IMP  2.0.0
The Integrative Modeling Platform
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 12345678]
oCIMP.isd.AbstractGrid.AbstractGridGrid main functionality: manage services
oCIMP.isd.AbstractGrid.AbstractServiceWrapper around Grid services, facilitating non parameter-specific usage of the remote objects
oCIMP::base::AddBoolFlag
oCIMP::base::AddFloatFlag
oCIMP::base::AddIntFlag
oCIMP::base::AddStringFlag
oCIMP.multifit.cluster.AlignmentClusteringClusters assembly models
oCIMP::cnmultifit::AlignSymmetricA class for fast alignment of a cyclic model to its density
oCIMP.isd.Analysis.AnalysisClass that produces analysis-related output, and is able to parse the output of a file produced by the Statistics class
oCIMP::atom::AtomTypeThe type of an atom
oCIMP::modeller::BinormalTermA single binormal term in a MultipleBinormalRestraint
oCIMP::atom::BondGraphRepresent a bond graph as a boost graph
oCIMP::algebra::BoundedGridRangeD< D >
oCIMP::algebra::BoundedGridRangeD< 3 >
oCIMP::algebra::BoundingBoxD< D >An axis-aligned bounding box
oCIMP::algebra::BoundingBoxD< 3 >
oCIMP::em2d::CenteredMat
oCIMP::atom::CHARMMAtomTopologyA single atom in a CHARMM topology
oCIMP::atom::CHARMMBondEndpointThe end of a bond, angle, dihedral, improper, or internal coordinate
oCIMP::atom::CHARMMBondParametersThe parameters for a CHARMM bond or angle
oCIMP::atom::CHARMMConnection< D >A connection (bond, angle, dihedral) between some number of endpoints
oCIMP::atom::CHARMMConnection< 4 >
oCIMP::atom::CHARMMDihedralParametersThe parameters for a CHARMM dihedral or improper
oCIMP.em2d.solutions_io.ClusterRecordSimple named tuple class
oCIMP::em::CoarseConvolutionConvolutes two grids
oCIMP.kernel.CommandDispatcherAllow applications to easily implement commmands
oCIMP.parallel.ContextA collection of tasks that run in the same environment
oCIMP.isd.TuneRex.CvEstimatorWhen created, estimates the heat capacity from the energies or from the indicator functions using the specified method
oCIMP.em2d.Database.Database2Class to manage a SQL database built with sqlite3
oCIMP::multifit::DataPointsAssignment
oCIMP::algebra::DefaultEmbeddingD< D >
oCIMP::algebra::DefaultEmbeddingD< 3 >
oCIMP::multifit::DensityDataPointsStores density voxels as a vector of Array1D
oCIMP::em::DensityHeader
oCIMP::kernel::DerivativeAccumulatorClass for adding derivatives from restraints to the model
oCIMP::core::DerivativesFromRefinedAccumulate the derivatives of the refined particles
oCIMP::core::DerivativesToRefinedCopy the derivatives from the particle to its refined particles
oCIMP.test.DirectorObjectCheckerCheck to make sure the number of director references is as expected
oCIMP.restrainer._display.DisplayStore Display
oCIMP::em::DistanceMaskCalculates and stores a distance mask
oCIMP.em2d.buildxlinks.DockOrderCompute the order of the docking experiments
oCIMP.em2d.DominoModel.DominoModelManagement of a model using DOMINO
oCIMP::atom::ElementTable
oCIMP.isd.Entry.EntryThe entry class represents a column in the statistics file
oCIMP.parallel.ErrorBase class for all errors specific to the parallel module
oCIMP::kernel::EvaluationState
oCIMP::example::ExampleTemplateClassD< D >A line segment templated on the dimension
oCIMP::base::ExceptionThe general base class for IMP exceptions
oCIMP.isd.FIFOBasedGrid.FIFOBasedRemoteObjectFilebased proxy instance
