  IMP::AddBoolFlag | |
| IMP::AddFloatFlag | |
| IMP::AddIntFlag | |
| IMP::AddStringFlag | |
| IMP::AdvancedFlag< T, ENABLED > | Use this to add an advanced flag to the program |
| IMP.pmi.analysis.Alignment | Performs alignment and RMSD calculation for two sets of coordinates |
| IMP.multifit.cluster.AlignmentClustering | Clusters assembly models |
| IMP::cnmultifit::AlignSymmetric | A class for fast alignment of a cyclic model to its density |
| IMP.pmi.restraints.proteomics.AmbiguousCompositeRestraint | This restraint allows ambiguous crosslinking between multiple copies excluding between symmetric copies It allows name ambiguity |
| IMP.isd.Analysis.Analysis | Class that produces analysis-related output, and is able to parse the output of a file produced by the Statistics class |
| IMP.pmi.macros.AnalysisReplicaExchange0 | A macro for running all the basic operations of analysis |
| IMP::multifit::AnchorsData | Storage of anchors (points and edges) |
| IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint | Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes' theory of probability |
| IMP::atom::AtomType | The type of an atom |
| IMP::em2d::AverageDistanceLinkage | Functor for hierarchical clustering based on average-linkage |
| IMP::modeller::BinormalTerm | A single binormal term in a MultipleBinormalRestraint |
| IMP::atom::ForceFieldParameters::Bond | |
| IMP::atom::BondGraph | Represent a bond graph as a boost graph |
 IMP::algebra::BoundedGridRangeD< D > | |
 IMP::algebra::DenseGridStorageD< 3, int > | |
 IMP::algebra::GridD< 3, DenseGridStorageD< 3, int >, int, LogEmbeddingD< 3 > > | |
  IMP::algebra::DenseIntLogGrid3D | |
| IMP::algebra::DenseGridStorageD< 3, VT > | |
| IMP::algebra::GridD< 3, DenseGridStorageD< 3, VT >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::DenseGrid3D< VT > | A dense grid of values |
| IMP::algebra::DenseGridStorageD<-1, float > | |
| IMP::algebra::GridD<-1, DenseGridStorageD<-1, float >, float, LogEmbeddingD<-1 > > | |
| IMP::algebra::DenseFloatLogGridKD | |
| IMP::algebra::DenseGridStorageD< D, VT > | |
| IMP::algebra::GridD< D, DenseGridStorageD< D, VT >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::BoundedGridRangeD< 3 > | |
| IMP::algebra::SparseGridStorageD< 3, VT, BoundedGridRangeD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, VT, BoundedGridRangeD< 3 > >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::SparseGrid3D< VT > | A sparse grid of values |
| IMP::algebra::BoundingBoxD< D > | An axis-aligned bounding box |
| IMP::algebra::BoundingBoxD< 3 > | |
| IMP.pmi.macros.BuildModel | A macro to build a Representation based on a Topology and lists of movers DEPRECATED - Use BuildSystem instead |
| IMP.pmi.macros.BuildModel1 | Deprecated building macro - use BuildSystem() |
| IMP.pmi.macros.BuildSystem | A macro to build a IMP::pmi::topology::System based on a TopologyReader object |
| IMP::kinematics::CCDLoopClosure | |
| IMP::em2d::CenteredMat | |
| IMP::atom::CHARMMAtomTopology | A single atom in a CHARMM topology |
| IMP::atom::CHARMMBondEndpoint | The end of a bond, angle, dihedral, improper, or internal coordinate |
| IMP::atom::CHARMMBondParameters | The parameters for a CHARMM bond or angle |
| IMP::atom::CHARMMConnection< D > | A connection (bond, angle, dihedral) between some number of endpoints |
| IMP::atom::CHARMMConnection< 4 > | |
| IMP::atom::CHARMMInternalCoordinate | A geometric relationship between four atoms |
| IMP::atom::CHARMMDihedralParameters | The parameters for a CHARMM dihedral or improper |
| IMP.pmi.restraints.stereochemistry.CharmmForceFieldRestraint | Enable CHARMM force field |
| IMP.pmi.analysis.Clustering | A class to cluster structures |
| IMP::em2d::ClusterSet | A class to store the clusters generated during hierarchical clustering |
| IMP::cnmultifit::CnSymmAxisDetector | Detect cn symmetry in proteins and density maps |
| IMP::em::CoarseConvolution | Convolutes two grids |
| IMP.pmi.tools.ColorChange | Change color code to hexadecimal to rgb |
| IMP.CommandDispatcher | Allow command line tools to easily implement multiple commands |
| IMP::multi_state::CompareMultiStateModels | Utility class to help sort MultiStateModel objects |
| IMP::em2d::CompleteLinkage | Functor for hierarchical clustering based on complete linkage |
| IMP.pmi.topology.ComponentTopology | Stores the components required to build a standard IMP hierarchy using IMP.pmi.BuildModel() |
| IMP.pmi.restraints.proteomics.CompositeRestraint | Handleparticles is a selection tuple compositeparticles is a list of selection tuples |
| IMP.pmi.samplers.ConjugateGradients | Sample using conjugate gradients |
| IMP.pmi.restraints.crosslinking.ConnectivityCrossLinkMS | This restraint allows ambiguous crosslinking between multiple copies it is a variant of the SimplifiedCrossLinkMS |
| IMP.pmi.restraints.proteomics.ConnectivityRestraint | Generate 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 |
| IMP.pmi.restraints.stereochemistry.ConnectivityRestraint | This class creates a restraint between consecutive TempResidue objects OR an entire PMI MOlecule object |
| IMP::algebra::ConnollySurfacePoint | Represent a point on the Connolly surface |
| IMP.parallel.Context | A collection of tasks that run in the same environment |
| IMP.pmi.restraints.em.CrossCorrelationRestraint | Fit particles to an EM map |
| IMP.pmi.io.crosslink.CrossLinkDataBaseFromStructure | This class generates a CrossLinkDataBase from a given structure |
| IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter | This class is needed to convert the keywords from a generic database to the standard ones |
| IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint | Setup cross-link distance restraints from mass spectrometry data |
| IMP.pmi.nonmantained.CrossLinkMS | This 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 |
| IMP.pmi.analysis.CrossLinkTable | Visualization of crosslinks |
| IMP.isd.TuneRex.CvEstimator | When created, estimates the heat capacity from the energies or from the indicator functions using the specified method |
| IMP.EMageFit.database.Database2 | Class to manage a SQL database built with sqlite3 |
| IMP.EMageFit.solutions_io.ResultsDB | Class for managing the results of the experiments |
| IMP::multifit::DataPointsAssignment | |
| IMP::algebra::DefaultEmbeddingD< D > | |
| IMP::algebra::GridD< D, DenseGridStorageD< D, VT >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::GridD< D, SparseGridStorageD< D, VT, UnboundedGridRangeD< D > >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::SparseUnboundedGridD< D, VT > | A sparse, infinite grid of values |
| IMP::algebra::DefaultEmbeddingD< 3 > | |
| IMP::algebra::GridD< 3, DenseGridStorageD< 3, VT >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, Ints, UnboundedGridRangeD< 3 > >, Ints, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, VT, BoundedGridRangeD< 3 > >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, VT, UnboundedGridRangeD< 3 > >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::SparseUnboundedGrid3D< VT > | A sparse, infinite grid of values |
| IMP.pmi.dof.DegreesOfFreedom | A class to simplify create of constraints and movers for an IMP Hierarchy |
| IMP.isd.demux_trajs.Demuxer | Uses column to demux a replica trajectory |
| IMP::multifit::DensityDataPoints | Stores density voxels as a vector of Array1D |
| IMP::em::DensityHeader | |
| IMP::DerivativeAccumulator | Class for adding derivatives from restraints to the model |
| IMP.test.DirectorObjectChecker | Check to make sure the number of director references is as expected |
| IMP::em::DistanceMask | Calculates and stores a distance mask |
| IMP.pmi.restraints.basic.DistanceRestraint | A simple distance restraint |
| IMP.EMageFit.buildxlinks.DockOrder | Compute the order of the docking experiments |
| IMP.EMageFit.domino_model.DominoModel | Management of a model using DOMINO |
| IMP.pmi.restraints.stereochemistry.ElasticNetworkRestraint | Add harmonic restraints between all pairs |
| IMP.pmi.restraints.em2d.ElectronMicroscopy2D | Fit particles against a set of class averages by principal components |
| IMP.pmi.restraints.em2d.ElectronMicroscopy2D_FFT | FFT based image alignment, developed by Javier Velazquez-Muriel |
| IMP::atom::ElementTable | |
| IMP::multi_state::EnsembleGenerator | Enumeration of an ensemble of good scoring MultiStateModels |
| IMP.isd.Entry.Entry | The entry class represents a column in the statistics file |
| IMP::EvaluationState | |
| IMP::example::ExampleTemplateClassD< D > | A line segment templated on the dimension |
| IMP::Exception | The general base class for IMP exceptions |
| IMP::EventException | An exception that signifies some event occurred |
| IMP::IndexException | An exception for a request for an invalid member of a container |
| IMP::IOException | An input/output exception |
| IMP::ModelException | An exception which is thrown when the Model has attributes with invalid values |
| IMP.parallel.Error | Base class for all errors specific to the parallel module |
| IMP.parallel.NetworkError | Error raised if a problem occurs with the network |
| IMP.parallel.NoMoreSlavesError | Error raised if all slaves failed, so tasks cannot be run |
| IMP.parallel.RemoteError | Error raised if a slave has an unhandled exception |
| IMP::TypeException | An exception for an invalid type being passed to IMP |
| IMP::ValueException | An exception for an invalid value being passed to IMP |
| IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere | A class to create an excluded volume restraint for a set of particles at a given resolution |
| IMP.pmi.io.crosslink.FilterOperator | This class allows to create filter functions that can be passed to the CrossLinkDataBase in this way: |
| IMP::saxs::FitParameters | Parameters of a fit, from ProfileFitter |
| IMP::saxs::WeightedFitParameters | Parameters of a weighted fit, from WeightedProfileFitter |
| IMP::multifit::FittingSolutionRecord | A fitting solution record |
