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IMP Reference Guide  develop.8b7eb21230,2024/06/24
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::AddBoolFlag
oCIMP::AddFloatFlag
oCIMP::AddIntFlag
oCIMP::AddStringFlag
oCIMP::AdvancedFlag< T, ENABLED >Use this to add an advanced flag to the program
oCIMP.pmi.analysis.AlignmentPerforms alignment and RMSD calculation for two sets of coordinates
oCIMP.pmi1.analysis.AlignmentPerforms 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.pmi.restraints.proteomics.AmbiguousCompositeRestraintThis restraint allows ambiguous cross-linking between multiple copies excluding between symmetric copies It allows name ambiguity
oCIMP.pmi1.restraints.proteomics.AmbiguousCompositeRestraintThis restraint allows ambiguous crosslinking between multiple copies excluding between symmetric copies It allows name ambiguity
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.AnalysisReplicaExchangeThis class contains analysis utilities to investigate ReplicaExchange results
oCIMP.pmi1.macros.AnalysisReplicaExchangeThis class contains analysis utilities to investigate ReplicaExchange results
oCIMP.pmi.macros.AnalysisReplicaExchange0A macro for running all the basic operations of analysis
oCIMP.pmi1.macros.AnalysisReplicaExchange0A macro for running all the basic operations of analysis
oCIMP::multifit::AnchorsDataStorage of anchors (points and edges)
oCIMP.ArgumentParserIMP-specific subclass of argparse.ArgumentParser
oCIMP.pmi.mmcif.AsymUnitA single asymmetric unit in the system
oCIMP.pmi1.mmcif.AsymUnitA single asymmetric unit in the system
oCIMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraintSetup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian
oCIMP::atom::AtomTypeThe type of an atom
oCIMP::em2d::AverageDistanceLinkageFunctor for hierarchical clustering based on average-linkage
oCIMP::core::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.pmi1.macros.BuildModelA macro to build a Representation based on a Topology and lists of movers
oCIMP.pmi1.macros.BuildModel1Building macro
oCIMP.pmi.macros.BuildSystemA macro to build a IMP::pmi::topology::System based on a TopologyReader object
oCIMP::kinematics::CCDLoopClosureCCD loop closure
oCIMP::atom::ChainTypeThe type for a chain
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.pmi.restraints.stereochemistry.CharmmForceFieldRestraintEnable CHARMM force field
oCIMP.pmi1.restraints.stereochemistry.CharmmForceFieldRestraintEnable CHARMM force field
oCIMP.multifit.transforms.ChimeraFormatterEach line in 'chimera' format lists the transformation index, the cross correlation score, and then the transformation for each component, as a rotation matrix (row-major order) and a translation in angstroms
oCIMP.pmi.output.ClusterA container for models organized into clusters
oCIMP.pmi1.output.ClusterA container for models organized into clusters
oCIMP.pmi.analysis.ClusteringA class to cluster structures
oCIMP.pmi1.analysis.ClusteringA class to cluster structures
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.ColorChangeChange color code to hexadecimal to rgb
oCIMP.pmi1.tools.ColorChangeChange color code to hexadecimal to rgb
oCIMP.CommandDispatcherAllow command line tools to easily implement multiple commands
oCIMP::multi_state::CompareMultiStateModelsUtility class to help sort MultiStateModel objects
oCIMP::em2d::CompleteLinkageFunctor for hierarchical clustering based on complete linkage
oCIMP.pmi.restraints.proteomics.CompositeRestraintHandleparticles a list of particles compositeparticles is a list of list of particles
oCIMP.pmi1.restraints.proteomics.CompositeRestraintHandleparticles is a selection tuple compositeparticles is a list of selection tuples
oCIMP.pmi.samplers.ConjugateGradientsSample using conjugate gradients
oCIMP.pmi1.samplers.ConjugateGradientsSample using conjugate gradients
oCIMP.pmi1.restraints.crosslinking.ConnectivityCrossLinkMSThis restraint allows ambiguous crosslinking between multiple copies it is a variant of the SimplifiedCrossLinkMS
oCIMP.pmi.restraints.proteomics.ConnectivityRestraintGenerate a connectivity restraint between domains setting up the restraint example: sel1 = IMP.atom.Selection(root_hier, molecule="Rpb3", residue_indexes=range(1,100)) sel2 = IMP.atom.Selection(root_hier, molecule="Rpb4", residue_indexes=range(1,100)) cr=restraints.ConnectivityRestraint((sel1, sel2), label='CR1') cr.add_to_model() Multistate support =No Resolution=Yes
oCIMP.pmi.restraints.stereochemistry.ConnectivityRestraintCreate a restraint between consecutive TempResidue objects or an entire PMI Molecule object
oCIMP.pmi1.restraints.proteomics.ConnectivityRestraintGenerate a connectivity restraint between domains setting up the restraint example: cr=restraints.ConnectivityRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")]) cr.add_to_model() cr.set_label("CR1") Multistate support =No Selection type=selection tuple Resolution=Yes
oCIMP.pmi1.restraints.stereochemistry.ConnectivityRestraintThis class creates a restraint between consecutive TempResidue objects OR an entire PMI MOlecule object
oCIMP::algebra::ConnollySurfacePointRepresent a point on the Connolly surface
oCIMP.parallel.ContextA collection of tasks that run in the same environment
oCIMP.pmi1.restraints.em.CrossCorrelationRestraintFit particles to an EM map
oCIMP.pmi.io.crosslink.CrossLinkDataBaseThis class handles a cross-link dataset and do filtering operations, adding cross-links, merge datasets..
