IMP::em2d)   TripletConstraint (IMP::core)   
CHARMMResidueTopology (IMP::atom)   ExampleSubsetFilterTable (IMP::example)   Model (IMP::kernel)   RelativePositionMover (IMP::em2d)   TripletContainer (IMP::kernel)   
CHARMMResidueTopologyBase (IMP::atom)   ExampleTemplateClassD (IMP::example)   ModelException (IMP::base)   RemoteError (IMP.parallel)   TripletContainerAdaptor (IMP::kernel)   
CHARMMSegmentTopology (IMP::atom)   ExampleUnaryFunction (IMP::example)   ModellerRestraints (IMP.modeller)   RemoveRigidMotionOptimizerState (IMP::atom)   TripletContainerSet (IMP::container)   
CHARMMStereochemistryRestraint (IMP::atom)   Exception (IMP::base)   ModelLoader (IMP.modeller)   RemoveTranslationOptimizerState (IMP::atom)   TripletContainerStatistics (IMP::container)   
CHARMMTopology (IMP::atom)   ExcludedVolumeRestraint (IMP::core)   ModelObject (IMP::kernel)   ReplicaExchange (IMP.pmi.samplers)   TripletModifier (IMP::kernel)   
ChecksScoreState (IMP::core)   ExcludedVolumeSphere (IMP.pmi.restraints.stereochemistry)   ModifierVisitor (IMP::core)   ReplicaExchange (IMP::mpi)   TripletPredicate (IMP::kernel)   
ChiFreeScore (IMP::saxs)   ExclusionSubsetFilterTable (IMP::domino)   Mol2Selector (IMP::atom)   ReplicaExchange0 (IMP.pmi.macros)   TripletRestraint (IMP::core)   
ChildrenRefiner (IMP::core)   ExclusiveConsecutivePairContainer (IMP::container)   MolCnSymmAxisDetector (IMP::cnmultifit)   Representation (IMP.pmi.representation)   TripletsConstraint (IMP::container)   
ChimeraWriter (IMP::display)   ExclusiveConsecutivePairFilter (IMP::container)   MolecularDynamics (IMP::atom)   Representation (IMP::atom)   TripletScore (IMP::kernel)   
ChiScore (IMP::saxs)   ExtendedGridIndexD (IMP::algebra)   MolecularDynamics (IMP.pmi.samplers)   RepulsiveDistancePairScore (IMP::isd)   TripletsOptimizerState (IMP::container)   
ChiScoreLog (IMP::saxs)   EzRestraint (IMP::atom)   MolecularDynamics (IMP::isd)   Residue (IMP::atom)   TripletsRestraint (IMP::container)   
ChiSquaredScore (IMP::em2d)   
  F  
MolecularDynamicsMover (IMP::isd)   ResidueAngleRestraint (IMP.pmi.restraints.stereochemistry)   TruncatedHarmonic (IMP::core)   
ChiSquareMetric (IMP::statistics)   Molecule (IMP::atom)   ResidueBondRestraint (IMP.pmi.restraints.stereochemistry)   Typed (IMP::core)   
CloseBipartitePairContainer (IMP::container)   FFTFitting (IMP::multifit)   MonteCarlo (IMP.pmi.samplers)   ResidueDihedralRestraint (IMP.pmi.restraints.stereochemistry)   TypedPairScore (IMP::core)   
ClosedCubicSpline (IMP::core)   FFTFittingOutput (IMP::multifit)   MonteCarlo (IMP::core)   ResidueRotamer (IMP::rotamer)   
  U  
ClosePairContainer (IMP::container)   FilterGeometry (IMP::display)   MonteCarloMover (IMP::core)   ResidueType (IMP::atom)   
ClosePairsFinder (IMP::core)   Fine2DRegistrationRestraint (IMP::em2d)   MonteCarloMoverResult (IMP::core)   Resolution (IMP::pmi)   UnaryFunction (IMP::kernel)   
ClosePairsPairScore (IMP::core)   FitRestraint (IMP::em)   MonteCarloRelativeMoves (IMP.EMageFit.monte_carlo)   Restraint (IMP::kernel)   UnaryFunctionEvaluate (IMP::score_functor)   
Clustering (IMP.pmi.analysis)   FittingSolutionRecord (IMP::multifit)   MonteCarloWithBasinHopping (IMP::core)   Restraint (IMP::saxs)   UnboundedGridRangeD (IMP::algebra)   
ClusterSet (IMP::em2d)   FittingSolutions (IMP::em)   MonteCarloWithLocalOptimization (IMP::core)   RestraintCache (IMP::domino)   Uncertainty (IMP::pmi)   