| IMP::em::FittingSolutions | A simple list of fitting solutions |
| IMP.pmi.io.crosslink.FixedFormatParser | A class to handle different XL format with fixed format currently support ProXL |
| IMP::Flag< T, ENABLED > | |
| IMP::saxs::FormFactorTable | |
| IMP.pmi.restraints.proteomics.FuzzyBoolean | Fully Ambiguous Restraint that can be built using boolean logic R |
| IMP.pmi.restraints.em.GaussianEMRestraint | Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) |
| IMP::multifit::GeometricHash< T, D > | Geometric Hash table |
| IMP::algebra::GeometricPrimitiveD< D > | Base class for geometric types |
| IMP::algebra::GridD< 3, DenseGridStorageD< 3, int >, int, LogEmbeddingD< 3 > > | |
| IMP::algebra::GridD< 3, DenseGridStorageD< 3, VT >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, Ints, UnboundedGridRangeD< 3 > >, Ints, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, VT, BoundedGridRangeD< 3 > >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, VT, UnboundedGridRangeD< 3 > >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::GridD< D, DenseGridStorageD< D, VT >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::GridD< D, SparseGridStorageD< D, VT, UnboundedGridRangeD< D > >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::GridD<-1, DenseGridStorageD<-1, float >, float, LogEmbeddingD<-1 > > | |
| IMP::algebra::GridD< D, StorageT, Value, EmbeddingT > | A voxel grid in d-dimensional space space |
| IMP::algebra::PrincipalComponentAnalysisD< D > | |
| IMP::algebra::SphereD< D > | Represent a sphere in D-dimensions |
| IMP::algebra::VectorBaseD< D > | A Cartesian vector in D-dimensions |
| IMP::algebra::VectorD< D > | A Cartesian vector in D-dimensions |
| IMP::algebra::VectorD< 2 > | |
| IMP::algebra::VectorD< 3 > | |
| IMP::algebra::VectorD< 4 > | |
| IMP::statistics::HistogramD< D, Grid > | Dynamically build a histogram embedded in D-dimensional space |
| IMP::algebra::SphereD< 3 > | |
| IMP::algebra::VectorBaseD< 1 > | |
| IMP::algebra::VectorBaseD< 2 > | |
| IMP::algebra::VectorBaseD< 3 > | |
| IMP::algebra::VectorBaseD< 4 > | |
| IMP::algebra::VectorBaseD< 5 > | |
| IMP::algebra::VectorBaseD< 6 > | |
| IMP::algebra::VectorBaseD<-1 > | |
| IMP::algebra::GeometricPrimitiveD< 2 > | |
| IMP::algebra::LinearFit2D | Calculate line that fits best the input data points (Linear least squares) |
| IMP::algebra::ParabolicFit2D | Calculate parabola that fits best the input data points |
| IMP::algebra::Rotation2D | Stores a 2D rotation matrix |
| IMP::algebra::Transformation2D | Simple 2D transformation class |
| IMP::algebra::GeometricPrimitiveD< 3 > | |
| IMP::algebra::Cone3D | Represent a cone in 3D |
| IMP::algebra::Cylinder3D | Represent a cylinder in 3D |
| IMP::algebra::Ellipsoid3D | Represent an ellipsoid in 3D |
| IMP::algebra::FixedXYZ | A simple class for returning XYZ Euler angles |
| IMP::algebra::Gaussian3D | A Gaussian distribution in 3D |
| IMP::algebra::Plane3D | Represent a plane in 3D |
| IMP::algebra::Reflection3D | Reflect about a plane in 3D |
| IMP::algebra::Rotation3D | 3D rotation class |
| IMP::algebra::Segment3D | Simple implementation of segments in 3D |
| IMP::algebra::SpherePatch3D | A sphere patch is defined as all points above the plane and on the sphere |
| IMP::algebra::SphericalVector3D | Class to represent a 3D point in spherical coordinates |
| IMP::algebra::Transformation3D | Simple 3D transformation class |
| IMP::algebra::Triangle3D | Represent a triangle in 3D |
| IMP::display::GeometryProcessor | Provide a standard geometry processing framework |
| IMP::display::FilterGeometry | Remove geometry which is not above a plane |
| IMP::display::Writer | Base class for writing geometry to a file |
| IMP::display::PivyWriter | |
| IMP::display::TextWriter | |
| IMP::display::PymolWriter | Write a CGO file with the geometry |
| IMP.pmi.analysis.GetModelDensity | Compute mean density maps from structures |
| IMP::em2d::HasHigherCCC< T > | Comparison by value of the ccc |
| IMP::em2d::HasLowerScore< T > | Compare two classes that return a score |
| IMP.EMageFit.solutions_io.HeapRecord | The heapq algorithm is a min-heap |
| IMP.pmi.tools.HierarchyDatabase | Store the representations for a system |
| IMP::core::HierarchyTraits | Define the type for a type of hierarchy |
| IMP::core::HierarchyVisitor | A visitor for traversal of a hierarchy |
| IMP::core::HierarchyCounter | A simple functor to count the number of particles in a hierarchy |
| IMP::core::ModifierVisitor | A visitor which applies a modifier to each Particle in a hierarchy |
| IMP.isd.History.History | Class that contains the output of one replica, used by the Analysis class |
| IMP::em::ImageHeader | Class to deal with the header of Electron Microscopy images in IMP |
| IMP.modeller.IMPRestraints | A Modeller restraint which evaluates an IMP scoring function |
| IMP.EMageFit.buildxlinks.InitialDockingFromXlinks | Puts two subunits together using the Xlinkins restraints |
| IMP::InputAdaptor | |
| IMP::atom::Selection | Select hierarchy particles identified by the biological name |
| IMP::display::WriterAdaptor | |
| IMP::domino::ParticlesAdaptor | |
| IMP::PairContainerAdaptor | |
| IMP::ParticleAdaptor | |
| IMP::ParticleIndexAdaptor | |
| IMP::ParticleIndexesAdaptor | |
| IMP::ParticleIndexPairsAdaptor | |
| IMP::QuadContainerAdaptor | |
| IMP::RestraintsAdaptor | Provide a consistent interface for things that take Restraints as arguments |
| IMP::ScoringFunctionAdaptor | |
| IMP::SingletonContainerAdaptor | |
| IMP::TextInput | |
| IMP::TextOutput | |
| IMP::TripletContainerAdaptor | |
| IMP::InternalException | A general exception for an internal error in IMP |
| IMP::em2d::IntsOrder | |
| IMP::em::KernelParameters | Calculates and stores Gaussian kernel parameters |
| IMP::em2d::LessPairBySecond< T > | Comparison of pairs by checking the second element |
| IMP::algebra::LogEmbeddingD< D > | |
| IMP::algebra::LogEmbeddingD< 3 > | |
| IMP::algebra::GridD< 3, DenseGridStorageD< 3, int >, int, LogEmbeddingD< 3 > > | |
| IMP::algebra::LogEmbeddingD<-1 > | |
| IMP::algebra::GridD<-1, DenseGridStorageD<-1, float >, float, LogEmbeddingD<-1 > > | |
| IMP.isd.demux_trajs.LogHolder | Manages information on a given simulation |
| IMP::LRUCache< Generator, Checker > | |
| IMP.parallel.Manager | Manages slaves and contexts |
| IMP::em2d::MasksManager | Management of projection masks |
| IMP.parallel.master_communicator.MasterCommunicator | For communicating from the master to slaves |
| IMP::em2d::MatchTemplateResult | |
| IMP::Memoizer< Generator, Checker > | |
| IMP::multifit::MergeTreeBuilder | Utility class for building merge trees |
| IMP.modeller.ModelLoader | Read a Modeller model into IMP |
| IMP::cnmultifit::MolCnSymmAxisDetector | Molecule symmetry detector |
| IMP.pmi.samplers.MolecularDynamics | Sample using molecular dynamics |
| IMP.pmi.topology.Molecule | Stores a named protein chain |
| IMP.pmi.samplers.MonteCarlo | Sample using Monte Carlo |
| IMP.EMageFit.monte_carlo.MonteCarloRelativeMoves | Class to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies |
| IMP::multi_state::MultiStateModel | Keep track of multiple states |
| IMP::multi_state::MultiStateModelScore | Base class for MultiStateModel scoring classes |
| IMP::multi_state::SAXSMultiStateModelScore< ScoringFunctionT > | |
| IMP::NonCopyable | |
| IMP::Object | Common base class for heavy weight IMP objects |
| IMP::algebra::DynamicNearestNeighbor3D | |
| IMP::algebra::NearestNeighborD< D > | |
| IMP::algebra::VectorKDMetric | |
| IMP::algebra::EuclideanVectorKDMetric | |
| IMP::algebra::MaxVectorKDMetric | |
| IMP::atom::CHARMMResidueTopologyBase | Base class for all CHARMM residue-based topology |
| IMP::atom::CHARMMIdealResidueTopology | The ideal topology of a single residue |
| IMP::atom::CHARMMResidueTopology | The topology of a single residue in a model |
| IMP::atom::CHARMMPatch | A CHARMM patch residue |
| IMP::atom::CHARMMSegmentTopology | The topology of a single CHARMM segment in a model |
| IMP::atom::CHARMMTopology | The topology of a complete CHARMM model |
| IMP::atom::ForceFieldParameters | Storage and access to force field |
| IMP::atom::CHARMMParameters | CHARMM force field parameters |
| IMP::atom::Mol2Selector | A base class for choosing which Mol2 atoms to read |
| IMP::atom::AllMol2Selector | Read all atoms |
| IMP::atom::NonHydrogenMol2Selector | Defines a selector that will pick only non-hydrogen atoms |
| IMP::atom::PDBSelector | Select which atoms to read from a PDB file |
| IMP::atom::AllPDBSelector | Defines a selector that will pick every ATOM and HETATM record |
| IMP::atom::AndPDBSelector | Select atoms which are selected by both selectors |
| IMP::atom::AtomTypePDBSelector | Select all atoms of the given types |
| IMP::atom::NonAlternativePDBSelector | Select all ATOM and HETATM records which are not alternatives |
| IMP::atom::ATOMPDBSelector | Select all non-alternative ATOM records |
| IMP::atom::CAlphaPDBSelector | Select all CA ATOM records |
| IMP::atom::CBetaPDBSelector | Select all CB ATOM records |
| IMP::atom::ChainPDBSelector | Select all ATOM and HETATM records with the given chain ids |
| IMP::atom::CPDBSelector | Select all C (not CA or CB) ATOM records |
| IMP::atom::HydrogenPDBSelector | Select all hydrogen ATOM and HETATM records |
| IMP::atom::NonWaterNonHydrogenPDBSelector | Select non water and non hydrogen atoms |
| IMP::atom::BackbonePDBSelector | Select all backbone (N,CA,C,O) ATOM records |
| IMP::atom::NonWaterPDBSelector | Select all non-water non-alternative ATOM and HETATM records |
| IMP::atom::NPDBSelector | Select all N ATOM records |
| IMP::atom::PPDBSelector | Select all P (= phosphate) ATOM records |
| IMP::atom::WaterPDBSelector | Select all non-water ATOM and HETATM records |
| IMP::atom::NotPDBSelector | Select atoms which are not selected by a given selector |
| IMP::atom::OrPDBSelector | Select atoms which are selected by either or both selectors |
