IMP  2.3.0
The Integrative Modeling Platform
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234567]
oCIMP::base::AddBoolFlag
oCIMP::base::AddFloatFlag
oCIMP::base::AddIntFlag
oCIMP::base::AddStringFlag
oCIMP::base::AdvancedFlag< T, ENABLED >Use this to add an advanced flag to the program
oCIMP.pmi.analysis.AlignmentThis class performs alignment and RMSD calculation for two sets of coordinates
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.pmi.macros.AnalysisReplicaExchange0A macro for running all the basic operations of analysis
oCIMP::multifit::AnchorsDataStorage of anchors (points and edges)
oCIMP::atom::AtomTypeThe type of an atom
oCIMP::em2d::AverageDistanceLinkageFunctor for hierarchical clustering based on average-linkage
oCIMP::modeller::BinormalTermA single binormal term in a MultipleBinormalRestraint
oCIMP::atom::ForceFieldParameters::Bond
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.pmi.macros.BuildModel1This building scheme needs a data structure with the following fields comp_name hier_name color fasta_file fasta_id pdb_name chain_id res_range read_em_files bead_size rb super_rb em_num_components em_txt_file_name em_mrc_file_name
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::saxs::ChiFreeScore
oCIMP::saxs::ChiScore
oCIMP::saxs::ChiScoreLog
oCIMP.pmi.analysis.ClusteringA class to cluster structures
oCIMP.em2d.solutions_io.ClusterRecordSimple named tuple class
oCIMP::em2d::ClusterSetA class to store the clusters generated during hierarchical clustering
oCIMP::cnmultifit::CnSymmAxisDetectorDetect cn symmetry in proteins and density maps
oCIMP::em::CoarseConvolutionConvolutes two grids
oCIMP.pmi.tools.ColorChangeClass to change color code to hexadecimal to rgb
oCIMP.kernel.CommandDispatcherAllow applications to easily implement commmands
oCIMP::em2d::CompleteLinkageFunctor for hierarchical clustering based on complete linkage
oCIMP::core::ConjugateGradientsSimple conjugate gradients optimizer
oCIMP::algebra::ConnollySurfacePointRepresent a point on the Connolly surface
oCIMP.parallel.ContextA collection of tasks that run in the same environment
oCIMP.pmi.nonmantained.CrossLinkMSThis class initialize a CrossLinkMS restraint and contains all useful informations, such as the cross-link database, contained in self.pairs If restraint_file=None, it will proceed creating simulated data
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.isd.demux_trajs.DemuxerUses column to demux a replica trajectory
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 a coarse particle to its refined particles
oCIMP.test.DirectorObjectCheckerCheck to make sure the number of director references is as expected
oCIMP::em::DistanceMaskCalculates and stores a distance mask
oCIMP.em2d.buildxlinks.DockOrderCompute the order of the docking experiments
oCIMP.pmi.dof.dofDegrees of Freedom Tasks: define rigid bodies and super rigid bodies define symmetries (see representation.py) create nuisances and their parameters generate lists of MC or MD movers
oCIMP.em2d.DominoModel.DominoModelManagement of a model using DOMINO
oCIMP::atom::ElementTable
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::multifit::FittingSolutionRecordA fitting solution record
oCIMP::em::FittingSolutionsA simple list of fitting solutions
oCIMP::base::Flag< T, ENABLED >
oCIMP::saxs::FormFactorTable
oCIMP::multifit::GeometricHash< T, D >Geometric Hash table
oCIMP::algebra::GeometricPrimitiveD< D >Base class for geometric types
oCIMP::algebra::GeometricPrimitiveD< 2 >
oCIMP::algebra::GeometricPrimitiveD< 3 >
oCIMP::display::GeometryProcessorProvide a standard geometry processing framework
oCIMP.pmi.analysis.GetModelDensityA class to compute mean density maps from structures
oCIMP::gsl::GSLOptimizerA base class for GSL-based optimizers
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.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 Microscopy 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 internal error in IMP