oCIMP.pmi.io.crosslink.CrossLinkDataBaseFromStructureThis class generates a CrossLinkDataBase from a given structure
oCIMP.pmi1.io.crosslink.CrossLinkDataBaseFromStructureThis class generates a CrossLinkDataBase from a given structure
oCIMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverterThis class is needed to convert the keywords from a generic database to the standard ones
oCIMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverterThis class is needed to convert the keywords from a generic database to the standard ones
oCIMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraintSetup cross-link distance restraints from mass spectrometry data
oCIMP.pmi1.nonmantained.CrossLinkMSThis class initializes a CrossLinkMS restraint and contains all useful information, such as the cross-link database, contained in self.pairs If restraint_file=None, it will proceed creating simulated data
oCIMP.pmi.analysis.CrossLinkTableVisualization of cross-links
oCIMP.pmi1.analysis.CrossLinkTableVisualization of crosslinks
oCIMP.isd.TuneRex.CvEstimatorWhen created, estimates the heat capacity from the energies or from the indicator functions using the specified method
oCIMP.EMageFit.database.Database2Class to manage a SQL database built with sqlite3
oCIMP.pmi.output.DataEntryA class to store data associated to a model
oCIMP.pmi1.output.DataEntryA class to store data associated to a model
oCIMP::multifit::DataPointsAssignment
oCIMP::algebra::DefaultEmbeddingD< D >Embed a grid as an evenly spaced axis aligned grid
oCIMP::algebra::DefaultEmbeddingD< 3 >
oCIMP.pmi.dof.DegreesOfFreedomSimplify creation of constraints and movers for an IMP Hierarchy
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::DerivativeAccumulatorClass for adding derivatives from restraints to the model
oCIMP.test.DirectorObjectCheckerCheck to make sure the number of director references is as expected
oCIMP::em::DistanceMaskCalculates and stores a distance mask
oCIMP.pmi.restraints.basic.DistanceRestraintA simple distance restraint
oCIMP.pmi.restraints.basic.DistanceToPointRestraintAnchor a particle to a specific coordinate
oCIMP.EMageFit.buildxlinks.DockOrderCompute the order of the docking experiments
oCIMP.multifit.transforms.DockRefFormatterEach line in 'dockref' format lists the transformation for each component, as a set of three Euler angles (in radians about the fixed x, y and z axes) and a translation in angstroms
oCIMP.EMageFit.domino_model.DominoModelManagement of a model using DOMINO
oCIMP.pmi.restraints.stereochemistry.ElasticNetworkRestraintAdd harmonic restraints between all pairs
oCIMP.pmi1.restraints.stereochemistry.ElasticNetworkRestraintAdd harmonic restraints between all pairs
oCIMP.pmi.restraints.em2d.ElectronMicroscopy2DFit particles against a set of class averages by principal components
oCIMP.pmi1.restraints.em2d.ElectronMicroscopy2DFit particles against a set of class averages by principal components
oCIMP.pmi.restraints.em2d.ElectronMicroscopy2D_FFTFFT based image alignment, developed by Javier Velazquez-Muriel
oCIMP.pmi1.restraints.em2d.ElectronMicroscopy2D_FFTFFT based image alignment, developed by Javier Velazquez-Muriel
oCIMP::atom::ElementTable
oCIMP::multi_state::EnsembleGeneratorEnumeration of an ensemble of good scoring MultiStateModels
oCIMP.pmi.mmcif.EntityA single entity in the system
oCIMP.pmi1.mmcif.EntityA single entity in the system
oCIMP.isd.Entry.EntryThe entry class represents a column in the statistics file
oCIMP::npctransport::LinearInteractionPairScore::EvaluationCache
oCIMP::EvaluationState
oCIMP::example::ExampleTemplateClassD< D >A line segment templated on the dimension
oCIMP::ExceptionThe general base class for IMP exceptions
oCIMP.pmi.restraints.stereochemistry.ExcludedVolumeSphereA class to create an excluded volume restraint for a set of particles at a given resolution
oCIMP.pmi1.restraints.stereochemistry.ExcludedVolumeSphereA class to create an excluded volume restraint for a set of particles at a given resolution
oCIMP.pmi.restraints.basic.ExternalBarrierKeeps all structures inside a sphere
oCIMP.pmi.io.crosslink.FilterOperatorThis class allows to create filter functions that can be passed to the CrossLinkDataBase in this way:
oCIMP.pmi1.io.crosslink.FilterOperatorThis class allows to create filter functions that can be passed to the CrossLinkDataBase in this way:
oCIMP::saxs::FitParametersParameters of a fit, from ProfileFitter