| IMP::atom::ResidueTypePDBSelector | Select all atoms in residues of the given types |
| IMP::atom::XorPDBSelector | Select atoms which are selected by either selector but not both |
| IMP::atom::SmoothingFunction | Base class for smoothing nonbonded interactions as a function of distance |
| IMP::atom::ForceSwitch | Smooth interaction scores by switching the derivatives (force switch) |
| IMP::Configuration | A class to store a configuration of a model |
| IMP::ConfigurationSet | A class to store a set of configurations of a model |
| IMP::core::ClosePairsFinder | A base class for algorithms to find spatial proximities |
| IMP::core::BoxSweepClosePairsFinder | Find all nearby pairs by sweeping the bounding boxes |
| IMP::core::GridClosePairsFinder | Find all nearby pairs by testing all pairs |
| IMP::core::NearestNeighborsClosePairsFinder | Find all nearby pairs using the algebra::NearestNeighbor code |
| IMP::core::QuadraticClosePairsFinder | Find all nearby pairs by testing all pairs |
| IMP::core::RigidClosePairsFinder | Perform more efficient close pair finding when rigid bodies are involved |
| IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound > | |
| IMP::core::DataObject< Data > | |
| IMP::display::Geometry | The base class for geometry |
| IMP::atom::SelectionGeometry | Display a Selection |
| IMP::display::BoundingBoxGeometry | Display a bounding box |
| IMP::display::CylinderGeometry | Display a cylinder |
| IMP::display::EllipsoidGeometry | Display a ellipsoid |
| IMP::display::FilterGeometry | Remove geometry which is not above a plane |
| IMP::display::GeometrySet | Group of set of geometric elements |
| IMP::display::LabelGeometry | A text label for a ball in space |
| IMP::display::PairGeometry | A base class for geometry contained in particles |
| IMP::core::EdgePairGeometry | Display a segment connecting a pair of particles |
| IMP::display::PairsGeometry | A base class for geometry from a set of particles |
| IMP::core::EdgePairsGeometry | Display a segment for each pair in a IMP::PairContainer |
| IMP::display::PlaneGeometry | Display a plane as truncated to a bounding box |
| IMP::display::PointGeometry | Display a point |
| IMP::display::PolygonGeometry | |
| IMP::display::ReferenceFrameGeometry | Display a reference frame |
| IMP::display::RestraintGeometry | Try to draw some stuff for a generic restraint |
| IMP::display::RestraintSetGeometry | Geometry for a whole set of restraints |
| IMP::display::SegmentGeometry | Display a segment |
| IMP::core::RigidBodyTorque | |
| IMP::display::SingletonGeometry | A base class for geometry contained in particles |
| IMP::atom::BondGeometry | Display a Bond particle as a segment |
| IMP::atom::HierarchyGeometry | Display an IMP::atom::Hierarchy particle as balls |
| IMP::core::RigidBodyDerivativeGeometry | |
| IMP::core::RigidBodyFrameGeometry | |
| IMP::core::RigidBodyHierarchyGeometry | |
| IMP::core::XYZDerivativeGeometry | |
| IMP::core::XYZRGeometry | Display an IMP::core::XYZR particle as a ball |
| IMP::display::SingletonsGeometry | A base class for geometry from a set of particles |
| IMP::atom::BondsGeometry | Display an IMP::SingletonContainer of Bond particles as segments |
| IMP::atom::HierarchiesGeometry | Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls |
| IMP::core::RigidBodyDerivativesGeometry | |
| IMP::core::RigidBodyFramesGeometry | |
| IMP::core::XYZDerivativesGeometry | |
| IMP::core::XYZRsGeometry | Display an IMP::SingletonContainer of IMP::core::XYZR particles as balls |
| IMP::display::SphereGeometry | Display a sphere |
| IMP::display::SurfaceMeshGeometry | Display a surface mesh |
| IMP::display::IsosurfaceGeometry | Display an isosurface of a density map |
| IMP::display::SkinSurfaceGeometry | Display an isosurface of a density map |
| IMP::display::TriangleGeometry | Display a triangle |
| IMP::display::Writer | Base class for writing geometry to a file |
| IMP::domino::AssignmentContainer | |
| IMP::domino::CappedAssignmentContainer | |
| IMP::domino::HeapAssignmentContainer | |
| IMP::domino::ListAssignmentContainer | |
| IMP::domino::PackedAssignmentContainer | |
| IMP::domino::RangeViewAssignmentContainer | |
| IMP::domino::ReadAssignmentContainer | |
| IMP::domino::ReadHDF5AssignmentContainer | |
| IMP::domino::SampleAssignmentContainer | |
| IMP::domino::WriteAssignmentContainer | |
| IMP::domino::WriteHDF5AssignmentContainer | |
| IMP::domino::AssignmentsTable | |
| IMP::domino::BranchAndBoundAssignmentsTable | |
| IMP::domino::ListAssignmentsTable | |
| IMP::domino::RecursiveAssignmentsTable | |
| IMP::domino::SimpleAssignmentsTable | |
| IMP::domino::ParticleStates | |
| IMP::domino::CompoundStates | |
| IMP::domino::IndexStates | |
| IMP::domino::NestedRigidBodyStates | |
| IMP::domino::PermutationStates | |
| IMP::domino::RecursiveStates | |
| IMP::domino::RigidBodyStates | |
| IMP::domino::XYZStates | |
| IMP::em2d::GridStates | |
| IMP::em2d::ProjectionStates | |
| IMP::multifit::FittingStates | |
| IMP::domino::ParticleStatesTable | |
| IMP::domino::RestraintCache | |
| IMP::domino::SubsetFilter | |
| IMP::em2d::DistanceFilter | SubsetFilter for checking overlap between projections and images |
| IMP::domino::SubsetFilterTable | |
| IMP::domino::DisjointSetsSubsetFilterTable | A base class |
| IMP::domino::EqualitySubsetFilterTable | Do not allow two particles to be in the same state |
| IMP::domino::EquivalenceAndExclusionSubsetFilterTable | Define sets of equivalent and exclusive particles |
| IMP::domino::EquivalenceSubsetFilterTable | Define sets of equivalent particles |
| IMP::domino::ExclusionSubsetFilterTable | Do not allow two particles to be in the same state |
| IMP::domino::ListSubsetFilterTable | Maintain an explicit list of what states each particle is allowed to have |
| IMP::domino::MinimumRestraintScoreSubsetFilterTable | Filter a configuration of the subset using the Model thresholds |
| IMP::domino::PairListSubsetFilterTable | |
| IMP::domino::ProbabilisticSubsetFilterTable | |
| IMP::domino::RestraintScoreSubsetFilterTable | Filter a configuration of the subset using the Model thresholds |
| IMP::em2d::DistanceFilterTable | |
| IMP::example::ExampleSubsetFilterTable | |
| IMP::em2d::CollisionCrossSection | Determine the collision cross section for some projections of particles |
| IMP::em2d::Image | 2D Electron Microscopy images in IMP |
| IMP::em2d::ImageReaderWriter | Virtual class for reader/writers of images |
| IMP::em2d::JPGImageReaderWriter | Class to read and write EM images in JPG format |
| IMP::em2d::SpiderImageReaderWriter | |
| IMP::em2d::TIFFImageReaderWriter | Management of reading/writing TIFF images |
| IMP::em2d::ProjectionFinder | Class to perform registration of model projections to images |
| IMP::em2d::ScoreFunction | Base class for all scoring functions related to em2d |
| IMP::em2d::ChiSquaredScore | Score based on Chi^2 = ((pixels_image - pixels_projection)/stddev_image)^2 |
| IMP::em2d::EM2DScore | |
| IMP::em2d::MeanAbsoluteDifference | Score based on the mean of the absolute difference |
| IMP::em::CoarseCC | Responsible for performing coarse fitting between two density objects |
| IMP::em::CoarseCCatIntervals | Cross correlation coefficient calculator |
| IMP::em::DensityMap | Class for handling density maps |
| IMP::em::MapDistanceTransform | Class for getting the distance from the map envelope |
| IMP::em::SampledDensityMap | Class for sampling a density map from particles |
| IMP::em::SurfaceShellDensityMap | The class represents a molecule as shells of distance from the surface |
| IMP::em::EnvelopeScore | Class for envelope based scoring using MapDistanceTransform |
| IMP::em::MapReaderWriter | The base class to handle reading and writing of density maps |
| IMP::em::EMReaderWriter | |
| IMP::em::MRCReaderWriter | |
| IMP::em::SpiderMapReaderWriter | Class to read EM maps (3D) in Spider and Xmipp formats |
| IMP::em::XplorReaderWriter | |
| IMP::em::PCAAligner | Fast alignment of points to a density map using principal components |
| IMP::example::ExampleObject | An example simple object which is reference counted |
| IMP::isd::BivariateFunction | Base class for functions of two variables |
| IMP::isd::Covariance1DFunction | Covariance function |
| IMP::isd::CrossLinkData | CrossLinkData |
| IMP::isd::CysteineCrossLinkData | CysteineCrossLinkData |
| IMP::isd::FNormal | FNormal |
| IMP::isd::FretData | Auxiliary class for FRET_R restraint |
| IMP::isd::GaussianProcessInterpolation | GaussianProcessInterpolation |
| IMP::isd::MultivariateFNormalSufficient | MultivariateFNormalSufficient |
| IMP::isd::UnivariateFunction | Base class for functions of one variable |
| IMP::isd::GeneralizedGuinierPorodFunction | 1D mean function for SAS data |
| IMP::isd::Linear1DFunction | Linear one-dimensional function |
| IMP::isd::vonMises | VonMises |
| IMP::isd::vonMisesSufficient | VonMisesSufficient |
| IMP::kinematics::DOF | |
| IMP::kinematics::DOFsSampler | |
| IMP::kinematics::UniformBackboneSampler | |
| IMP::kinematics::Joint | |
| IMP::kinematics::CompositeJoint | |
| IMP::kinematics::PrismaticJoint | |
| IMP::kinematics::RevoluteJoint | |
| IMP::kinematics::BondAngleRevoluteJoint | |
| IMP::kinematics::DihedralAngleRevoluteJoint | |
| IMP::kinematics::TransformationJoint | |
| IMP::kinematics::KinematicForest | |
| IMP::kinematics::LocalPlanner | |
| IMP::kinematics::PathLocalPlanner | |
| IMP::kmeans::KMeans | |
| IMP::Model | Class for storing model, its restraints, constraints, and particles |
| IMP::ModelObject | |
| IMP::Container | Abstract class for containers of particles |
| IMP::PairContainer | A shared container for Pairs |
| IMP::atom::BondPairContainer | A container that returns pairs of the endpoints of the bonds |
| IMP::container::AllBipartitePairContainer | Return all bipartite pairs between two containers |
| IMP::container::AllPairContainer | Return all unordered pairs of particles taken from the SingletonContainer |