CnSymmAxisDetector (IMP::cnmultifit)   FittingStates (IMP::multifit)   MoveStatisticsScoreState (IMP::core)   RestraintGeometry (IMP::display)   UncheckedWeakPointer (IMP::base)   
CoarseCARestraint (IMP.pmi.restraints_new.stereochemistry)   FixedRefiner (IMP::core)   MRCReaderWriter (IMP::em)   RestraintsAdaptor (IMP::kernel)   Undecorator (IMP::kernel)   
CoarseCC (IMP::em)   FixedXYZ (IMP::algebra)   MSConnectivityRestraint (IMP::core)   RestraintScoreSubsetFilterTable (IMP::domino)   UniformBackboneSampler (IMP::kinematics)   
CoarseCCatIntervals (IMP::em)   Flag (IMP::base)   MultipleBinormalRestraint (IMP::modeller)   RestraintSet (IMP::kernel)   UniformPrior (IMP::isd)   
CoarseConvolution (IMP::em)   FloatIndex (IMP::kernel)   MultivariateFNormalSufficient (IMP::isd)   RestraintSetGeometry (IMP::display)   UnivariateFunction (IMP::isd)   
CoinFlipPairPredicate (IMP::core)   FNormal (IMP::isd)   MyMetric (write_a_metric)   RestraintsScoringFunction (IMP::core)   UnorderedTypePairPredicate (IMP::core)   
CoinFlipQuadPredicate (IMP::core)   ForceFieldParameters (IMP::atom)   
  N  
ResultsDB (IMP.EMageFit.solutions_io)   UnorderedTypeQuadPredicate (IMP::core)   
CoinFlipSingletonPredicate (IMP::core)   ForceSwitch (IMP::atom)   RevoluteJoint (IMP::kinematics)   UnorderedTypeSingletonPredicate (IMP::core)   
CoinFlipTripletPredicate (IMP::core)   FormFactorTable (IMP::saxs)   NearestNeighborD (IMP::algebra)   RigidBodiesImageFitRestraint (IMP::em2d)   UnorderedTypeTripletPredicate (IMP::core)   
CollisionCrossSection (IMP::em2d)   Fragment (IMP::atom)   NearestNeighborsClosePairsFinder (IMP::core)   RigidBodiesProfileHandler (IMP::saxs)   UsageException (IMP::base)   
Color (IMP::display)   FretData (IMP::isd)   NeighborsTable (IMP::core)   RigidBody (IMP::core)   
  V  
ColorChange (IMP.pmi.tools)   FretRestraint (IMP::isd)   NestedRigidBodyStates (IMP::domino)   RigidBodyDerivativeGeometry (IMP::core)   
Colored (IMP::display)   
  G  
NetworkError (IMP.parallel)   RigidBodyDerivativesGeometry (IMP::core)   Value (IMP::base)   
CommandDispatcher (IMP.kernel)   NOERestraint (IMP::isd)   RigidBodyDiffusion (IMP::atom)   ValueException (IMP::base)   
CommonEndpointPairFilter (IMP::misc)   Gaussian (IMP::core)   NoMoreSlavesError (IMP.parallel)   RigidBodyDistancePairScore (IMP::core)   Vector (IMP::base)   
ComplementarityRestraint (IMP::multifit)   Gaussian3D (IMP::algebra)   NonAlternativePDBSelector (IMP::atom)   RigidBodyFrameGeometry (IMP::core)   VectorBaseD (IMP::algebra)   
CompleteLinkage (IMP::em2d)   GaussianEMRestraint (IMP::isd)   NonCopyable (IMP::base)   RigidBodyFramesGeometry (IMP::core)   VectorD (IMP::algebra)   
ComponentHeader (IMP::multifit)   GaussianProcessInterpolation (IMP::isd)   NonHydrogenMol2Selector (IMP::atom)   RigidBodyHierarchyGeometry (IMP::core)   VectorDEmbedding (IMP::statistics)   
ComponentTopology (IMP.pmi.topology)   GaussianProcessInterpolationRestraint (IMP::isd)   NonRigidMember (IMP::core)   RigidBodyMember (IMP::core)   VectorKDMetric (IMP::algebra)   
CompositeJoint (IMP::kinematics)   GaussianRestraint (IMP::isd)   NonWaterNonHydrogenPDBSelector (IMP::atom)   RigidBodyMover (IMP::symmetry)   VelocityScalingOptimizerState (IMP::atom)   
CompositeRestraint (IMP.pmi.restraints.proteomics)   GeneralizedGuinierPorodFunction (IMP::isd)   NonWaterPDBSelector (IMP::atom)   RigidBodyMover (IMP::core)   VersionInfo (IMP::base)   
CompositeRestraint (IMP::pmi)   GenericAttributeSingletonScore (IMP::core)   NormalizedSphereDistancePairScore (IMP::core)   RigidBodyStates (IMP::domino)   VolumeRestraint (IMP::core)   