oCIMP::multifit::FittingSolutionRecordA fitting solution record
oCIMP::em::FittingSolutionsA simple list of fitting solutions
oCIMP.pmi.io.crosslink.FixedFormatParserA class to handle different XL format with fixed format currently support ProXL
oCIMP.pmi1.io.crosslink.FixedFormatParserA class to handle different XL format with fixed format currently support ProXL
oCIMP::Flag< T, ENABLED >
oCIMP::saxs::FormFactorTable
oCIMP.pmi.restraints.stereochemistry.FusionRestraintCreates a restraint between the termini two polypeptides, to simulate the sequence connectivity
oCIMP.pmi1.restraints.stereochemistry.FusionRestraintThis class creates a restraint between the termini two polypeptides, to simulate the sequence connectivity
oCIMP.pmi.restraints.proteomics.FuzzyBooleanFully Ambiguous Restraint that can be built using boolean logic R
oCIMP.pmi1.restraints.proteomics.FuzzyBooleanFully Ambiguous Restraint that can be built using boolean logic R
oCIMP.pmi.restraints.em.GaussianEMRestraintFit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians)
oCIMP.pmi1.restraints.em.GaussianEMRestraintFit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians)
oCIMP.bayesianem.restraint.GaussianEMRestraintWrapperFit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians)
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.GetModelDensityCompute mean density maps from structures
oCIMP.pmi1.analysis.GetModelDensityCompute mean density maps from structures
oCIMP.sampcon.precision_rmsd.GetModelDensityCompute mean density maps from structures
oCIMP.pmi.mmcif.GMMParserExtract metadata from an EM density GMM file
oCIMP.sampcon.good_scoring_model_selector.GoodScoringModelSelectorSelect good-scoring models based on scores and/or data satisfaction
oCIMP.spatiotemporal.graphNode.graphNodeA class to represent a node in a spatiotemporal process
oCIMP::em2d::HasHigherCCC< T >Comparison by value of the ccc
oCIMP::em2d::HasLowerScore< T >Compare two classes that return a score
oCIMP.EMageFit.solutions_io.HeapRecordThe heapq algorithm is a min-heap
oCIMP.pmi.restraints.stereochemistry.HelixRestraintEnforce ideal Helix dihedrals and bonds for a selection at resolution 0
oCIMP.pmi1.restraints.stereochemistry.HelixRestraintEnforce ideal Helix dihedrals and bonds for a selection at resolution 0
oCIMP.pmi1.tools.HierarchyDatabaseStore the representations for a system
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 an IMP scoring function
oCIMP::Index< Tag >A typed index
oCIMP::Index< ParticleIndexTag >
oCIMP.EMageFit.buildxlinks.InitialDockingFromXlinksPuts two subunits together using the Xlinkins restraints
oCIMP::InputAdaptorConvenience class to accept multiple input types
oCIMP::InternalExceptionA general exception for an internal error in IMP
oCIMP::em2d::IntsOrder
oCIMP.pmi.io.crosslink.JaccardDistanceMatrixThis class allows to compute and plot the distance between datasets
oCIMP.pmi1.io.crosslink.JaccardDistanceMatrixThis class allows to compute and plot the distance between datasets
oCIMP.pmi.restraints.parameters.JeffreysPriorWrapper for IMP.isd.JeffreysRestraint
oCIMP::em::KernelParametersCalculates and stores Gaussian kernel parameters
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::LRUCache< Generator, Checker >Implement a simple least recently used cache
oCIMP.parallel.ManagerManages workers and contexts
oCIMP.parallel.manager_communicator.ManagerCommunicatorFor communicating from the manager to workers
oCIMP.pmi.io.crosslink.MapCrossLinkDataBaseOnStructureThis class maps a CrossLinkDataBase on a given structure and save an rmf file with color-coded cross-links
oCIMP.pmi1.io.crosslink.MapCrossLinkDataBaseOnStructureThis class maps a CrossLinkDataBase on a given structure and save an rmf file with color-coded crosslinks
oCIMP::em2d::MasksManagerManagement of projection masks
oCIMP::em2d::MatchTemplateResult
oCIMP.pmi.restraints.npc.MembraneExclusionRestraintKeep protein away from a half torus in the xy plane
oCIMP.pmi1.restraints.npc.MembraneExclusionRestraintCreate Membrane Exclusion Restraint
oCIMP.pmi.restraints.basic.MembraneRestraintRestrain particles to be above, below, or inside a planar membrane
oCIMP.pmi.restraints.npc.MembraneSurfaceLocationConditionalRestraintLocalize one protein on the surface of a half torus in the xy plane