oCIMP.isd.FileBasedGrid.FileBasedRemoteObjectFilebased proxy instance
oCIMP::multifit::FittingSolutionRecordA fitting solution record
oCIMP::em::FittingSolutionsA simple list of fitting solutions
oCIMP::saxs::FormFactorTable
oCIMP::algebra::GeometricPrimitiveD< D >
oCIMP::algebra::GeometricPrimitiveD< 2 >
oCIMP::algebra::GeometricPrimitiveD< 3 >
oCIMP::display::GeometryProcessorProvide a standard geometry processing framework
oCIMP::em2d::HasHigherCCC< T >Comparison by value of the ccc
oCIMP::em2d::HasLowerScore< T >Compare two classes that return a score
oCIMP.em2d.solutions_io.HeapRecordThe heapq algorithm is a min-heap
oCIMP::core::HierarchyTraitsDefine the type for a type of hierarchy
oCIMP::core::HierarchyVisitorA visitor for traversal of a hierarchy
oCIMP::statistics::HistogramHistogram
oCIMP.isd.History.HistoryClass that contains the output of one replica, used by the Analysis class
oCIMP::em::ImageHeaderClass to deal with the header of Electron Microsocopy images in IMP
oCIMP.modeller.IMPRestraintsA Modeller restraint which evaluates all defined IMP restraints
oCIMP.em2d.buildxlinks.InitialDockingFromXlinksPuts two subunits together using the Xlinkins restraints
oCIMP::base::InputAdaptor
oCIMP::base::InternalExceptionA general exception for an intenal error in IMP
oCIMP::em2d::JPGImageReaderWriterClass to read and write EM images in JPG format
oCIMP::em::KernelParameters
oCIMP::em2d::LessPairBySecond< T >Comparison of pairs by checking the second element
oCIMP::algebra::LogEmbeddingD< D >
oCIMP::base::LRUCache< Generator, Checker >
oCIMP::base::LRUCache< Generator, ApproximatelyEqual >
oCIMP.parallel.ManagerManages slaves and contexts
oCIMP::base::map< Key, Data >
oCIMP::base::map< base::Object *, Statistics >
oCIMP::base::map< const IMP::kernel::Particle *, int >
oCIMP::base::map< core::RigidBody, Particles >
oCIMP::base::map< DGVertex, Particle * >
oCIMP::base::map< Element, std::string >
oCIMP::base::map< GridIndexD< D >, Ints >
oCIMP::base::map< GridIndexD< D >, VT >
oCIMP::base::map< IMP::base::Array, unsigned int >
oCIMP::base::map< IMP::base::Array, Vector< IntPair > >
oCIMP::base::map< IMP::domino::Subset, IMP::OwnerPointer< IMP::domino::AssignmentContainer > >
oCIMP::base::map< IMP::kernel::Key, FloatRange >
oCIMP::base::map< IMP::kernel::ModelObject *, ScoreStatesTemp >
oCIMP::base::map< IMP::kernel::Particle *, ConstData >
oCIMP::base::map< IMP::kernel::Particle *, Data >
oCIMP::base::map< IMP::kernel::Particle *, Particles >
oCIMP::base::map< IMP::kernel::Particle *, Pointer< display::Geometry > >
oCIMP::base::map< IMP::kernel::Particle *, Pointer< Geometry > >
oCIMP::base::map< IMP::kernel::Particle *, unsigned int >
oCIMP::base::map< Index< ParticleIndexTag >, Vector< ParticleIndex > >
oCIMP::base::map< Particle *, DGVertex >
oCIMP::base::map< Particle *, IMP::OwnerPointer< ParticleStates > >
oCIMP::base::map< ParticleIndex, base::OwnerPointer< internal::SingleParticleScoringFunction > >
oCIMP::base::map< Pointer< Restraint >, int >
oCIMP::base::map< Pointer< Restraint >, Subset >
oCIMP::base::map< Restraint *, RestraintData >
oCIMP::base::map< Restraint *, SetData >
oCIMP::base::map< std::string, Element >
oCIMP::base::map< Tracked *, std::string >
oCIMP::base::map< unsigned int, ParticlesTemp >
oCIMP::em2d::MasksManagerManage of projection masks
oCIMP::em2d::MatchTemplateResult
oCIMP::base::Memoizer< Generator, Checker >