| IMP::container::CloseBipartitePairContainer | Return all close ordered pairs of particles taken from the two SingletonContainers |
| IMP::container::ClosePairContainer | Return all close unordered pairs of particles taken from the SingletonContainer |
| IMP::container::ConnectingPairContainer | A container which keeps a set of pairs that connect a set of spheres |
| IMP::container::ConsecutivePairContainer | A container which contains all consecutive particle pairs from an input list |
| IMP::container::DynamicListPairContainer | Store a ParticleIndexPairs |
| IMP::container::ExclusiveConsecutivePairContainer | |
| IMP::container::ListPairContainer | Store a list of ParticleIndexPairs |
| IMP::container::PairContainerSet | Stores a set of PairContainers |
| IMP::QuadContainer | A shared container for Quads |
| IMP::container::DynamicListQuadContainer | Store a ParticleIndexQuads |
| IMP::container::ListQuadContainer | Store a list of ParticleIndexQuads |
| IMP::container::QuadContainerSet | Stores a set of QuadContainers |
| IMP::SingletonContainer | A shared container for Singletons |
| IMP::container::DynamicListSingletonContainer | Store a ParticleIndexes |
| IMP::container::ListSingletonContainer | Store a list of ParticleIndexes |
| IMP::container::SingletonContainerSet | Stores a set of SingletonContainers |
| IMP::TripletContainer | A shared container for Triplets |
| IMP::container::DynamicListTripletContainer | Store a ParticleIndexTriplets |
| IMP::container::ListTripletContainer | Store a list of ParticleIndexTriplets |
| IMP::container::TripletContainerSet | Stores a set of TripletContainers |
| IMP::core::MonteCarloMover | A base class for classes which perturb particles |
| IMP::core::BallMover | Modify a set of continuous variables by perturbing them within a ball |
| IMP::core::NormalMover | Modify a set of continuous variables using a normal distribution |
| IMP::core::RigidBodyMover | Modify the transformation of a rigid body |
| IMP::em2d::RelativePositionMover | |
| IMP::core::RigidBodyTunneler | Modify the transformation of a rigid body |
| IMP::core::SerialMover | Applies a list of movers one at a time |
| IMP::core::TransformationSymmetryMover | Modify the given TransformationSymmetry |
| IMP::isd::MolecularDynamicsMover | Modify a set of continuous variables using a MD simulation |
| IMP::isd::WeightMover | A mover that perturbs a Weight particle |
| IMP::kinematics::RevoluteJointMover | Modify a set of joints using a normal distribution with zero mean and |
| IMP::pmi::TransformMover | Modify the transformation of a rigid body |
| IMP::symmetry::BallMover | Move a particle and keep it in the primitive cell of a periodic lattice |
| IMP::symmetry::RigidBodyMover | Move a rigid body and keep it in the primitive cell of a periodic lattice |
| IMP::Optimizer | Base class for all optimizers |
| IMP::atom::Simulator | The base class for simulators |
| IMP::atom::BrownianDynamics | Simple Brownian dynamics simulator |
| IMP::atom::BrownianDynamicsTAMD | Simple Brownian dynamics simulator |
| IMP::atom::MolecularDynamics | Simple molecular dynamics optimizer |
| IMP::isd::MolecularDynamics | Molecular dynamics optimizer on 1-D and 3-D particles |
| IMP::AttributeOptimizer | Base class for optimizers that act on individual attributes |
| IMP::core::ConjugateGradients | Simple conjugate gradients optimizer |
| IMP::core::SteepestDescent | A simple steepest descent optimizer |
| IMP::gsl::GSLOptimizer | A base class for GSL-based optimizers |
| IMP::gsl::ConjugateGradients | A conjugate gradients optimizer taken from GSL |
| IMP::gsl::QuasiNewton | A quasi-Newton optimizer taken from GSL |
| IMP::gsl::Simplex | A simplex optimizer taken from GSL |
| IMP::core::MonteCarlo | A Monte Carlo optimizer |
| IMP::core::MonteCarloWithLocalOptimization | This variant of Monte Carlo that relaxes after each move |
| IMP::core::MonteCarloWithBasinHopping | This variant of Monte Carlo uses basis hopping |
| IMP::isd::HybridMonteCarlo | Hybrid Monte Carlo optimizer |
| IMP::OptimizerState | Shared optimizer state that is invoked upon commitment of new coordinates |
| IMP::atom::BerendsenThermostatOptimizerState | Maintains temperature during molecular dynamics |
| IMP::atom::LangevinThermostatOptimizerState | Maintains temperature during molecular dynamics |
| IMP::atom::RemoveRigidMotionOptimizerState | Removes rigid translation and rotation from the particles |
| IMP::atom::RemoveTranslationOptimizerState | Removes rigid translation from the particles |
| IMP::atom::VelocityScalingOptimizerState | Maintains temperature during molecular dynamics by velocity scaling |
| IMP::atom::WritePDBOptimizerState | |
| IMP::container::EventPairsOptimizerState | |
| IMP::container::EventQuadsOptimizerState | |
| IMP::container::EventSingletonsOptimizerState | |
| IMP::container::EventTripletsOptimizerState | |
| IMP::container::PairsOptimizerState | Apply a PairFunction to a PairContainer to maintain an invariant |
| IMP::container::QuadsOptimizerState | Apply a QuadFunction to a QuadContainer to maintain an invariant |
| IMP::container::SingletonsOptimizerState | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
| IMP::container::TripletsOptimizerState | Apply a TripletFunction to a TripletContainer to maintain an invariant |
| IMP::core::WriteRestraintScoresOptimizerState | Write the scores of the passed restraints to a file during optimization |
| IMP::display::WriteOptimizerState | |
| IMP::misc::DecayPairContainerOptimizerState | Maintain a pair container with a decaying list of pairs |
| IMP::rmf::SaveOptimizerState | |
| IMP::SaveToConfigurationSetOptimizerState | |
| IMP::Particle | Class to handle individual model particles |
| IMP::Restraint | A restraint is a term in an IMP ScoringFunction |
| IMP::atom::CAAngleRestraint | Angle restraint between three residues in CA-only representation |
| IMP::atom::CADihedralRestraint | Dihedral restraint between five residues in CA-only representation |
| IMP::atom::CHARMMStereochemistryRestraint | Enforce CHARMM stereochemistry on the given Hierarchy |
| IMP::atom::EzRestraint | Ez Potential restraint |
| IMP::container::MinimumPairRestraint | Score based on the min or max PairScore over a set |
| IMP::container::MinimumQuadRestraint | Score based on the min or max QuadScore over a set |
| IMP::container::MinimumSingletonRestraint | Score based on the min or max SingletonScore over a set |
| IMP::container::MinimumTripletRestraint | Score based on the min or max TripletScore over a set |
| IMP::container::PairsRestraint | Applies a PairScore to each Pair in a list |
| IMP::atom::ProteinLigandRestraint | Score a pair of molecules |
| IMP::container::PredicatePairsRestraint | Applies a PairScore to each Pair in a list based on a predicate |
| IMP::container::PredicateQuadsRestraint | Applies a QuadScore to each Quad in a list based on a predicate |
| IMP::container::PredicateSingletonsRestraint | Applies a SingletonScore to each Singleton in a list based on a predicate |
| IMP::container::PredicateTripletsRestraint | Applies a TripletScore to each Triplet in a list based on a predicate |
| IMP::container::QuadsRestraint | Applies a QuadScore to each Quad in a list |
| IMP::container::SingletonsRestraint | Applies a SingletonScore to each Singleton in a list |
| IMP::container::TripletsRestraint | Applies a TripletScore to each Triplet in a list |
| IMP::core::ConnectivityRestraint | Ensure that a set of particles remains connected with one another |
| IMP::core::ConstantRestraint | Return a constant value |
| IMP::core::DiameterRestraint | Restrain the diameter of a set of points |
| IMP::core::DihedralRestraint | Dihedral restraint between four particles |
| IMP::core::DistanceRestraint | Distance restraint between two particles |
| IMP::core::ExcludedVolumeRestraint | Prevent a set of particles and rigid bodies from inter-penetrating |
| IMP::core::MinimumRestraint | Score based on the minimum scoring members of a set of restraints |
| IMP::core::MSConnectivityRestraint | Ensure that a set of particles remains connected with one another |
| IMP::core::PairRestraint | Applies a PairScore to a Pair |
| IMP::core::QuadRestraint | Applies a QuadScore to a Quad |
| IMP::core::RigidBodyUmbrella | Umbrella-like restraint for rigid bodies |
| IMP::core::SingletonRestraint | Applies a SingletonScore to a Singleton |
| IMP::core::TripletRestraint | Applies a TripletScore to a Triplet |
| IMP::core::AngleRestraint | Angle restraint between three particles |
| IMP::core::VolumeRestraint | A restraint that prevents spheres from inter-penetrating |
| IMP::em2d::DummyRestraint | Dummy restraint between two particles |
| IMP::em2d::Em2DRestraint | |
| IMP::em2d::Fine2DRegistrationRestraint | |
| IMP::em2d::ParticlesDummyRestraint | Dummy restraint for a set of particles. Same use as DummyRestraint |
| IMP::em2d::PCAFitRestraint | Fast scoring of Particles against electron microscopy class averages |
| IMP::em2d::RigidBodiesImageFitRestraint | Fit rigid bodies to an image |
| IMP::em::DensityFillingRestraint | Calculate score based on fit to EM map |
| IMP::em::EnvelopeFitRestraint | A restraint for envelope-based scoring of particles in the density map |
| IMP::em::EnvelopePenetrationRestraint | Calculate score based on fit to EM map |
| IMP::em::FitRestraint | Calculate score based on fit to EM map |
| IMP::em::PCAFitRestraint | Calculate score based on fit to EM map |
| IMP::example::ExampleComplexRestraint | Restrain the diameter of a set of points |
| IMP::example::ExampleRestraint | Restrain a particle to be in the x,y plane |
| IMP.example.PythonExampleRestraint | An example restraint written in Python |
| IMP::isd::AmbiguousNOERestraint | Ambiguous NOE distance restraint between a number of pairs of particles |
| IMP::isd::AmbiguousRestraint | Apply an ambiguous restraint by computing the d-norm |
| IMP::isd::AtomicCrossLinkMSRestraint | Restrain atom pairs based on a set of crosslinks |