oCIMP::em2d::IntsOrder
oCIMP::em::KernelParameters
oCIMP::em2d::LessPairBySecond< T >Comparison of pairs by checking the second element
oCIMP::algebra::LogEmbeddingD< D >
oCIMP::algebra::LogEmbeddingD< 3 >
oCIMP::algebra::LogEmbeddingD<-1 >
oCIMP.isd.demux_trajs.LogHolderManages information on a given simulation
oCIMP::base::LRUCache< Generator, Checker >
oCIMP.parallel.ManagerManages slaves and contexts
oCIMP::base::map< Key, Data >
oCIMP::em2d::MasksManagerManagement of projection masks
oCIMP.parallel.master_communicator.MasterCommunicatorFor communicating from the master to slaves
oCIMP::em2d::MatchTemplateResult
oCIMP::base::Memoizer< Generator, Checker >
oCIMP::multifit::MergeTreeBuilderUtility class for building merge trees
oCIMP.modeller.ModelLoaderRead a Modeller model into IMP
oCIMP::cnmultifit::MolCnSymmAxisDetectorMolecule symmetry detector
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.pmi.output.OutputClass for easy writing of PDBs, RMFs, and stat files
oCIMP::kernel::ParticleInputs
oCIMP::kernel::ParticleOutputs
oCIMP::base::piecewise_linear_distribution< T >
oCIMP.isd.utils.PipeImplements a FIFO pipe that merges lists (see self.put)
oCIMP::base::Pointer< O >A smart pointer to a reference counted object
oCIMP::base::Pointer< base::Object >
oCIMP::base::Pointer< const IMP::atom::CHARMMParameters >
oCIMP::base::Pointer< const IMP::statistics::internal::XYZDataPoints >
oCIMP::base::Pointer< container::DynamicListPairContainer >
oCIMP::base::Pointer< core::HarmonicUpperBound >
oCIMP::base::Pointer< domino::ParticleStatesTable >
oCIMP::base::Pointer< domino::RestraintCache >
oCIMP::base::Pointer< em::DensityMap >
oCIMP::base::Pointer< em::SampledDensityMap >
oCIMP::base::Pointer< IMP::atom::CHARMMIdealResidueTopology >
oCIMP::base::Pointer< IMP::atom::CHARMMPatch >
oCIMP::base::Pointer< IMP::core::IncrementalScoringFunction >
oCIMP::base::Pointer< IMP::domino::AssignmentContainer >
oCIMP::base::Pointer< IMP::domino::AssignmentsTable >
oCIMP::base::Pointer< IMP::domino::ParticleStatesTable >
oCIMP::base::Pointer< IMP::domino::RestraintCache >
oCIMP::base::Pointer< IMP::em2d::Image >
oCIMP::base::Pointer< IMP::em2d::ImageReaderWriter >
oCIMP::base::Pointer< IMP::em2d::ProjectionFinder >
oCIMP::base::Pointer< IMP::em2d::ScoreFunction >
oCIMP::base::Pointer< IMP::isd::GaussianProcessInterpolation >
oCIMP::base::Pointer< IMP::isd::MolecularDynamics >
oCIMP::base::Pointer< IMP::isd::vonMisesSufficient >
oCIMP::base::Pointer< IMP::kernel::Configuration >
oCIMP::base::Pointer< IMP::kernel::ConfigurationSet >
oCIMP::base::Pointer< IMP::kernel::IMP::kernel::Particle >
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::ScoreState >
oCIMP::base::Pointer< IMP::kernel::ScoringFunction >
oCIMP::base::Pointer< IMP::kernel::SingletonContainer >
oCIMP::base::Pointer< IMP::kernel::TripletContainer >
oCIMP::base::Pointer< IMP::kernel::UnaryFunction >
oCIMP::base::Pointer< IMP::kinematics::IMP::kinematics::KinematicForest >
oCIMP::base::Pointer< IMP::saxs::DerivativeCalculator >
oCIMP::base::Pointer< IMP::saxs::ProfileFitter< IMP::saxs::ChiScore > >
oCIMP::base::Pointer< IMP::saxs::RigidBodiesProfileHandler >
oCIMP::base::Pointer< internal::ConjugateGradientEigen >
oCIMP::base::Pointer< internal::KMdata >
oCIMP::base::Pointer< internal::KMfilterCenters >
oCIMP::base::Pointer< internal::ListSelectionPredicate >
oCIMP::base::Pointer< internal::RigidBodyHierarchy >
oCIMP::base::Pointer< kernel::IMP::kernel::Particle >
oCIMP::base::Pointer< kernel::IMP::kernel::RestraintSet >
oCIMP::base::PointerMember< O >A smart pointer to a ref-counted Object that is a class member
oCIMP::base::PointerMember< algebra::NearestNeighbor3D >
oCIMP::base::PointerMember< algebra::NearestNeighbor6D >
oCIMP::base::PointerMember< const IMP::rotamer::RotamerLibrary >
oCIMP::base::PointerMember< const IMP::saxs::Profile >
oCIMP::base::PointerMember< core::internal::MovedSingletonContainer >