oCIMP.pmi1.restraints.npc.MembraneSurfaceLocationConditionalRestraintCreate Membrane Surface Location CONDITIONAL Restraint for Nup120 ALPS Motifs - Mutually Exclusive from (135,152,'Nup120') and (197,216,'Nup120')
oCIMP.pmi.restraints.npc.MembraneSurfaceLocationRestraintLocalize protein on the surface of a half torus in the xy plane
oCIMP.pmi1.restraints.npc.MembraneSurfaceLocationRestraintCreate Membrane Surface Location Restraint
oCIMP::Memoizer< Generator, Checker >Helper class for writing memoizers
oCIMP::multifit::MergeTreeBuilderUtility class for building merge trees
oCIMP.pmi.MissingFileWarningWarning for an expected, but missing, file
oCIMP.modeller.ModelLoaderRead a Modeller model into IMP
oCIMP::cnmultifit::MolCnSymmAxisDetectorMolecule symmetry detector
oCIMP.pmi.samplers.MolecularDynamicsSample using molecular dynamics
oCIMP.pmi1.samplers.MolecularDynamicsSample using molecular dynamics
oCIMP.pmi.topology.MoleculeStores a named protein chain
oCIMP.pmi.samplers.MonteCarloSample using Monte Carlo
oCIMP.pmi1.samplers.MonteCarloSample using Monte Carlo
oCIMP.EMageFit.monte_carlo.MonteCarloRelativeMovesClass to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies
oCIMP::multi_state::MultiStateModelKeep track of multiple states
oCIMP::multi_state::MultiStateModelScoreBase class for MultiStateModel scoring classes
oCIMP::NonCopyableBase class for all objects that cannot be copied
oCIMP.pmi.tools.OrderedDefaultDictStore objects in order they were added, but with default type
oCIMP.pmi1.tools.OrderedDefaultDictStore objects in order they were added, but with default type
oCIMP.pmi.output.OutputClass for easy writing of PDBs, RMFs, and stat files
oCIMP.pmi1.output.OutputClass for easy writing of PDBs, RMFs, and stat files
oCIMP.pmi.output.OutputStatisticsCollect statistics from ProcessOutput.get_fields()
oCIMP.pmi1.output.OutputStatisticsCollect statistics from ProcessOutput.get_fields()
oCIMP.pmi.ParameterWarningWarning for probably incorrect input parameters
oCIMP::ParticleInputsBase class for objects that take particle arguments and read from them
oCIMP::ParticleOutputsBase class for objects that take particle arguments and modify them
oCIMP.pmi.topology.PDBSequencesData structure for reading and storing sequence data from PDBs
oCIMP.isd.utils.PipeImplements a FIFO pipe that merges lists (see self.put)
oCIMP.pmi.restraints.stereochemistry.PlaneDihedralRestraintRestrain the dihedral between planes defined by three particles
oCIMP::Pointer< O >A smart pointer to a reference counted object
oCIMP::Pointer< const IMP::atom::CHARMMParameters >
oCIMP::Pointer< const IMP::statistics::internal::XYZDataPoints >
oCIMP::Pointer< container::DynamicListPairContainer >
oCIMP::Pointer< core::HarmonicUpperBound >
oCIMP::Pointer< domino::ParticleStatesTable >
oCIMP::Pointer< domino::RestraintCache >
oCIMP::Pointer< em::DensityMap >
oCIMP::Pointer< em::SampledDensityMap >
oCIMP::Pointer< IMP::atom::CHARMMIdealResidueTopology >
oCIMP::Pointer< IMP::atom::CHARMMPatch >
oCIMP::Pointer< IMP::Configuration >
oCIMP::Pointer< IMP::ConfigurationSet >
oCIMP::Pointer< IMP::domino::AssignmentContainer >
oCIMP::Pointer< IMP::domino::AssignmentsTable >
oCIMP::Pointer< IMP::domino::ParticleStatesTable >
oCIMP::Pointer< IMP::domino::RestraintCache >
oCIMP::Pointer< IMP::em2d::Image >
oCIMP::Pointer< IMP::em2d::ImageReaderWriter >
oCIMP::Pointer< IMP::em2d::ProjectionFinder >
oCIMP::Pointer< IMP::em2d::ScoreFunction >
oCIMP::Pointer< IMP::IMP::Particle >
oCIMP::Pointer< IMP::isd::FStudentT >
oCIMP::Pointer< IMP::isd::MolecularDynamics >
oCIMP::Pointer< IMP::isd::PenalizedComplexityPrior >
oCIMP::Pointer< IMP::isd::vonMisesSufficient >
oCIMP::Pointer< IMP::Model >
oCIMP::Pointer< IMP::Object >
oCIMP::Pointer< IMP::PairContainer >
oCIMP::Pointer< IMP::Particle >
oCIMP::Pointer< IMP::QuadContainer >
oCIMP::Pointer< IMP::RestraintSet >
oCIMP::Pointer< IMP::saxs::DerivativeCalculator >
oCIMP::Pointer< IMP::saxs::Profile >
oCIMP::Pointer< IMP::saxs::ProfileFitter< IMP::saxs::ChiScore > >
oCIMP::Pointer< IMP::saxs::RigidBodiesProfileHandler >
oCIMP::Pointer< IMP::ScoreState >
oCIMP::Pointer< IMP::ScoringFunction >
oCIMP::Pointer< IMP::SingletonContainer >
oCIMP::Pointer< IMP::TripletContainer >
oCIMP::Pointer< IMP::UnaryFunction >
oCIMP::Pointer< internal::ConjugateGradientEigen >
oCIMP::Pointer< internal::KMdata >
oCIMP::Pointer< internal::KMfilterCenters >
oCIMP::Pointer< internal::ListSelectionPredicate >
oCIMP::Pointer< internal::RigidBodyHierarchy >