| IMP::isd::CrossLinkMSRestraint | A restraint for ambiguous cross-linking MS data and multiple state approach |
| IMP::isd::CysteineCrossLinkRestraint | A restraint for cysteine cross-linking data |
| IMP::isd::FretRestraint | |
| IMP::isd::GaussianEMRestraint | Creates a restraint between two Gaussian Mixture Models, "model" and "density" |
| IMP::isd::GaussianProcessInterpolationRestraint | Gaussian process restraint |
| IMP::isd::GaussianRestraint | Normal probability distribution as a restraint |
| IMP::isd::ISDRestraint | A base class for ISD Restraints |
| IMP::pmi::MembraneRestraint | Membrane Restraint |
| IMP::isd::JeffreysRestraint | |
| IMP::isd::LognormalAmbiguousRestraint | |
| IMP::isd::LognormalRestraint | Normal probability distribution as a restraint |
| IMP::isd::LogWrapper | Calculate the -Log of a list of restraints |
| IMP::isd::MarginalHBondRestraint | Apply a lognormal distance restraint between two particles |
| IMP::isd::MarginalNOERestraint | Apply an NOE distance restraint between two particles |
| IMP::isd::NOERestraint | Apply an NOE distance restraint between two particles |
| IMP::isd::TALOSRestraint | Phi/psi dihedral restraint between four particles, using data from TALOS |
| IMP::isd::UniformPrior | Uniform distribution with harmonic boundaries |
| IMP::isd::vonMisesKappaConjugateRestraint | Conjugate prior for the concentration parameter of a von Mises distribution |
| IMP::isd::vonMisesKappaJeffreysRestraint | Jeffreys prior for the \(\kappa\) concentration parameter of a von Mises distribution |
| IMP::isd::WeightRestraint | |
| IMP.modeller.ModellerRestraints | An IMP restraint using all defined Modeller restraints |
| IMP::modeller::MultipleBinormalRestraint | Modeller-style multiple binormal (phi/psi) restraint |
| IMP::multifit::ComplementarityRestraint | Compute the complementarity between two molecules |
| IMP::multifit::DummyRestraint | A simple Restraint that always returns a score of zero |
| IMP::multifit::RadiusOfGyrationRestraint | Ensure the radius of gyration of particles fits the predicted one |
| IMP::multifit::WeightedExcludedVolumeRestraint | Calculate score based on fit to EM map |
| IMP::pmi::CompositeRestraint | A restraint for ambiguous cross-linking MS data and multiple state approach |
| IMP.pmi.restraints.basic.BiStableDistanceRestraint | Python restraint with bistable potential Authors: G |
| IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint | Python restraint that computes the score for a composite of proteins Authors: G |
| IMP.pmi.restraints.proteomics.FuzzyRestraint | Fully Ambiguous Restraint that can be built using boolean logic R |
| IMP::pmi::SigmoidRestraintSphere | Simple sigmoidal score calculated between sphere surfaces |
| IMP::RestraintSet | Object used to hold a set of restraints |
| IMP::saxs::Restraint | Calculate score based on fit to SAXS profile |
| IMP::saxs::RadiusOfGyrationRestraint | Calculate score based on radius of gyration, taken from saxs profile |
| IMP::ScoreState | ScoreStates maintain invariants in the Model |
| IMP::Constraint | Implement a constraint on the Model |
| IMP::container::PairsConstraint | Apply a PairFunction to a PairContainer to maintain an invariant |
| IMP::container::QuadsConstraint | Apply a QuadFunction to a QuadContainer to maintain an invariant |
| IMP::container::SingletonsConstraint | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
| IMP::container::TripletsConstraint | Apply a TripletFunction to a TripletContainer to maintain an invariant |
| IMP::core::PairConstraint | Apply a PairFunction to a Pair |
| IMP::core::QuadConstraint | Apply a QuadFunction to a Quad |
| IMP::core::SingletonConstraint | Apply a SingletonFunction to a Singleton |
| IMP::core::TripletConstraint | Apply a TripletFunction to a Triplet |
| IMP::example::ExampleConstraint | A trivial constraint that just increments a counter |
| IMP.example.PythonExampleConstraint | An example Constraint written in Python |
| IMP::container::DistributePairsScoreState | Distribute contents of one container into several based on predicates |
| IMP::container::DistributeQuadsScoreState | Distribute contents of one container into several based on predicates |
| IMP::container::DistributeSingletonsScoreState | Distribute contents of one container into several based on predicates |
| IMP::container::DistributeTripletsScoreState | Distribute contents of one container into several based on predicates |
| IMP::container::PairContainerStatistics | Track statistics on a PairContainer |
| IMP::container::QuadContainerStatistics | Track statistics on a QuadContainer |
| IMP::container::SingletonContainerStatistics | Track statistics on a SingletonContainer |
| IMP::container::TripletContainerStatistics | Track statistics on a TripletContainer |
| IMP::core::ChecksScoreState | |
| IMP::core::MoveStatisticsScoreState | Keep track of statistics about how particles move |
| IMP::core::NeighborsTable | |
| IMP::domino::DependencyScoreState | Add a dependency to the dependency graph |
| IMP::em2d::ProjectionParametersScoreState | |
| IMP::kinematics::KinematicForestScoreState | |
| IMP::misc::StateAdaptor | Allow OptimizerStates to be used as ScoreStates |
| IMP::ScoringFunction | Represents a scoring function on the model |
| IMP::core::IncrementalScoringFunction | Score the model efficiently when a small number of particles are changed |
| IMP::core::RestraintsScoringFunction | |
| IMP::mpi::ReplicaExchange | A class to implement Hamiltonian Replica Exchange |
| IMP::multifit::AssemblyHeader | Holds data about the assembly density needed for optimization |
| IMP::multifit::ComponentHeader | Holds data about a component needed for optimization |
| IMP::multifit::Ensemble | An ensemble of fitting solutions |
| IMP::multifit::FFTFitting | Fit a molecule inside its density by local or global FFT |
| IMP::multifit::FFTFittingOutput | Storage of the results from an FFT fit |
| IMP::multifit::ProbabilisticAnchorGraph | Probabilistic anchor graph |
| IMP::multifit::ProteomicsData | Storage of proteomics data |
| IMP::multifit::ProteomicsEMAlignmentAtomic | Align proteomics graph to EM density map |
| IMP::multifit::SettingsData | Holds header data for optimization |
| IMP::PairModifier | A base class for modifiers of ParticlePairsTemp |
| IMP::PairPredicate | Abstract predicate function |
| IMP::atom::BondedPairFilter | A filter for bonds |
| IMP::atom::SameResiduePairFilter | |
| IMP::atom::SoapPairFilter | Filter atom pairs for SOAP |
| IMP::atom::StereochemistryPairFilter | A filter that excludes bonds, angles and dihedrals |
| IMP::container::ConsecutivePairFilter | |
| IMP::container::ExclusiveConsecutivePairFilter | |
| IMP::container::InContainerPairFilter | A filter which returns true if a container containers the Pair |
| IMP::core::AllSamePairPredicate | |
| IMP::core::CoinFlipPairPredicate | |
| IMP::core::ConstantPairPredicate | |
| IMP::core::IsCollisionPairPredicate | Return 1 if two XYZRs collide |
| IMP::core::OrderedTypePairPredicate | |
| IMP::core::UnorderedTypePairPredicate | |
| IMP::misc::CommonEndpointPairFilter | Return true for any pair of bonds sharing an endpoint |
| IMP::PairScore | Abstract class for scoring object(s) of type ParticleIndexPair |
| IMP::score_functor::DistancePairScore< score_functor::Dope > | |
| IMP::atom::DopePairScore | |
| IMP::score_functor::DistancePairScore< score_functor::OrientedSoap > | |
| IMP::atom::OrientedSoapPairScore | Score a pair of atoms using an orientation-dependent SOAP score |
| IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > > | |
| IMP::core::StatisticalPairScore< Key, BIPARTITE, INTERPOLATE, SPARSE > | |
| IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > > | |
| IMP::core::StatisticalPairScore< ProteinLigandType, true, false > | |
| IMP::atom::ProteinLigandAtomPairScore | |
| IMP::atom::CoulombPairScore | Coulomb (electrostatic) score between a pair of particles |
| IMP::atom::LennardJonesPairScore | Lennard-Jones score between a pair of particles |
| IMP::container::MinimumPairScore | Evaluate the min or max n particle_pair scores of the passed set |
| IMP::core::ClosePairsPairScore | |
| IMP::core::DistancePairScore | |
| IMP::core::HarmonicDistancePairScore | |
| IMP::core::HarmonicSphereDistancePairScore | A harmonic score on the distance between two spheres |
| IMP::core::HarmonicUpperBoundSphereDiameterPairScore | A harmonic upper bound on the diameter of the span of two spheres |
| IMP::core::HarmonicUpperBoundSphereDistancePairScore | A harmonic upper bound on the distance between two spheres |
| IMP::core::KClosePairsPairScore | |
| IMP::core::RigidBodyDistancePairScore | Accelerated computation of the distance between two rigid bodies |
| IMP::core::NormalizedSphereDistancePairScore | A score on the normalized distance between the surfaces of two spheres |
| IMP::core::RefinedPairsPairScore | Generate pairs to score by applying a Refiner |
| IMP::core::RigidBodyAnglePairScore | Score on the crossing angle between two rigid bodies |
| IMP::core::SoftSpherePairScore | |
| IMP::core::SphereDistancePairScore | A score on the distance between the surfaces of two spheres |
| IMP::core::TransformedDistancePairScore | Apply a function to the distance between two particles after transforming the first |
| IMP::core::TypedPairScore | Delegate to another PairScore depending on particle types |
| IMP::core::WeightedSphereDistancePairScore | A score on a weighted distance between the surfaces of two spheres |
| IMP::example::ExamplePairScore | Apply a harmonic to the distance between two particles |
| IMP.example.PythonExamplePairScore | An example PairScore written in Python |
| IMP::isd::RepulsiveDistancePairScore | A repulsive potential on the distance between two atoms |
| IMP::misc::LogPairScore | Track the pairs of particles passed |
| IMP::misc::LowestRefinedPairScore | Refine both particles with the refiner and score on the lowest pair |