oCIMP::base::PointerMember< domino::ParticleStatesTable >
oCIMP::base::PointerMember< domino::RestraintScoreSubsetFilterTable >
oCIMP::base::PointerMember< em::DensityMap >
oCIMP::base::PointerMember< GaussianProcessInterpolationScoreState >
oCIMP::base::PointerMember< IMP::atom::AngleSingletonScore >
oCIMP::base::PointerMember< IMP::atom::BondSingletonScore >
oCIMP::base::PointerMember< IMP::atom::DihedralSingletonScore >
oCIMP::base::PointerMember< IMP::atom::ImproperSingletonScore >
oCIMP::base::PointerMember< IMP::atom::PDBSelector >
oCIMP::base::PointerMember< IMP::atom::SmoothingFunction >
oCIMP::base::PointerMember< IMP::container::ConsecutivePairContainer >
oCIMP::base::PointerMember< IMP::core::ClosePairsFinder >
oCIMP::base::PointerMember< IMP::core::RigidClosePairsFinder >
oCIMP::base::PointerMember< IMP::core::SoftSpherePairScore >
oCIMP::base::PointerMember< IMP::display::Writer >
oCIMP::base::PointerMember< IMP::domino::AssignmentsTable >
oCIMP::base::PointerMember< IMP::domino::ParticleStates >
oCIMP::base::PointerMember< IMP::domino::ParticleStatesTable >
oCIMP::base::PointerMember< IMP::domino::RestraintCache >
oCIMP::base::PointerMember< IMP::em::DensityMap >
oCIMP::base::PointerMember< IMP::em::EnvelopeScore >
oCIMP::base::PointerMember< IMP::em::MapDistanceTransform >
oCIMP::base::PointerMember< IMP::em::PCAAligner >
oCIMP::base::PointerMember< IMP::em::SampledDensityMap >
oCIMP::base::PointerMember< IMP::IMP::kernel::UnaryFunction >
oCIMP::base::PointerMember< IMP::internal::IMP::core::RestraintsScoringFunction >
oCIMP::base::PointerMember< IMP::isd::BivariateFunction >
oCIMP::base::PointerMember< IMP::isd::CrossLinkData >
oCIMP::base::PointerMember< IMP::isd::CysteineCrossLinkData >
oCIMP::base::PointerMember< IMP::isd::FretData >
oCIMP::base::PointerMember< IMP::isd::MolecularDynamics >
oCIMP::base::PointerMember< IMP::isd::MolecularDynamicsMover >
oCIMP::base::PointerMember< IMP::isd::MultivariateFNormalSufficient >
oCIMP::base::PointerMember< IMP::isd::UnivariateFunction >
oCIMP::base::PointerMember< IMP::kernel::Configuration >
oCIMP::base::PointerMember< IMP::kernel::ConfigurationSet >
oCIMP::base::PointerMember< IMP::kernel::Model >
oCIMP::base::PointerMember< IMP::kernel::Optimizer >
oCIMP::base::PointerMember< IMP::kernel::OptimizerState >
oCIMP::base::PointerMember< IMP::kernel::PairContainer >
oCIMP::base::PointerMember< IMP::kernel::PairModifier >
oCIMP::base::PointerMember< IMP::kernel::PairPredicate >
oCIMP::base::PointerMember< IMP::kernel::PairScore >
oCIMP::base::PointerMember< IMP::kernel::QuadContainer >
oCIMP::base::PointerMember< IMP::kernel::QuadModifier >
oCIMP::base::PointerMember< IMP::kernel::QuadPredicate >
oCIMP::base::PointerMember< IMP::kernel::QuadScore >
oCIMP::base::PointerMember< IMP::kernel::Refiner >
oCIMP::base::PointerMember< IMP::kernel::RestraintSet >
oCIMP::base::PointerMember< IMP::kernel::ScoreState >
oCIMP::base::PointerMember< IMP::kernel::ScoringFunction >
oCIMP::base::PointerMember< IMP::kernel::SingletonContainer >
oCIMP::base::PointerMember< IMP::kernel::SingletonModifier >
oCIMP::base::PointerMember< IMP::kernel::SingletonPredicate >
oCIMP::base::PointerMember< IMP::kernel::SingletonScore >
oCIMP::base::PointerMember< IMP::kernel::TripletContainer >
oCIMP::base::PointerMember< IMP::kernel::TripletModifier >
oCIMP::base::PointerMember< IMP::kernel::TripletPredicate >
oCIMP::base::PointerMember< IMP::kernel::TripletScore >
oCIMP::base::PointerMember< IMP::kernel::UnaryFunction >
oCIMP::base::PointerMember< IMP::multifit::AssemblyHeader >
oCIMP::base::PointerMember< IMP::saxs::Profile >
oCIMP::base::PointerMember< IMP::statistics::Embedding >
oCIMP::base::PointerMember< IMP::statistics::Metric >
oCIMP::base::PointerMember< IMP::statistics::PartitionalClustering >
oCIMP::base::PointerMember< internal::PairContainerIndex >
oCIMP::base::PointerMember< internal::QuadContainerIndex >
oCIMP::base::PointerMember< internal::SingletonContainerIndex >