oCIMP::PointerMember< O >A smart pointer to a ref-counted Object that is a class member
oCIMP::PointerMember< algebra::NearestNeighbor3D >
oCIMP::PointerMember< algebra::NearestNeighbor6D >
oCIMP::PointerMember< atom::BrownianDynamics >
oCIMP::PointerMember< const IMP::rotamer::RotamerLibrary >
oCIMP::PointerMember< const IMP::saxs::Profile >
oCIMP::PointerMember< const saxs::Profile >
oCIMP::PointerMember< container::CloseBipartitePairContainer >
oCIMP::PointerMember< container::ClosePairContainer >
oCIMP::PointerMember< container::PredicatePairsRestraint >
oCIMP::PointerMember< core::Harmonic >
oCIMP::PointerMember< core::HarmonicDistancePairScore >
oCIMP::PointerMember< core::internal::MovedSingletonContainer >
oCIMP::PointerMember< core::TableRefiner >
oCIMP::PointerMember< display::Geometry >
oCIMP::PointerMember< domino::ParticleStatesTable >
oCIMP::PointerMember< domino::RestraintScoreSubsetFilterTable >
oCIMP::PointerMember< em2d::Image >
oCIMP::PointerMember< em::DensityMap >
oCIMP::PointerMember< GaussianProcessInterpolationScoreState >
oCIMP::PointerMember< IMP::atom::AngleSingletonScore >
oCIMP::PointerMember< IMP::atom::BondSingletonScore >
oCIMP::PointerMember< IMP::atom::DihedralSingletonScore >
oCIMP::PointerMember< IMP::atom::ImproperSingletonScore >
oCIMP::PointerMember< IMP::atom::PDBSelector >
oCIMP::PointerMember< IMP::atom::SmoothingFunction >
oCIMP::PointerMember< IMP::Configuration >
oCIMP::PointerMember< IMP::ConfigurationSet >
oCIMP::PointerMember< IMP::container::CloseBipartitePairContainer >
oCIMP::PointerMember< IMP::container::ConsecutivePairContainer >
oCIMP::PointerMember< IMP::core::ClosePairsFinder >
oCIMP::PointerMember< IMP::core::OrderedTypePairPredicate >
oCIMP::PointerMember< IMP::core::RestraintsScoringFunction >
oCIMP::PointerMember< IMP::core::RigidClosePairsFinder >
oCIMP::PointerMember< IMP::core::SoftSpherePairScore >
oCIMP::PointerMember< IMP::core::SurfaceGeometry >
oCIMP::PointerMember< IMP::core::TransformationSymmetry >
oCIMP::PointerMember< IMP::display::Writer >
oCIMP::PointerMember< IMP::domino::AssignmentsTable >
oCIMP::PointerMember< IMP::domino::ParticleStates >
oCIMP::PointerMember< IMP::domino::ParticleStatesTable >
oCIMP::PointerMember< IMP::domino::RestraintCache >
oCIMP::PointerMember< IMP::em2d::ScoreFunction >
oCIMP::PointerMember< IMP::em::DensityMap >
oCIMP::PointerMember< IMP::em::EnvelopeScore >
oCIMP::PointerMember< IMP::em::MapDistanceTransform >
oCIMP::PointerMember< IMP::em::PCAAligner >
oCIMP::PointerMember< IMP::em::SampledDensityMap >
oCIMP::PointerMember< IMP::IMP::PairContainer >
oCIMP::PointerMember< IMP::IMP::Particle >
oCIMP::PointerMember< IMP::IMP::Restraint >
oCIMP::PointerMember< IMP::IMP::SingletonContainer >
oCIMP::PointerMember< IMP::IMP::UnaryFunction >
oCIMP::PointerMember< IMP::isd::BivariateFunction >
oCIMP::PointerMember< IMP::isd::CrossLinkData >
oCIMP::PointerMember< IMP::isd::CysteineCrossLinkData >
oCIMP::PointerMember< IMP::isd::FNormal >
oCIMP::PointerMember< IMP::isd::FretData >
oCIMP::PointerMember< IMP::isd::GaussianProcessInterpolation >
oCIMP::PointerMember< IMP::isd::MolecularDynamics >
oCIMP::PointerMember< IMP::isd::MolecularDynamicsMover >
oCIMP::PointerMember< IMP::isd::MultivariateFNormalSufficient >
oCIMP::PointerMember< IMP::isd::UnivariateFunction >
oCIMP::PointerMember< IMP::kinematics::DirectionalDOF >
oCIMP::PointerMember< IMP::kinematics::DOFsSampler >
oCIMP::PointerMember< IMP::kinematics::LocalPlanner >
oCIMP::PointerMember< IMP::Model >
oCIMP::PointerMember< IMP::multifit::AssemblyHeader >
oCIMP::PointerMember< IMP::npctransport::GlobalStatisticsOptimizerState >
oCIMP::PointerMember< IMP::npctransport::IMP::npctransport::Scoring >
oCIMP::PointerMember< IMP::npctransport::IMP::npctransport::Statistics >
oCIMP::PointerMember< IMP::Object >
oCIMP::PointerMember< IMP::Optimizer >
oCIMP::PointerMember< IMP::OptimizerState >
oCIMP::PointerMember< IMP::PairContainer >
oCIMP::PointerMember< IMP::PairModifier >
oCIMP::PointerMember< IMP::PairPredicate >
oCIMP::PointerMember< IMP::PairScore >
oCIMP::PointerMember< IMP::Particle >
oCIMP::PointerMember< IMP::QuadContainer >
oCIMP::PointerMember< IMP::QuadModifier >
oCIMP::PointerMember< IMP::QuadPredicate >
oCIMP::PointerMember< IMP::QuadScore >
oCIMP::PointerMember< IMP::Refiner >
oCIMP::PointerMember< IMP::Restraint >
oCIMP::PointerMember< IMP::RestraintSet >