| IMP::misc::SoftCylinderPairScore | Apply a function to the distance between the cylinders defined by two bonds |
| IMP::score_functor::DistancePairScore< DistanceScoreT > | Create efficient distance-based pair scores |
| IMP::QuadModifier | A base class for modifiers of ParticleQuadsTemp |
| IMP::QuadPredicate | Abstract predicate function |
| IMP::container::InContainerQuadFilter | A filter which returns true if a container containers the Quad |
| IMP::core::AllSameQuadPredicate | |
| IMP::core::CoinFlipQuadPredicate | |
| IMP::core::ConstantQuadPredicate | |
| IMP::core::OrderedTypeQuadPredicate | |
| IMP::core::UnorderedTypeQuadPredicate | |
| IMP::QuadScore | Abstract class for scoring object(s) of type ParticleIndexQuad |
| IMP::container::MinimumQuadScore | Evaluate the min or max n particle_quad scores of the passed set |
| IMP::Refiner | Abstract class to implement hierarchical methods |
| IMP::atom::BondEndpointsRefiner | Return the endpoints of a bond |
| IMP::core::ChildrenRefiner | Return the hierarchy children of a particle |
| IMP::core::FixedRefiner | The refiner can refine any particle by returning a fixed set |
| IMP::core::LeavesRefiner | Return the hierarchy leaves under a particle |
| IMP::core::TableRefiner | A lookup based particle refiner |
| IMP::rmf::LoadLink | |
| IMP::rmf::SimpleLoadLink< O > | |
| IMP::rmf::SimpleLoadLink< Particle > | |
| IMP::rmf::HierarchyLoadLink | |
| IMP::rmf::SaveLink | |
| IMP::rmf::SimpleSaveLink< O > | |
| IMP::rmf::SimpleSaveLink< Particle > | |
| IMP::rmf::HierarchySaveLink | |
| IMP::rotamer::RotamerCalculator | A class performing the rotations of atoms in the residues |
| IMP::rotamer::RotamerLibrary | A class storing a whole rotamer library read from a file |
| IMP::Sampler | Base class for all samplers |
| IMP::core::MCCGSampler | A simple sampler |
| IMP::domino::DiscreteSampler | A base class for discrete samplers in Domino2 |
| IMP::domino::BranchAndBoundSampler | Sample best solutions using BranchAndBound |
| IMP::domino::DominoSampler | Sample best solutions using Domino |
| IMP::kinematics::RRT | |
| IMP::saxs::ChiFreeScore | |
| IMP::saxs::ChiScore | |
| IMP::saxs::ChiScoreLog | |
| IMP::saxs::DerivativeCalculator | |
| IMP::saxs::Profile | |
| IMP::saxs::ProfileFitter< ScoringFunctionT > | Fit two profiles with user-defined scoring function as a template parameter |
| IMP::saxs::WeightedProfileFitter< ScoringFunctionT > | Fitting of multiple profiles to the experimental one |
| IMP::saxs::RatioVolatilityScore | |
| IMP::saxs::RigidBodiesProfileHandler | Handle the profile for a set of particles, which may include rigid bodies |
| IMP::SingletonModifier | A base class for modifiers of ParticlesTemp |
| IMP::atom::CoverBond | Cover a bond with a sphere |
| IMP::core::CentroidOfRefined | |
| IMP::core::CoverRefined | This class sets the position and radius of each particle to enclose the refined |
| IMP::core::DerivativesFromRefined | Accumulate the derivatives of the refined particles |
| IMP::core::DerivativesToRefined | Copy the derivatives from a coarse particle to its refined particles |
| IMP::core::Transform | Apply a transformation to a passed particle |
| IMP::core::TransformationAndReflectionSymmetry | Set the coordinates of a particle to be a transformed version of a reference |
| IMP::core::TransformationSymmetry | Set the coordinates of a particle to be a transformed version of a reference |
| IMP::core::WeightedDerivativesToRefined | Copy the derivatives from a coarse particle to its refined particles |
| IMP::example::ExampleSingletonModifier | An example singleton modifier |
| IMP.example.PythonExampleSingletonModifier | An example SingletonModifier written in Python |
| IMP::SingletonPredicate | Abstract predicate function |
| IMP::container::InContainerSingletonFilter | A filter which returns true if a container containers the Singleton |
| IMP::core::AllSameSingletonPredicate | |
| IMP::core::AttributeSingletonPredicate | Return the value of an int attribute as the predicate value |
| IMP::core::CoinFlipSingletonPredicate | |
| IMP::core::ConstantSingletonPredicate | |
| IMP::core::InBoundingBox3DSingletonPredicate | Return 1 if the XYZ is in the bounding box, 0 otherwise |
| IMP::core::OrderedTypeSingletonPredicate | |
| IMP::core::UnorderedTypeSingletonPredicate | |
| IMP::SingletonScore | Abstract class for scoring object(s) of type ParticleIndex |
| IMP::atom::AngleSingletonScore | Score the angle based on a UnaryFunction, |
| IMP::atom::BondSingletonScore | Score the bond based on a UnaryFunction, |
| IMP::atom::DihedralSingletonScore | Score the dihedral angle |
| IMP::atom::ImproperSingletonScore | Score the improper dihedral based on a UnaryFunction, |
| IMP::container::MinimumSingletonScore | Evaluate the min or max n particle scores of the passed set |
| IMP::core::GenericAttributeSingletonScore< UF > | Apply a function to an attribute |
| IMP::core::GenericBoundingBox3DSingletonScore< UF > | Score particles based on how far outside a box they are |
| IMP::core::GenericDistanceToSingletonScore< UF > | Apply a function to the distance to a fixed point |
| IMP::core::PredicateSingletonScore< Predicate, Score > | |
| IMP::core::SphereDistanceToSingletonScore | Apply a function to the distance to a fixed point |
| IMP::statistics::Embedding | Store data to be clustered for embedding based algorithms |
| IMP::em::HighDensityEmbedding | |
| IMP::statistics::ConfigurationSetXYZEmbedding | Embed a configuration using the XYZ coordinates of a set of particles |
| IMP::statistics::ParticleEmbedding | |
| IMP::statistics::RecursivePartitionalClusteringEmbedding | |
| IMP::statistics::VectorDEmbedding | Simply return the coordinates of a VectorD |
| IMP::statistics::Metric | Store data to be clustered for distance metric based algorithms |
| IMP::statistics::ChiSquareMetric | Compute the distance between two configurations using chi2 |
| IMP::statistics::ConfigurationSetRMSDMetric | |
| IMP::statistics::EuclideanMetric | |
| IMP::statistics::RecursivePartitionalClusteringMetric | Represent a metric for clustering data that has already been clustered once |
| write_a_metric.MyMetric | |
| IMP::statistics::PartitionalClustering | A base class for clustering results where each item is in one cluster |
| IMP::statistics::PartitionalClusteringWithCenter | |
| IMP::TripletModifier | A base class for modifiers of ParticleTripletsTemp |
| IMP::TripletPredicate | Abstract predicate function |
| IMP::container::InContainerTripletFilter | A filter which returns true if a container containers the Triplet |
| IMP::core::AllSameTripletPredicate | |
| IMP::core::CoinFlipTripletPredicate | |
| IMP::core::ConstantTripletPredicate | |
| IMP::core::OrderedTypeTripletPredicate | |
| IMP::core::UnorderedTypeTripletPredicate | |
| IMP::TripletScore | Abstract class for scoring object(s) of type ParticleIndexTriplet |
| IMP::container::MinimumTripletScore | Evaluate the min or max n particle_triplet scores of the passed set |
| IMP::core::AngleTripletScore | Apply a function to the angle between three particles |
| IMP::UnaryFunction | Abstract single variable functor class for score functions |
| IMP::core::ClosedCubicSpline | Closed cubic spline function |
| IMP::core::Cosine | Cosine function |
| IMP::core::Harmonic | Harmonic function (symmetric about the mean) |
| IMP::core::HarmonicLowerBound | Lower bound harmonic function (non-zero when feature < mean) |
| IMP::core::HarmonicUpperBound | Upper bound harmonic function (non-zero when feature > mean) |
| IMP::core::HarmonicWell | A well with harmonic barriers |
| IMP::core::Linear | Linear function |
| IMP::core::TruncatedHarmonic< DIRECTION > | A function that is harmonic over an interval |
| IMP::example::ExampleUnaryFunction | A simple unary function |
| IMP.example.PythonExampleUnaryFunction | An example UnaryFunction written in Python |
| IMP::misc::WormLikeChain | Worm-like-chain energy for polymer chains |
| IMP::score_functor::ScoreUnaryFunction< Score, D > | |
| IMP::score_functor::ScoreUnaryFunction< score_functor::OpenCubicSpline > | |
| IMP::core::OpenCubicSpline | An OpenCubicSpline |
| IMP::Undecorator | |
| IMP::RAII | Temporarily change something; undo the change when this object is destroyed |
| IMP::benchmark::Profiler | |
| IMP::CreateLogContext | Create a new log context |
| IMP::ScopedAddCacheAttribute< Key, Value > | |
| IMP::ScopedSetAttribute< Key, Value > | |
| IMP::SetCheckState | A class to change and restore check state |
| IMP::SetLogState | A class to change and restore log state |
| IMP::SetLogTarget | |
| IMP::SetNumberOfThreads | |
| IMP::Timer | |
| IMP.OptionParser | IMP-specific subclass of optparse.OptionParser |
| IMP.pmi.tools.OrderedDefaultDict | Store objects in order they were added, but with default type |
| IMP.pmi.output.Output | Class for easy writing of PDBs, RMFs, and stat files |
| IMP::ParticleInputs | |
| IMP::core::ClosePairsFinder | A base class for algorithms to find spatial proximities |
| IMP::PairModifier | A base class for modifiers of ParticlePairsTemp |
| IMP::PairPredicate | Abstract predicate function |
| IMP::PairScore | Abstract class for scoring object(s) of type ParticleIndexPair |
| IMP::QuadModifier | A base class for modifiers of ParticleQuadsTemp |
| IMP::QuadPredicate | Abstract predicate function |
| IMP::QuadScore | Abstract class for scoring object(s) of type ParticleIndexQuad |
| IMP::Refiner | Abstract class to implement hierarchical methods |
| IMP::SingletonModifier | A base class for modifiers of ParticlesTemp |
| IMP::SingletonPredicate | Abstract predicate function |
| IMP::SingletonScore | Abstract class for scoring object(s) of type ParticleIndex |
| IMP::TripletModifier | A base class for modifiers of ParticleTripletsTemp |
| IMP::TripletPredicate | Abstract predicate function |
| IMP::TripletScore | Abstract class for scoring object(s) of type ParticleIndexTriplet |
| IMP::ParticleOutputs | |