oCIMP.modeller.ModelLoaderRead a Modeller model into IMP
oCIMP.em2d.MonteCarloRelativeMoves.MonteCarloRelativeMovesClass to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies
oCIMP::base::NonCopyable
oCIMP.kernel.OptionParserIMP-specific subclass of optparse.OptionParser
oCIMP::base::OwnerPointer< O >A reference counted pointer to an Object
oCIMP::base::OwnerPointer< algebra::NearestNeighbor3D >
oCIMP::base::OwnerPointer< algebra::NearestNeighbor6D >
oCIMP::base::OwnerPointer< IMP::container::ConsecutivePairContainer >
oCIMP::base::OwnerPointer< IMP::core::SoftSpherePairScore >
oCIMP::base::OwnerPointer< IMP::display::Writer >
oCIMP::base::OwnerPointer< IMP::IMP::kernel::UnaryFunction >
oCIMP::base::OwnerPointer< IMP::kernel::PairContainer >
oCIMP::base::OwnerPointer< IMP::kernel::PairPredicate >
oCIMP::base::OwnerPointer< IMP::kernel::PairScore >
oCIMP::base::OwnerPointer< IMP::kernel::QuadContainer >
oCIMP::base::OwnerPointer< IMP::kernel::QuadPredicate >
oCIMP::base::OwnerPointer< IMP::kernel::QuadScore >
oCIMP::base::OwnerPointer< IMP::kernel::Restraint >
oCIMP::base::OwnerPointer< IMP::kernel::ScoringFunction >
oCIMP::base::OwnerPointer< IMP::kernel::SingletonContainer >
oCIMP::base::OwnerPointer< IMP::kernel::SingletonPredicate >
oCIMP::base::OwnerPointer< IMP::kernel::SingletonScore >
oCIMP::base::OwnerPointer< IMP::kernel::TripletContainer >
oCIMP::base::OwnerPointer< IMP::kernel::TripletPredicate >
oCIMP::base::OwnerPointer< IMP::kernel::TripletScore >
oCIMP::base::OwnerPointer< IMP::kernel::UnaryFunction >
oCIMP::base::OwnerPointer< IMP::statistics::Embedding >
oCIMP::base::OwnerPointer< internal::PairContainerIndex >
oCIMP::base::OwnerPointer< internal::QuadContainerIndex >
oCIMP::base::OwnerPointer< internal::SingletonContainerIndex >
oCIMP::base::OwnerPointer< internal::TripletContainerIndex >
oCIMP::base::OwnerPointer< multifit::ProteomicsData >
oCIMP::base::OwnerPointer< PairScore >
oCIMP::base::piecewise_linear_distribution< T >
oCIMP.isd.utils.PipeImplements a FIFO pipe that merges lists (see self.put)
oCIMP::base::Pointer< O >A reference counted pointer to an object
oCIMP::base::Pointer< IMP::internal::InternalDynamicListPairContainer >
oCIMP::base::Pointer< IMP::kernel::Model >
oCIMP::base::Pointer< IMP::kernel::PairContainer >
oCIMP::base::Pointer< IMP::kernel::Particle >
oCIMP::base::Pointer< IMP::kernel::QuadContainer >
oCIMP::base::Pointer< IMP::kernel::RestraintSet >
oCIMP::base::Pointer< IMP::kernel::ScoringFunction >
oCIMP::base::Pointer< IMP::kernel::SingletonContainer >
oCIMP::base::Pointer< IMP::kernel::TripletContainer >
oCIMP::base::Pointer< List >
oCIMP::base::Pointer< SS >
oCIMP::em2d::PolarResamplingParameters
oCIMP::saxs::Profile
oCIMP::em2d::ProjectionMask
oCIMP::multifit::ProteinsAnchorsSamplingSpaceStores the anchors sampling space for each protein
oCIMP.isd.PyroGrid.PyroHandlerRuns on remote side, non-specific object
oCIMP.isd.PyroGrid.PyroProxyThis is high level wrapper of Pyro proxy objects, returns immediately with an empty Result object
oCIMP::kernel::PythonDirectedGraph
oCIMP::em::RadiusDependentKernelParametersCalculates kernel parameters as a function of a specific radius
oCIMP.test.RefCountCheckerCheck to make sure the number of C++ object references is as expected
oCIMP::algebra::ReferenceFrame3DA reference frame in 3D
oCIMP::em2d::RegistrationResultClass to manage registration results