oCIMP::PointerMember< IMP::saxs::Profile >
oCIMP::PointerMember< IMP::ScoreState >
oCIMP::PointerMember< IMP::ScoringFunction >
oCIMP::PointerMember< IMP::SingletonContainer >
oCIMP::PointerMember< IMP::SingletonModifier >
oCIMP::PointerMember< IMP::SingletonPredicate >
oCIMP::PointerMember< IMP::SingletonScore >
oCIMP::PointerMember< IMP::statistics::Embedding >
oCIMP::PointerMember< IMP::statistics::Metric >
oCIMP::PointerMember< IMP::statistics::PartitionalClustering >
oCIMP::PointerMember< IMP::TripletContainer >
oCIMP::PointerMember< IMP::TripletModifier >
oCIMP::PointerMember< IMP::TripletPredicate >
oCIMP::PointerMember< IMP::TripletScore >
oCIMP::PointerMember< IMP::UnaryFunction >
oCIMP::PointerMember< internal::PairContainerIndex >
oCIMP::PointerMember< internal::QuadContainerIndex >
oCIMP::PointerMember< internal::SingletonContainerIndex >
oCIMP::PointerMember< internal::TripletContainerIndex >
oCIMP::PointerMember< kinematics::IMP::kinematics::KinematicForest >
oCIMP::PointerMember< multifit::IMP::multifit::ProteomicsData >
oCIMP::PointerMember< PairScore >
oCIMP::PointerMember< Predicate >
oCIMP::PointerMember< rmf::SaveOptimizerState >
oCIMP::PointerMember< ScoringFunctionT >
oCIMP::PointerMember< Table >
oCIMP::PointerMember< UF >
oCIMP::score_functor::PointToSphereDistance< BaseDistanceScore >
oCIMP::em2d::PolarResamplingParameters
oCIMP.pmi.analysis.PrecisionA class to evaluate the precision of an ensemble
oCIMP.pmi1.analysis.PrecisionA class to evaluate the precision of an ensemble
oCIMP.pmi.output.ProcessOutputA class for reading stat files (either rmf or ascii v1 and v2)
oCIMP.pmi1.output.ProcessOutputA class for reading stat files (either rmf or ascii v1 and v2)
oCIMP::saxs::ProfileClustering
oCIMP::em2d::ProjectingParametersParameters needed for the core projection routine
oCIMP::em2d::ProjectionMask
oCIMP::multifit::ProteinsAnchorsSamplingSpaceStores the anchors sampling space for each protein
oCIMP.pmi.output.ProtocolOutputBase class for capturing a modeling protocol
oCIMP.pmi1.output.ProtocolOutputBase class for capturing a modeling protocol
oCIMP.pmi.restraints.stereochemistry.PseudoAtomicRestraintAdd bonds and improper dihedral restraints for the CBs
oCIMP.pmi1.restraints.stereochemistry.PseudoAtomicRestraintAdd bonds and improper dihedral restraints for the CBs
oCIMP::PythonDirectedGraph
oCIMP::em::RadiusDependentDistanceMask
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.samplers.ReplicaExchangeSample using replica exchange
oCIMP.pmi1.samplers.ReplicaExchangeSample using replica exchange
oCIMP.pmi.macros.ReplicaExchangeA macro to help setup and run replica exchange
oCIMP.pmi1.macros.ReplicaExchange0A macro to help setup and run replica exchange
oCIMP.pmi1.representation.RepresentationSet up the representation of all proteins and nucleic acid macromolecules
oCIMP.pmi.alphabets.ResidueAlphabetMap between FASTA codes and residue types
oCIMP.pmi.restraints.stereochemistry.ResidueAngleRestraintAdd angular restraint between triplets of consecutive residues/beads to enforce the stereochemistry
oCIMP.pmi1.restraints.stereochemistry.ResidueAngleRestraintAdd angular restraint between triplets of consecutive residues/beads to enforce the stereochemistry
oCIMP.pmi.restraints.stereochemistry.ResidueBondRestraintAdd bond restraint between pair of consecutive residues/beads to enforce the stereochemistry
oCIMP.pmi1.restraints.stereochemistry.ResidueBondRestraintAdd bond restraint between pair of consecutive residues/beads to enforce the stereochemistry
oCIMP.pmi.restraints.stereochemistry.ResidueDihedralRestraintAdd dihedral restraints between quadruplet of consecutive residues/beads to enforce the stereochemistry
oCIMP.pmi1.restraints.stereochemistry.ResidueDihedralRestraintAdd dihedral restraints between quadruplet of consecutive residues/beads to enforce the stereochemistry
oCIMP.pmi.io.crosslink.ResiduePairListParserA class to handle different styles of site pairs parsers
oCIMP.pmi1.io.crosslink.ResiduePairListParserA class to handle different styles of site pairs parsers
oCIMP.pmi.restraints.basic.ResidueProteinProximityRestraintRestrain residue/residues to bind to unknown location in a target
oCIMP::rotamer::ResidueRotamerA class storing the rotated coordinates of the atoms in the residue
oCIMP::atom::ResidueTypeThe type for a residue
oCIMP.pmi1.restraints.RestraintBaseBase class for PMI restraints, which wrap IMP.Restraint(s)