| IMP::PairModifier | A base class for modifiers of ParticlePairsTemp |
| IMP::QuadModifier | A base class for modifiers of ParticleQuadsTemp |
| IMP::SingletonModifier | A base class for modifiers of ParticlesTemp |
| IMP::TripletModifier | A base class for modifiers of ParticleTripletsTemp |
| IMP::piecewise_linear_distribution< T > | |
| IMP.isd.utils.Pipe | Implements a FIFO pipe that merges lists (see self.put) |
| IMP::Pointer< O > | A smart pointer to a reference counted object |
| IMP::Pointer< const IMP::atom::CHARMMParameters > | |
| IMP::Pointer< const IMP::statistics::internal::XYZDataPoints > | |
| IMP::Pointer< container::ClosePairContainer > | |
| IMP::Pointer< container::DynamicListPairContainer > | |
| IMP::Pointer< core::HarmonicUpperBound > | |
| IMP::Pointer< domino::ParticleStatesTable > | |
| IMP::Pointer< domino::RestraintCache > | |
| IMP::Pointer< em::DensityMap > | |
| IMP::Pointer< em::SampledDensityMap > | |
| IMP::Pointer< IMP::atom::CHARMMIdealResidueTopology > | |
| IMP::Pointer< IMP::atom::CHARMMPatch > | |
| IMP::Pointer< IMP::Configuration > | |
| IMP::Pointer< IMP::ConfigurationSet > | |
| IMP::Pointer< IMP::core::IncrementalScoringFunction > | |
| IMP::Pointer< IMP::domino::AssignmentContainer > | |
| IMP::Pointer< IMP::domino::AssignmentsTable > | |
| IMP::Pointer< IMP::domino::ParticleStatesTable > | |
| IMP::Pointer< IMP::domino::RestraintCache > | |
| IMP::Pointer< IMP::em2d::Image > | |
| IMP::Pointer< IMP::em2d::ImageReaderWriter > | |
| IMP::Pointer< IMP::em2d::ProjectionFinder > | |
| IMP::Pointer< IMP::em2d::ScoreFunction > | |
| IMP::Pointer< IMP::IMP::Particle > | |
| IMP::Pointer< IMP::isd::MolecularDynamics > | |
| IMP::Pointer< IMP::isd::vonMisesSufficient > | |
| IMP::Pointer< IMP::Model > | |
| IMP::Pointer< IMP::Object > | |
| IMP::Pointer< IMP::PairContainer > | |
| IMP::Pointer< IMP::Particle > | |
| IMP::Pointer< IMP::QuadContainer > | |
| IMP::Pointer< IMP::RestraintSet > | |
| IMP::Pointer< IMP::saxs::DerivativeCalculator > | |
| IMP::Pointer< IMP::saxs::ProfileFitter< IMP::saxs::ChiScore > > | |
| IMP::Pointer< IMP::saxs::RigidBodiesProfileHandler > | |
| IMP::Pointer< IMP::ScoreState > | |
| IMP::Pointer< IMP::ScoringFunction > | |
| IMP::Pointer< IMP::SingletonContainer > | |
| IMP::Pointer< IMP::TripletContainer > | |
| IMP::Pointer< IMP::UnaryFunction > | |
| IMP::Pointer< internal::ConjugateGradientEigen > | |
| IMP::Pointer< internal::KMdata > | |
| IMP::Pointer< internal::KMfilterCenters > | |
| IMP::Pointer< internal::ListSelectionPredicate > | |
| IMP::Pointer< internal::RigidBodyHierarchy > | |
| IMP::Pointer< kinematics::IMP::kinematics::KinematicForest > | |
| IMP::PointerMember< O > | A smart pointer to a ref-counted Object that is a class member |
| IMP::PointerMember< algebra::NearestNeighbor3D > | |
| IMP::PointerMember< algebra::NearestNeighbor6D > | |
| IMP::PointerMember< const IMP::rotamer::RotamerLibrary > | |
| IMP::PointerMember< const IMP::saxs::Profile > | |
| IMP::PointerMember< const saxs::Profile > | |
| IMP::PointerMember< container::CloseBipartitePairContainer > | |
| IMP::PointerMember< core::internal::MovedSingletonContainer > | |
| IMP::PointerMember< domino::ParticleStatesTable > | |
| IMP::PointerMember< domino::RestraintScoreSubsetFilterTable > | |
| IMP::PointerMember< em::DensityMap > | |
| IMP::PointerMember< GaussianProcessInterpolationScoreState > | |
| IMP::PointerMember< IMP::atom::AngleSingletonScore > | |
| IMP::PointerMember< IMP::atom::BondSingletonScore > | |
| IMP::PointerMember< IMP::atom::DihedralSingletonScore > | |
| IMP::PointerMember< IMP::atom::ImproperSingletonScore > | |
| IMP::PointerMember< IMP::atom::PDBSelector > | |
| IMP::PointerMember< IMP::atom::SmoothingFunction > | |
| IMP::PointerMember< IMP::Configuration > | |
| IMP::PointerMember< IMP::ConfigurationSet > | |
| IMP::PointerMember< IMP::container::ConsecutivePairContainer > | |
| IMP::PointerMember< IMP::core::ClosePairsFinder > | |
| IMP::PointerMember< IMP::core::RigidClosePairsFinder > | |
| IMP::PointerMember< IMP::core::SoftSpherePairScore > | |
| IMP::PointerMember< IMP::core::TransformationSymmetry > | |
| IMP::PointerMember< IMP::display::Writer > | |
| IMP::PointerMember< IMP::domino::AssignmentsTable > | |
| IMP::PointerMember< IMP::domino::ParticleStates > | |
| IMP::PointerMember< IMP::domino::ParticleStatesTable > | |
| IMP::PointerMember< IMP::domino::RestraintCache > | |
| IMP::PointerMember< IMP::em2d::ScoreFunction > | |
| IMP::PointerMember< IMP::em::DensityMap > | |
| IMP::PointerMember< IMP::em::EnvelopeScore > | |
| IMP::PointerMember< IMP::em::MapDistanceTransform > | |
| IMP::PointerMember< IMP::em::PCAAligner > | |
| IMP::PointerMember< IMP::em::SampledDensityMap > | |
| IMP::PointerMember< IMP::IMP::UnaryFunction > | |
| IMP::PointerMember< IMP::internal::IMP::core::RestraintsScoringFunction > | |
| IMP::PointerMember< IMP::isd::BivariateFunction > | |
| IMP::PointerMember< IMP::isd::CrossLinkData > | |
| IMP::PointerMember< IMP::isd::CysteineCrossLinkData > | |
| IMP::PointerMember< IMP::isd::FretData > | |
| IMP::PointerMember< IMP::isd::GaussianProcessInterpolation > | |
| IMP::PointerMember< IMP::isd::MolecularDynamics > | |
| IMP::PointerMember< IMP::isd::MolecularDynamicsMover > | |
| IMP::PointerMember< IMP::isd::MultivariateFNormalSufficient > | |
| IMP::PointerMember< IMP::isd::UnivariateFunction > | |
| IMP::PointerMember< IMP::Model > | |
| IMP::PointerMember< IMP::multifit::AssemblyHeader > | |
| IMP::PointerMember< IMP::Optimizer > | |
| IMP::PointerMember< IMP::OptimizerState > | |
| IMP::PointerMember< IMP::PairContainer > | |
| IMP::PointerMember< IMP::PairModifier > | |
| IMP::PointerMember< IMP::PairPredicate > | |
| IMP::PointerMember< IMP::PairScore > | |
| IMP::PointerMember< IMP::Particle > | |
| IMP::PointerMember< IMP::QuadContainer > | |
| IMP::PointerMember< IMP::QuadModifier > | |
| IMP::PointerMember< IMP::QuadPredicate > | |
| IMP::PointerMember< IMP::QuadScore > | |
| IMP::PointerMember< IMP::Refiner > | |
| IMP::PointerMember< IMP::Restraint > | |
| IMP::PointerMember< IMP::saxs::Profile > | |
| IMP::PointerMember< IMP::ScoreState > | |
| IMP::PointerMember< IMP::ScoringFunction > | |
| IMP::PointerMember< IMP::SingletonContainer > | |
| IMP::PointerMember< IMP::SingletonModifier > | |
| IMP::PointerMember< IMP::SingletonPredicate > | |
| IMP::PointerMember< IMP::SingletonScore > | |
| IMP::PointerMember< IMP::statistics::Embedding > | |
| IMP::PointerMember< IMP::statistics::Metric > | |
| IMP::PointerMember< IMP::statistics::PartitionalClustering > | |
| IMP::PointerMember< IMP::TripletContainer > | |
| IMP::PointerMember< IMP::TripletModifier > | |
| IMP::PointerMember< IMP::TripletPredicate > | |
| IMP::PointerMember< IMP::TripletScore > | |
| IMP::PointerMember< IMP::UnaryFunction > | |
| IMP::PointerMember< internal::PairContainerIndex > | |
| IMP::PointerMember< internal::QuadContainerIndex > | |
| IMP::PointerMember< internal::SingletonContainerIndex > | |
| IMP::PointerMember< internal::TripletContainerIndex > | |
| IMP::PointerMember< multifit::IMP::multifit::ProteomicsData > | |
| IMP::PointerMember< PairScore > | |
| IMP::PointerMember< Predicate > | |
| IMP::PointerMember< ScoringFunctionT > | |
| IMP::PointerMember< Table > | |
| IMP::PointerMember< UF > | |
| IMP::em2d::PolarResamplingParameters | |
| IMP.pmi.analysis.Precision | A class to evaluate the precision of an ensemble |
| IMP.pmi.output.ProcessOutput | A class for reading stat files |
| IMP::saxs::ProfileClustering | |
| IMP::em2d::ProjectingParameters | Parameters needed for the core projection routine |
| IMP::em2d::Em2DRestraintParameters | Parameters used by Em2DRestraint and ProjectionFinder |
| IMP::em2d::ProjectingOptions | Parameters given as options to the get_projections() functions |
| IMP::em2d::ProjectionMask | |
| IMP::kinematics::ProteinKinematics | |
| IMP::multifit::ProteinsAnchorsSamplingSpace | Stores the anchors sampling space for each protein |
| IMP.pmi.restraints.stereochemistry.PseudoAtomicRestraint | Add bonds and improper dihedral restraints for the CBs |
| IMP::PythonDirectedGraph | |
| IMP::em::RadiusDependentDistanceMask | |
| IMP.test.RefCountChecker | Check to make sure the number of C++ object references is as expected |
| IMP::algebra::ReferenceFrame3D | A reference frame in 3D |
| IMP::em2d::RegistrationResult | Class to manage registration results |
| IMP.pmi.samplers.ReplicaExchange | Sample using replica exchange |
| IMP.pmi.macros.ReplicaExchange0 | A macro to help setup and run replica exchange |
| IMP.pmi.representation.Representation | Set up the representation of all proteins and nucleic acid macromolecules |
| IMP.pmi.restraints.stereochemistry.ResidueAngleRestraint | Add angular restraint between triplets of consecutive residues/beads to enforce the stereochemistry |
| IMP.pmi.restraints.stereochemistry.ResidueBondRestraint | Add bond restraint between pair of consecutive residues/beads to enforce the stereochemistry |
| IMP.pmi.restraints.stereochemistry.ResidueDihedralRestraint | Add dihedral restraints between quadruplet of consecutive residues/beads to enforce the stereochemistry |
| IMP.pmi.io.crosslink.ResiduePairListParser | A class to handle different styles of site pairs parsers |
| IMP::rotamer::ResidueRotamer | A class storing the rotated coordinates of the atoms in the residue |
| IMP::atom::ResidueType | The type for a residue |
| IMP.pmi.io.RMSDOutput | A helper output based on dist to initial coordinates |
| IMP::rotamer::RotamerAngleTuple | A simple class storing chi angles and their probability |
| IMP.test.RunInTempDir | Simple RAII-style class to run in a temporary directory |
| IMP::score_functor::Score | A functor for computing a distance based score for two particles |
| IMP::score_functor::AddScores< BaseDistanceScore0, BaseDistanceScore1 > | |
| IMP::score_functor::Harmonic | |
| IMP::score_functor::HarmonicLowerBound | |
| IMP::score_functor::HarmonicUpperBound | |