CompoundStates (IMP::domino)   GenericBoundingBox3DSingletonScore (IMP::core)   NormalMover (IMP::core)   RigidBodyTorque (IMP::core)   Voxel (IMP::em)   
Cone3D (IMP::algebra)   GenericDistanceToSingletonScore (IMP::core)   NotPDBSelector (IMP::atom)   RigidBodyTunneler (IMP::core)   
  W  
Configuration (IMP::kernel)   GeometricHash (IMP::multifit)   NPDBSelector (IMP::atom)   RigidBodyUmbrella (IMP::core)   
ConfigurationSet (IMP::kernel)   GeometricPrimitiveD (IMP::algebra)   Nuisance (IMP::isd)   RigidClosePairsFinder (IMP::core)   WarningContext (IMP::base)   
ConfigurationSetRMSDMetric (IMP::statistics)   Geometry (IMP::display)   
  O  
RigidMember (IMP::core)   WaterPDBSelector (IMP::atom)   
ConfigurationSetXYZEmbedding (IMP::statistics)   GeometryProcessor (IMP::display)   RotamerAngleTuple (IMP::rotamer)   WeakPointer (IMP::base)   
ConjugateGradients (IMP.pmi.samplers)   GeometrySet (IMP::display)   Object (IMP::base)   RotamerCalculator (IMP::rotamer)   Weight (IMP::isd)   
ConjugateGradients (IMP::gsl)   GetModelDensity (IMP.pmi.analysis)   OpenCubicSpline (IMP::core)   RotamerLibrary (IMP::rotamer)   WeightedDerivativesToRefined (IMP::core)   
ConjugateGradients (IMP::core)   GridClosePairsFinder (IMP::core)   OpenCubicSpline (IMP::score_functor)   Rotation2D (IMP::algebra)   WeightedExcludedVolumeRestraint (IMP::multifit)   
ConnectingPairContainer (IMP::container)   GridD (IMP::algebra)   Optimizer (IMP::kernel)   Rotation3D (IMP::algebra)   WeightedProfileFitter (IMP::saxs)   
ConnectivityCrossLinkMS (IMP.pmi.restraints.crosslinking)   GridIndexD (IMP::algebra)   OptimizerState (IMP::kernel)   RRT (IMP::kinematics)   WeightedSphereDistancePairScore (IMP::core)   
ConnectivityRestraint (IMP.pmi.restraints.proteomics)   GridStates (IMP::em2d)   OptionParser (IMP.kernel)   RunInTempDir (IMP.test)   WeightMover (IMP::isd)   
ConnectivityRestraint (IMP::core)   GSLOptimizer (IMP::gsl)   Order (IMP::domino)   
  S  
WeightRestraint (IMP::isd)   
ConnollySurfacePoint (IMP::algebra)   
  H  
OrderedTypePairPredicate (IMP::core)   WeightScore (IMP::score_functor)   
ConsecutivePairContainer (IMP::container)   OrderedTypeQuadPredicate (IMP::core)   SameResiduePairFilter (IMP::atom)   WormLikeChain (IMP::misc)   
ConsecutivePairFilter (IMP::container)   Harmonic (IMP::core)   OrderedTypeSingletonPredicate (IMP::core)   SampleAssignmentContainer (IMP::domino)   WriteAssignmentContainer (IMP::domino)   
ConstantPairPredicate (IMP::core)   Harmonic (IMP::score_functor)   OrderedTypeTripletPredicate (IMP::core)   SampledDensityMap (IMP::em)   WriteHDF5AssignmentContainer (IMP::domino)   
ConstantQuadPredicate (IMP::core)   HarmonicDistancePairScore (IMP::core)   OrientedSoap (IMP::score_functor)   SampleObjects (IMP.pmi.sampling_tools)   WriteOptimizerState (IMP::display)   
ConstantRestraint (IMP::core)   HarmonicLowerBound (IMP::core)   OrientedSoapPairScore (IMP::atom)   Sampler (IMP::kernel)   WritePDBOptimizerState (IMP::atom)   
ConstantSingletonPredicate (IMP::core)   HarmonicLowerBound (IMP::score_functor)   OrPDBSelector (IMP::atom)   SaveLink (IMP::rmf)   Writer (IMP::display)   
ConstantTripletPredicate (IMP::core)   HarmonicSphereDistancePairScore (IMP::core)   Output (IMP.pmi.output)   SaveOptimizerState (IMP::rmf)   WriterAdaptor (IMP::display)   
Constraint (IMP::kernel)   HarmonicUpperBound (IMP::core)   
  P  