oCIMP.pmi1.analysis.RMSDCompute the RMSD (without alignment) taking into account the copy ambiguity
oCIMP.pmi.analysis.RMSDCompute the RMSD (without alignment) taking into account the copy ambiguity
oCIMP.pmi1.io.RMSDOutputA helper output based on dist to initial coordinates
oCIMP::rotamer::RotamerAngleTupleA simple class storing chi angles and their probability
oCIMP::kinematics::RRT::RRTNodeSimple RRT node implementation
oCIMP.pmi.restraints.saxs.SAXSISDRestraintBasic SAXS restraint using ISD
oCIMP.pmi.restraints.saxs.SAXSRestraintBasic SAXS restraint
oCIMP::score_functor::ScoreA functor for computing a distance based score for D particles
oCIMP::score_functor::ScoreWithCacheA cached functor for computing a distance based score for D particles
oCIMP.pmi1.restraints.stereochemistry.SecondaryStructureExperimental, requires isd_emxl for now
oCIMP::em2d::SegmentationParametersClass to provide all the parameters to the segmentation function
oCIMP.pmi.tools.SegmentsThis class stores integers in ordered compact lists eg: [[1,2,3],[6,7,8]] the methods help splitting and merging the internal lists Example: s=Segments([1,2,3]) is [[1,2,3]] s.add(4) is [[1,2,3,4]] (add right) s.add(3) is [[1,2,3,4]] (item already existing) s.add(7) is [[1,2,3,4],[7]] (new list) s.add([8,9]) is [[1,2,3,4],[7,8,9]] (add item right) s.add([5,6]) is [[1,2,3,4,5,6,7,8,9]] (merge) s.remove(3) is [[1,2],[4,5,6,7,8,9]] (split) etc
oCIMP.pmi1.tools.SegmentsThis class stores integers in ordered compact lists eg: [[1,2,3],[6,7,8]] the methods help splitting and merging the internal lists Example: s=Segments([1,2,3]) is [[1,2,3]] s.add(4) is [[1,2,3,4]] (add right) s.add(3) is [[1,2,3,4]] (item already existing) s.add(7) is [[1,2,3,4],[7]] (new list) s.add([8,9]) is [[1,2,3,4],[7,8,9]] (add item right) s.add([5,6]) is [[1,2,3,4,5,6,7,8,9]] (merge) s.remove(3) is [[1,2],[4,5,6,7,8,9]] (split) etc
oCIMP.pmi1.topology.SequencesA dictionary-like wrapper for reading and storing sequence data
oCIMP.pmi.topology.SequencesA dictionary-like wrapper for reading and storing sequence data
oCIMP.pmi.restraints.proteomics.SetupConnectivityNetworkRestraintGenerates and wraps a IMP.pmi.ConnectivityRestraint between domains example: cr=restraints.ConnectivityNetworkRestraint( simo,["CCC",(1,100,"TTT"),(100,150,"AAA")]) cr.add_to_model() cr.set_label("CR1")
oCIMP.pmi1.restraints.proteomics.SetupConnectivityNetworkRestraintGenerates and wraps a IMP.pmi1.ConnectivityRestraint between domains example: cr=restraints.ConnectivityNetworkRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")]) cr.add_to_model() cr.set_label("CR1")
oCIMP.pmi1.restraints.proteomics.SetupMembraneRestraint
oCIMP.isd.shared_functions.sfo_commonNonspecific methods used across all shared function objects
oCIMP::score_functor::Shift< BaseDistanceScore >
oCIMP::ShowableHelper class to aid in output of IMP classes to streams
oCIMP::em2d::SingleLinkageFunctor for hierarchical clustering based on single linkage
oCIMP::score_functor::SingletonStatistical< Key, INTERPOLATE >Create a single key/single particle statistical potential from a file
oCIMP::npctransport::SitesPairScoreParameters
oCIMP::saxs::SolventAccessibleSurface
oCIMP::algebra::SparseGridStorageD< D, VT, Base, Map >
oCIMP::algebra::SparseGridStorageD< D, VT, Base >
oCIMP::SparseSymmetricPairMemoizer< Generator, Checker >
oCIMP::score_functor::SphereDistance< BaseDistanceScore >
oCIMP::em::SpiderHeaderHeader for Spider images. IMP-EM is designed to be compatible with it
oCIMP.pmi.topology.StateStores a list of Molecules all with the same State index
oCIMP.isd.Statistics.StatisticsStatistics gathering and printing class for ISD gibbs sampling
oCIMP.pmi.tools.StopwatchCollect timing information
oCIMP.pmi1.tools.StopwatchCollect timing information
oCIMP.pmi.StructureWarningWarning related to handling of structures
oCSurfacesGeometryDisplay an IMP::SingletonContainer of Surface particles as cylindrical disks
oCIMP.pmi1.restraints.stereochemistry.SymmetryRestraintCreate harmonic restraints between the reference and (transformed) clones
oCIMP.pmi.restraints.stereochemistry.SymmetryRestraintCreate harmonic restraints between the reference and (transformed) clones
oCIMP.pmi.topology.SystemRepresent the root node of the global IMP.atom.Hierarchy
oCIMP.isd.TALOSReader.TALOSReaderReads a TALOS file, or a TALOS folder, and stores the data