oCIMP::base::PointerMember< internal::TripletContainerIndex >
oCIMP::base::PointerMember< kernel::IMP::kernel::Model >
oCIMP::base::PointerMember< kernel::IMP::kernel::PairContainer >
oCIMP::base::PointerMember< kernel::IMP::kernel::PairPredicate >
oCIMP::base::PointerMember< kernel::IMP::kernel::Particle >
oCIMP::base::PointerMember< kernel::IMP::kernel::QuadContainer >
oCIMP::base::PointerMember< kernel::IMP::kernel::QuadPredicate >
oCIMP::base::PointerMember< kernel::IMP::kernel::Restraint >
oCIMP::base::PointerMember< kernel::IMP::kernel::ScoringFunction >
oCIMP::base::PointerMember< kernel::IMP::kernel::SingletonContainer >
oCIMP::base::PointerMember< kernel::IMP::kernel::SingletonPredicate >
oCIMP::base::PointerMember< kernel::IMP::kernel::TripletContainer >
oCIMP::base::PointerMember< kernel::IMP::kernel::TripletPredicate >
oCIMP::base::PointerMember< multifit::IMP::multifit::ProteomicsData >
oCIMP::base::PointerMember< PairScore >
oCIMP::base::PointerMember< Predicate >
oCIMP::base::PointerMember< Table >
oCIMP::base::PointerMember< UF >
oCIMP::em2d::PolarResamplingParameters
oCIMP.pmi.output.ProcessOutputA class for reading stat files
oCIMP::em2d::ProjectingParametersParameters needed for the core projection routine
oCIMP::em2d::ProjectionMask
oCIMP::kinematics::ProteinKinematics
oCIMP::multifit::ProteinsAnchorsSamplingSpaceStores the anchors sampling space for each protein
oCIMP::kernel::PythonDirectedGraph
oCIMP::em::RadiusDependentDistanceMask
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.pmi.macros.ReplicaExchange0A macro to help setup and run replica exchange, supporting monte carlo and molecular dynamics
oCIMP::rotamer::ResidueRotamerA class storing the rotated coordinates of the atoms in the residue
oCIMP::atom::ResidueTypeThe type for a residue
oCIMP::rotamer::RotamerAngleTupleA simple class storing chi angles and their probability
oCIMP.test.RunInTempDirSimple RAII-style class to run in a temporary directory
oCIMP.pmi.sampling_tools.SampleObjectsUseful tools for setting up sampling
oCIMP::score_functor::ScoreA functor for computing a distance based score for two particles
oCIMP::em2d::SegmentationParametersClass to provide all the parameters to the segmentation function
oCIMP::base::set< Key >
oCIMP.isd.shared_functions.sfo_commonNonspecific methods used across all shared function objects
oCIMP::score_functor::Shift< BaseDistanceScore >
oCIMP::base::Showable
oCIMP::em2d::SingleLinkageFunctor for hierarchical clustering based on single linkage
oCIMP::score_functor::SingletonStatistical< Key, INTERPOLATE >
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.isd.Statistics.StatisticsStatistics gathering and printing class for ISD gibbs sampling
oCIMP::core::SteepestDescentA simple steepest descent optimizer
oCIMP.isd.TALOSReader.TALOSReaderReads a TALOS file, or a TALOS folder, and stores the data
oCIMP.test.TempDirSimple RAII-style class to make a temporary directory
oCIMP.test.TestCaseSuper class for IMP test cases
oCIMP::algebra::UnboundedGridRangeD< D >
oCIMP::algebra::UnboundedGridRangeD< 3 >
oCIMP::base::UncheckedWeakPointer< O >A weak pointer to an Object or RefCountedObject
oCIMP::base::UncheckedWeakPointer< IMP::kernel::Optimizer >
oCIMP::base::UsageExceptionAn exception for an invalid usage of IMP
oCIMP::base::ValueBase for a simple primitive-like type
oCstd::vector< T >STL class
oCIMP::base::WarningContext
oCIMP::base::WeakPointer< O >
oCIMP::base::WeakPointer< atom::Simulator >
oCIMP::base::WeakPointer< IMP::kernel::Model >
oCIMP::base::WeakPointer< kernel::IMP::kernel::Particle >
oCIMP::base::WeakPointer< kernel::IMP::kernel::Restraint >
oCIMP::core::WeightedDerivativesToRefinedCopy the derivatives from a coarse particle to its refined particles
oCIMP::score_functor::WeightScore< BaseDistanceScore >
oCIMP.em2d.buildxlinks.XlinkClass defining a cross-link
\CIMP.em2d.buildxlinks.XlinksDictDescription of crosslinking restraints as a python dictionary