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IMP Reference Guide  2.8.0
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::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.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 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.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::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.pmi.macros.BuildModelA macro to build a Representation based on a Topology and lists of movers DEPRECATED - Use BuildSystem instead
oCIMP.pmi.macros.BuildModel1Deprecated building macro - use BuildSystem()
oCIMP.pmi.macros.BuildSystemA macro to build a IMP::pmi::topology::System based on a TopologyReader object
oCIMP::kinematics::CCDLoopClosureCCD loop closure
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.pmi.restraints.stereochemistry.CharmmForceFieldRestraintEnable CHARMM force field
oCIMP.pmi.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.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 is a selection tuple compositeparticles is a list of selection tuples
oCIMP.pmi.samplers.ConjugateGradientsSample using conjugate gradients
oCIMP.pmi.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: 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.pmi.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.pmi.restraints.em.CrossCorrelationRestraintFit particles to an EM map
oCIMP.pmi.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.pmi.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 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::multifit::DataPointsAssignment
oCIMP::algebra::DefaultEmbeddingD< D >Embed a grid as an evenly spaced axis aligned grid
oCIMP::algebra::DefaultEmbeddingD< 3 >
oCIMP.pmi.dof.DegreesOfFreedomA class to simplify create 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.EMageFit.buildxlinks.DockOrderCompute the order of the docking experiments
oCIMP.EMageFit.domino_model.DominoModelManagement of a model using DOMINO
oCIMP.pmi.restraints.stereochemistry.ElasticNetworkRestraintAdd harmonic restraints between all pairs
oCIMP.pmi.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::atom::ElementTable
oCIMP::multi_state::EnsembleGeneratorEnumeration of an ensemble of good scoring MultiStateModels
oCIMP.isd.Entry.EntryThe entry class represents a column in the statistics file
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.pmi.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::Flag< T, ENABLED >
oCIMP::saxs::FormFactorTable
oCIMP.pmi.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.pmi.restraints.em.GaussianEMRestraintFit 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::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.pmi.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.EMageFit.buildxlinks.InitialDockingFromXlinksPuts two subunits together using the Xlinkins restraints
oCIMP::InputAdaptor
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::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 >
oCIMP.parallel.ManagerManages slaves and contexts
oCIMP.pmi.io.crosslink.MapCrossLinkDataBaseOnStructureThis class maps a CrossLinkDataBase on a given structure and save an rmf file with the color coded crosslinks
oCIMP::em2d::MasksManagerManagement of projection masks
oCIMP.parallel.master_communicator.MasterCommunicatorFor communicating from the master to slaves
oCIMP::em2d::MatchTemplateResult
oCIMP::Memoizer< Generator, Checker >
oCIMP::multifit::MergeTreeBuilderUtility class for building merge trees
oCIMP.pmi.metadata.MetadataBase class for all metadata
oCIMP.modeller.ModelLoaderRead a Modeller model into IMP
oCIMP::cnmultifit::MolCnSymmAxisDetectorMolecule symmetry detector
oCIMP.pmi.samplers.MolecularDynamicsSample using molecular dynamics
oCIMP.pmi.topology.MoleculeStores a named protein chain
oCIMP.pmi.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::NonCopyable
oCIMP.OptionParserIMP-specific subclass of optparse.OptionParser
oCIMP.pmi.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::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 pdb
oCIMP::piecewise_linear_distribution< T >
oCIMP.isd.utils.PipeImplements a FIFO pipe that merges lists (see self.put)
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::core::IncrementalScoringFunction >
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::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::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< 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< core::HarmonicDistancePairScore >
oCIMP::PointerMember< core::internal::MovedSingletonContainer >
oCIMP::PointerMember< core::TableRefiner >
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::ConsecutivePairContainer >
oCIMP::PointerMember< IMP::core::ClosePairsFinder >
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::Particle >
oCIMP::PointerMember< IMP::IMP::UnaryFunction >
oCIMP::PointerMember< IMP::internal::IMP::core::RestraintsScoringFunction >
oCIMP::PointerMember< IMP::isd::BivariateFunction >
oCIMP::PointerMember< IMP::isd::CrossLinkData >
oCIMP::PointerMember< IMP::isd::CysteineCrossLinkData >
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::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< 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.pmi.output.ProcessOutputA class for reading stat files
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.pmi.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.pmi.macros.ReplicaExchange0A macro to help setup and run replica exchange
oCIMP.pmi.representation.RepresentationSet up the representation of all proteins and nucleic acid macromolecules
oCIMP.pmi.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.pmi.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::rotamer::ResidueRotamerA class storing the rotated coordinates of the atoms in the residue
oCIMP::atom::ResidueTypeThe type for a residue
oCIMP.pmi.restraints.RestraintBaseBase class for PMI restraints, which wrap IMP.Restraint(s)
oCIMP.pmi.analysis.RMSDCompute the RMSD (without alignment) taking into account the copy ambiguity
oCIMP.pmi.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.test.RunInTempDirSimple RAII-style class to run in a temporary directory
oCIMP::score_functor::ScoreA functor for computing a distance based score for two particles
oCIMP.pmi.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.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.pmi.restraints.proteomics.SetupMembraneRestraint
oCIMP.isd.shared_functions.sfo_commonNonspecific methods used across all shared function objects
oCIMP::score_functor::Shift< BaseDistanceScore >
oCIMP::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::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
oCSurfacesGeometryDisplay an IMP::SingletonContainer of Surface particles as cylindrical disks
oCIMP.pmi.restraints.stereochemistry.SymmetryRestraintCreate harmonic restraints between the reference and (transformed) clones
oCIMP.pmi.topology.SystemThis class initializes 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.test.TempDirSimple RAII-style class to make a temporary directory
oCIMP.pmi.topology.TempResidueTemporarily stores residue information, even without structure available
oCIMP.test.TestCaseSuper class for IMP test cases
oCIMP.pmi.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.pmi.topology.TopologyReaderAutomatically setup Sytem and Degrees of Freedom with a formatted text file
oCIMP.pmi.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::Optimizer >
oCIMP::UsageExceptionAn exception for an invalid usage of IMP
oCIMP::ValueBase for a simple primitive-like type
oCstd::vector< T >STL class
oCIMP::WarningContext
oCIMP::WeakPointer< O >Smart pointer to Object-derived classes that does not refcount
oCIMP::WeakPointer< atom::Simulator >
oCIMP::WeakPointer< IMP::Model >
oCIMP::WeakPointer< IMP::Particle >
oCIMP::WeakPointer< IMP::Restraint >
oCIMP::score_functor::WeightScore< BaseDistanceScore >
oCIMP.EMageFit.buildxlinks.XlinkClass defining a cross-link
oCIMP.EMageFit.buildxlinks.XlinksDictDescription of crosslinking restraints as a python dictionary
\CIMP.pmi.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