oCIMP.pmi.topology.TempResidueTemporarily stores residue information, even without structure available
oCIMP.test.TestCaseSuper class for IMP test cases
oCIMP.pmi1.tools.ThreeToOneConverterThis class converts three to one letter codes, and return X for any unknown codes
oCIMP.pmi.plotting.topology.TopologyPlotA class to read RMF files and make a network contact map
oCIMP.pmi1.plotting.topology.TopologyPlotA class to read RMF files and make a network contact map
oCIMP.pmi1.topology.TopologyReaderAutomatically setup System and Degrees of Freedom with a formatted text file
oCIMP.pmi.topology.TopologyReaderAutomatically setup System and Degrees of Freedom with a formatted text file
oCIMP.pmi.io.TotalScoreOutputA helper output for model evaluation
oCIMP.pmi1.io.TotalScoreOutputA helper output for model evaluation
oCIMP.EMageFit.imp_general.io.Transformation3DToTextParseable output for a IMP Transformation3D
oCIMP::algebra::UnboundedGridRangeD< D >
oCIMP::algebra::UnboundedGridRangeD< 3 >
oCIMP::UncheckedWeakPointer< O >A weak pointer to an Object or RefCountedObject
oCIMP::UncheckedWeakPointer< IMP::npctransport::SimulationData >
oCIMP::UncheckedWeakPointer< IMP::Optimizer >
oCIMP::UsageExceptionAn exception for an invalid usage of IMP
oCIMP::ValueBase class for a simple primitive-like type
oCstd::vector< T >STL class
oCIMP::WarningContextWarnings with the same key within the context are only output once
oCIMP::WeakPointer< O >Smart pointer to Object-derived classes that does not refcount
oCIMP::WeakPointer< atom::Simulator >
oCIMP::WeakPointer< IMP::atom::Simulator >
oCIMP::WeakPointer< IMP::Model >
oCIMP::WeakPointer< IMP::npctransport::IMP::npctransport::Statistics >
oCIMP::WeakPointer< IMP::npctransport::SimulationData >
oCIMP::WeakPointer< IMP::Particle >
oCIMP::WeakPointer< IMP::Restraint >
oCIMP.pmi.restraints.parameters.WeightRestraintWrapper for an IMP.isd.WeightRestraint
oCIMP::score_functor::WeightScore< BaseDistanceScore >
oCIMP.parallel.WorkerRepresentation of a single worker
oCIMP.parallel.WorkerArrayRepresentation of an array of workers
oCIMP.mmcif.util.WriterConvert one or more IMP Models and/or RMF frames to mmCIF or BinaryCIF
oCIMP.EMageFit.buildxlinks.XlinkClass defining a cross-link
oCIMP.EMageFit.buildxlinks.XlinksDictDescription of crosslinking restraints as a python dictionary
oCIMP.pmi1.io.xltable.XLTableClass to read, analyze, and plot xlink data on contact maps Canonical way to read the data: 1) load sequences and name them 2) load coordinates for those sequences from PDB file 3) add crosslinks 4) create contact map 5) plot
oCIMP.pmi1.restraints.npc.XYRadialPositionLowerRestraintCreate XYRadial Position Lower restraints
oCIMP.pmi.restraints.npc.XYRadialPositionLowerRestraintRestrain a protein's distance from the z axis to above a lower bound
oCIMP.pmi1.restraints.npc.XYRadialPositionRestraintCreate XYRadial Position Restraint
oCIMP.pmi.restraints.npc.XYRadialPositionRestraintRestrain a protein's distance from the z axis to within a given range
oCIMP.pmi1.restraints.npc.XYRadialPositionUpperRestraintCreate XYRadial Position Upper restraints
oCIMP.pmi.restraints.npc.XYRadialPositionUpperRestraintRestrain a protein's distance from the z axis to below an upper bound
oCIMP.pmi.restraints.npc.YAxialPositionLowerRestraintRestrain a protein's y coordinate to above a lower bound
oCIMP.pmi1.restraints.npc.YAxialPositionLowerRestraintCreate Y-Axial Position Lower restraints
oCIMP.pmi.restraints.npc.YAxialPositionRestraintRestrain a protein's y coordinate to within a given range
oCIMP.pmi1.restraints.npc.YAxialPositionRestraintCreate Y-Axial Position restraints
oCIMP.pmi.restraints.npc.YAxialPositionUpperRestraintRestrain a protein's y coordinate to below an upper bound
oCIMP.pmi1.restraints.npc.YAxialPositionUpperRestraintCreate Y-Axial Position Upper restraints
oCIMP.pmi.restraints.npc.ZAxialPositionLowerRestraintRestrain a protein's z coordinate to above a lower bound
oCIMP.pmi1.restraints.npc.ZAxialPositionLowerRestraintCreate Z-Axial Position Lower restraints
oCIMP.pmi.restraints.npc.ZAxialPositionRestraintRestrain a protein's z coordinate to within a given range
oCIMP.pmi1.restraints.npc.ZAxialPositionRestraintCreate Z-Axial Position restraints
oCIMP.pmi1.restraints.npc.ZAxialPositionUpperRestraintCreate Z-Axial Position Upper restraints
\CIMP.pmi.restraints.npc.ZAxialPositionUpperRestraintRestrain a protein's z coordinate to below an upper bound