SaveToConfigurationSetOptimizerState (IMP::kernel)   WriteRestraintScoresOptimizerState (IMP::core)   
ConstVector (IMP::base)   HarmonicUpperBound (IMP::score_functor)   SAXSMultiStateModelScore (IMP::multi_state)   
  X  
Container (IMP::kernel)   HarmonicUpperBoundSphereDiameterPairScore (IMP::core)   PackedAssignmentContainer (IMP::domino)   Scale (IMP::isd)   
Context (IMP.parallel)   HarmonicUpperBoundSphereDistancePairScore (IMP::core)   PairConstraint (IMP::core)   ScopedAddCacheAttribute (IMP::kernel)   Xlink (IMP.EMageFit.buildxlinks)   
Copy (IMP::atom)   HarmonicWell (IMP::core)   PairContainer (IMP::kernel)   ScopedSetAttribute (IMP::kernel)   XlinksDict (IMP.EMageFit.buildxlinks)   
Cosine (IMP::core)   HasHigherCCC (IMP::em2d)   PairContainerAdaptor (IMP::kernel)   Score (IMP::score_functor)   XplorReaderWriter (IMP::em)   
CoulombPairScore (IMP::atom)   HasLowerScore (IMP::em2d)   PairContainerSet (IMP::container)   ScoreAccumulator (IMP::kernel)   XYZ (IMP::core)   
Covariance1DFunction (IMP::isd)   HeapAssignmentContainer (IMP::domino)   PairContainerStatistics (IMP::container)   ScoreFunction (IMP::em2d)   XYZDerivativeGeometry (IMP::core)   
Cover (IMP::core)   HeapRecord (IMP.EMageFit.solutions_io)   PairGeometry (IMP::display)   ScoreState (IMP::kernel)   XYZDerivativesGeometry (IMP::core)   
CoverBond (IMP::atom)   HierarchiesGeometry (IMP::atom)   PairListSubsetFilterTable (IMP::domino)   ScoreUnaryFunction (IMP::score_functor)   XYZR (IMP::core)   
CoverRefined (IMP::core)   Hierarchy (IMP::core)   PairModifier (IMP::kernel)   ScoringFunction (IMP::kernel)   XYZRGeometry (IMP::core)   
CPDBSelector (IMP::atom)   Hierarchy (IMP::atom)   PairPredicate (IMP::kernel)   ScoringFunctionAdaptor (IMP::kernel)   XYZRsGeometry (IMP::core)   
CreateLogContext (IMP::base)   HierarchyCounter (IMP::core)   PairRestraint (IMP::core)   SecondaryStructureResidue (IMP::atom)   XYZStates (IMP::domino)   
CrossLink (IMP.pmi.io)   HierarchyDatabase (IMP.pmi.tools)   PairsConstraint (IMP::container)   Segment3D (IMP::algebra)   
  d  
CrossLinkData (IMP.pmi.io)   HierarchyGeometry (IMP::atom)   PairScore (IMP::kernel)   SegmentationParameters (IMP::em2d)   
CrossLinkData (IMP::isd)   HierarchyLoadLink (IMP::rmf)   PairsGeometry (IMP::display)   SegmentGeometry (IMP::display)   dof (IMP.pmi.dof)   
CrossLinkMS (IMP.pmi.nonmantained)   HierarchySaveLink (IMP::rmf)   PairsOptimizerState (IMP::container)   Selection (IMP::atom)   
  m  
CrossLinkMSRestraint (IMP::isd)   HierarchyTraits (IMP::core)   PairsRestraint (IMP::container)   SelectionGeometry (IMP::atom)   
CrossLinkTable (IMP.pmi.analysis)   HierarchyVisitor (IMP::core)   ParabolicFit2D (IMP::algebra)   Sequences (IMP.pmi.topology)   map (IMP::base)   
CustomXYZR (IMP::misc)   HighDensityEmbedding (IMP::em)   Particle (IMP::kernel)   SerialMover (IMP::core)   
  p  
CvEstimator (IMP.isd.TuneRex)   HistogramD (IMP::statistics)   ParticleAdaptor (IMP::kernel)   SetCheckState (IMP::base)   
Cylinder3D (IMP::algebra)   History (IMP.isd.History)   ParticleEmbedding (IMP::statistics)   SetLogState (IMP::base)   piecewise_linear_distribution (IMP::base)   
CylinderGeometry (IMP::display)   HybridMonteCarlo (IMP::isd)   ParticleIndexAdaptor (IMP::kernel)   SetLogTarget (IMP::base)   
  s  
CysteineCrossLinkData (IMP::isd)   HydrogenPDBSelector (IMP::atom)   ParticleIndexesAdaptor (IMP::kernel)   SetNumberOfThreads (IMP::base)   
set (IMP::base)   
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