oCIMP.restrainer._representation.RepresentationStore Representation
oCIMP::rotamer::ResidueRotamerA class storing the rotated coordinates of the atoms in the residue
oCIMP::atom::ResidueTypeThe type for a residue
oCIMP.restrainer._restraint.RestraintStore Restraint
oCIMP.isd.AbstractGrid.ResultA Result object is returned by a Proxy object, when some remote function invoked
oCIMP::atom::RMSDCalculatorUsed to calculate rmsd between multiple transformation that operate on the same particles
oCIMP::multifit::RMSDClustering< TransT >RMSD clustering
oCIMP::rotamer::RotamerAngleTupleA simple class storing chi angles and their probability
oCIMP.test.RunInTempDirSimple RAII-style class to run in a temporary directory
oCIMP::score_functor::Score
oCIMP::em2d::SegmentationParametersClass to provide all the parameters to the segmentation function
oCIMP.isd.AbstractGrid.ServerContains all the information that is required to use a remote object (alone and within a grid)
oCIMP::base::set< Key >
oCIMP::base::set< IMP::kernel::Particle * >
oCIMP::base::set< std::string >
oCIMP::base::set< Tracked * >
oCIMP.isd.shared_functions.sfo_commonNonspecific methods used across all shared function objects
oCIMP::score_functor::Shift< BaseDistanceScore >
oCIMP::base::Showable
oCIMP::restrainer::SimpleConnectivitySimple connectivity restraint
oCIMP::restrainer::SimpleDiameterSimple diameter restraint
oCIMP::restrainer::SimpleDistanceSimple distance restraint between two particles
oCIMP::restrainer::SimpleEMFitSimple EM fit restraint
oCIMP::restrainer::SimpleExcludedVolumeSimple excluded volume restraint
oCIMP.parallel.SlaveRepresentation of a single slave
oCIMP.parallel.SlaveArrayRepresentation of an array of slaves
oCIMP::saxs::SolventAccessibleSurface
oCIMP::algebra::SparseGridStorageD< D, VT, Base, Map >
oCIMP::algebra::SparseGridStorageD< D, VT, Base >
oCIMP::base::SparseSymmetricPairMemoizer< Generator, Checker >
oCIMP::score_functor::SphereDistance< BaseDistanceScore >
oCIMP::em::SpiderHeaderHeader for Spider images. IMP-EM is designed to be compatible with it
oCIMP::em2d::SpiderImageReaderWriter
oCIMP.isd.Statistics.StatisticsStatistics gathering and printing class for ISD gibbs sampling
oCIMP.isd.TALOSReader.TALOSReaderReads a TALOS file, or a TALOS folder, and stores the data
oCIMP.test.TestCaseSuper class for IMP test cases
oCIMP::base::Tracker< Tracked >
oCIMP::algebra::UnboundedGridRangeD< D >
oCIMP::algebra::UnboundedGridRangeD< 3 >
oCIMP::base::UncheckedWeakPointer< O >A weak pointer to an IMP::Object or IMP::RefCountedObject
oCIMP::base::UncheckedWeakPointer< IMP::base::Tracker >
oCIMP::base::UncheckedWeakPointer< Type >
oCIMP::base::UsageExceptionAn exception for an invalid usage of IMP
oCIMP::base::Value
oCstd::vector< T >STL class
oCIMP::base::WarningContext
oCIMP::base::WeakPointer< O >
oCIMP::base::WeakPointer< atom::Simulator >
oCIMP::base::WeakPointer< IMP::kernel::Particle >
oCIMP::score_functor::WeightScore< BaseDistanceScore >
oCIMP.em2d.buildxlinks.XlinkClass defining a cross-link
oCIMP.em2d.buildxlinks.XlinksDictDescription of crosslinking restraints as a python dictionary
oCIMP.restrainer._xml_parser.XMLDisplayConstruct Display from XML file
oCIMP.restrainer._xml_parser.XMLRepresentationConstruct Representation from XML file
\CIMP.restrainer._xml_parser.XMLRestraintConstruct Restraint from XML file