| IMP::score_functor::LinearLowerBound | |
| IMP::score_functor::OpenCubicSpline | Open cubic spline function |
| IMP::score_functor::OrientedSoap | Orientation-dependent SOAP score |
| IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > | |
| IMP::score_functor::UnaryFunctionEvaluate | |
| IMP::score_functor::Statistical< DopeType, false, false > | |
| IMP::score_functor::Soap | |
| IMP::score_functor::Statistical< DopeType, false, true > | |
| IMP::score_functor::Dope | |
| IMP::score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > | |
| IMP.pmi.restraints.stereochemistry.SecondaryStructure | Experimental, requires isd_emxl for now |
| IMP::em2d::SegmentationParameters | Class to provide all the parameters to the segmentation function |
| IMP.pmi.topology.Sequences | A dictionary-like wrapper for reading and storing sequence data |
| IMP.pmi.restraints.proteomics.SetupConnectivityNetworkRestraint | Generates 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") |
| IMP.pmi.restraints.proteomics.SetupMembraneRestraint | |
| IMP.isd.shared_functions.sfo_common | Nonspecific methods used across all shared function objects |
| IMP::score_functor::Shift< BaseDistanceScore > | |
| IMP::Showable | |
| IMP::em2d::SingleLinkage | Functor for hierarchical clustering based on single linkage |
| IMP::score_functor::SingletonStatistical< Key, INTERPOLATE > | |
| IMP.parallel.Slave | Representation of a single slave |
| IMP.parallel.LocalSlave | A slave running on the same machine as the master |
| IMP.parallel.SlaveArray | Representation of an array of slaves |
| IMP.parallel.SGEPESlaveArray | An array of slaves in a Sun Grid Engine system parallel environment |
| IMP.parallel.SGEQsubSlaveArray | An array of slaves on a Sun Grid Engine system, started with 'qsub' |
| IMP::saxs::SolventAccessibleSurface | |
| IMP::algebra::SparseGridStorageD< D, VT, Base, Map > | |
| IMP::algebra::SparseGridStorageD< D, VT, Base > | |
| IMP::SparseSymmetricPairMemoizer< Generator, Checker > | |
| IMP::score_functor::SphereDistance< BaseDistanceScore > | |
| IMP::em::SpiderHeader | Header for Spider images. IMP-EM is designed to be compatible with it |
| IMP.pmi.topology.State | Stores a list of Molecules all with the same State index |
| IMP.isd.Statistics.Statistics | Statistics gathering and printing class for ISD gibbs sampling |
| IMP.pmi.restraints.stereochemistry.SymmetryRestraint | Create harmonic restraints between the reference and (transformed) clones |
| IMP.pmi.topology.System | This class initializes the root node of the global IMP.atom.Hierarchy |
| IMP.isd.TALOSReader.TALOSReader | Reads a TALOS file, or a TALOS folder, and stores the data |
| IMP.test.TempDir | Simple RAII-style class to make a temporary directory |
| IMP.pmi.topology.TempResidue | Temporarily stores residue information, even without structure available |
| IMP.test.TestCase | Super class for IMP test cases |
| IMP.test.ApplicationTestCase | Super class for simple IMP application test cases |
| IMP.pmi.plotting.topology.TopologyPlot | A class to read RMF files and make a network contact map |
| IMP.pmi.topology.TopologyReader | Automatically setup Sytem and Degrees of Freedom with a formatted text file |
| IMP.pmi.io.TotalScoreOutput | A helper output for model evaluation |
| IMP.EMageFit.imp_general.io.Transformation3DToText | Parseable output for a IMP Transformation3D |
| IMP.EMageFit.imp_general.io.ReferenceFrameToText | Transform a IMP reference frame into parseable output |
| IMP::algebra::UnboundedGridRangeD< D > | |
| IMP::algebra::SparseGridStorageD< D, VT, UnboundedGridRangeD< D > > | |
| IMP::algebra::GridD< D, SparseGridStorageD< D, VT, UnboundedGridRangeD< D > >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::UnboundedGridRangeD< 3 > | |
| IMP::algebra::SparseGridStorageD< 3, Ints, UnboundedGridRangeD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, Ints, UnboundedGridRangeD< 3 > >, Ints, DefaultEmbeddingD< 3 > > | |
| IMP::algebra::SparseGridStorageD< 3, VT, UnboundedGridRangeD< 3 > > | |
| IMP::algebra::GridD< 3, SparseGridStorageD< 3, VT, UnboundedGridRangeD< 3 > >, VT, DefaultEmbeddingD< 3 > > | |
| IMP::UncheckedWeakPointer< O > | A weak pointer to an Object or RefCountedObject |
| IMP::UncheckedWeakPointer< IMP::Optimizer > | |
| IMP::UsageException | An exception for an invalid usage of IMP |
| IMP::Value | Base for a simple primitive-like type |
| IMP::Array< 2, Key > | |
| IMP::Array< 4, ParticleIndex > | |
| IMP::ConstVector< IMP::WeakPointer< Particle >, Particle * > | |
| IMP::domino::Subset | Represent a subset of the particles being optimized |
| IMP::ConstVector< int > | |
| IMP::domino::Assignment | Store a configuration of a subset |
| IMP::ConstVector< unsigned int > | |
| IMP::domino::Order | Store a persistent ordering for a subset based on the list |
| IMP::domino::Slice | Store a subset of a subset or assignment |
| IMP::algebra::ExtendedGridIndexD< D > | An index in an infinite grid on space |
| IMP::algebra::GridIndexD< D > | Represent a real cell in a grid (one within the bounding box) |
| IMP::Array< D, Data, SwigData > | A class to store an fixed array of same-typed values |
| IMP::ConstVector< Data, SwigData > | Store an array of values of the same type |
| IMP::core::MonteCarloMoverResult | |
| IMP::Decorator | Interface to specialized Particle types (e.g. atoms) |
| IMP::atom::Angle | A particle that describes an angle between three particles |
| IMP::atom::AngularVelocity | A particle with angular velocity |
| IMP::atom::Bond | A decorator for wrapping a particle representing a molecular bond |
| IMP::atom::Bonded | A decorator for a particle which has bonds |
| IMP::atom::CenterOfMass | A particle that is the center of mass of other particles |
| IMP::atom::Dihedral | A particle that describes a dihedral angle between four particles |
| IMP::atom::LinearVelocity | A particle with linear (XYZ) velocity |
| IMP::atom::Mass | Add mass to a particle |
| IMP::atom::SecondaryStructureResidue | A decorator for a residue with probability of secondary structure |
| IMP::atom::StructureSource | Store strings describing the source of this structure fragment |
| IMP::atom::TAMDParticle | |
| IMP::core::Hierarchy | A decorator for helping deal with a generalized hierarchy |
| IMP::atom::Hierarchy | The standard decorator for manipulating molecular structures |
| IMP::atom::Atom | A decorator for a particle representing an atom |
| IMP::atom::CHARMMAtom | A decorator for an atom that has a defined CHARMM type |
| IMP::atom::Chain | Store info for a chain of a protein |
| IMP::atom::Domain | A decorator to associate a particle with a part of a protein |
| IMP::atom::Fragment | A decorator to associate a particle with a part of a protein/DNA/RNA |
| IMP::atom::Molecule | A decorator for a molecule |
| IMP::atom::Copy | A decorator for keeping track of copies of a molecule |
| IMP::atom::Representation | A decorator for a representation |
| IMP::atom::Residue | A decorator for a residue |
| IMP::atom::State | Associate an integer "state" index with a hierarchy node |
| IMP::core::Reference | A particle that has an associated reference particle |
| IMP::core::Typed | A decorator for classifying particles in your system |
| IMP::core::XYZ | A decorator for a particle with x,y,z coordinates |
| IMP::atom::Charged | A decorator for a point particle that has an electrostatic charge |
| IMP::atom::Diffusion | A decorator for a diffusing particle with a diffusion coefficient |
| IMP::atom::RigidBodyDiffusion | |
| IMP::core::Centroid | A particle that is the geometric centroid of other particles |
| IMP::atom::TAMDCentroid | |
| IMP::core::RigidBody | A decorator for a rigid body |
| IMP::core::Gaussian | |
| IMP::kinematics::KinematicNode | |
| IMP::core::RigidBodyMember | A member of a rigid body, it has internal (local) coordinates |
| IMP::core::NonRigidMember | A decorator for a particle that is part of a rigid body but not rigid |
| IMP::core::RigidMember | |
| IMP::core::XYZR | A decorator for a particle with x,y,z coordinates and a radius |
| IMP::atom::LennardJones | A decorator for a particle that has a Lennard-Jones potential well |
| IMP::core::Cover | A particle which covers a set of other particles |
| IMP::misc::CustomXYZR | A decorator for a particle with x,y,z coordinates and a radius |
| IMP::display::Colored | A particle with a color |
| IMP::em2d::ProjectionParameters | |
| IMP::em::Voxel | |
| IMP::example::ExampleDecorator | A simple decorator which adds a name to a particle |
| IMP::isd::Nuisance | Add nuisance parameter to particle |
| IMP::isd::Scale | Add scale parameter to particle |
| IMP::isd::Switching | Add switching parameter to particle |
| IMP::isd::Weight | Add weights for a set of states to a particle |
| IMP::pmi::Resolution | Add resolution to a particle |
| IMP::pmi::Symmetric | Add symmetric attribute to a particle |
| IMP::pmi::Uncertainty | Add uncertainty to a particle |
| IMP::display::Color | Represent an RGB color |
| IMP::FloatIndex | |
| IMP::Index< Tag > | A typed index |
| IMP::Key< ID, LazyAdd > | A base class for Keys |
| IMP::ScoreAccumulator | Class for adding up scores during ScoringFunction evaluation |
| IMP::Vector< T > | |
| IMP::IndexVector< Tag, T > | |
| IMP::ParticleIndexPairsAdaptor | |
| IMP::VersionInfo | Version and module information for Objects |
| IMP::Index< ParticleIndexTag > | |
| IMP::ParticleIndexAdaptor | |
| IMP::Key< 0, true > | |
| IMP::Key< 1, true > | |
| IMP::Key< 3, true > | |
| IMP::Key< 4, true > | |
| IMP::Key< 6, true > | |
| IMP::Key< 8974343, false > | |
| IMP::Key< 90784334, true > | |
| IMP::Vector< algebra::Vector3D > | |
| IMP::Vector< algebra::Vector3Ds > | |
| IMP::Vector< algebra::VectorKD > | |
| IMP::Vector< AP > | |
| IMP::Vector< Assignment > | |
| IMP::Vector< AtomFactorCoefficients > | |
| IMP::Vector< CHARMMAngle > | |
| IMP::Vector< CHARMMBond > | |
| IMP::Vector< CHARMMDihedral > | |
| IMP::Vector< CHARMMInternalCoordinate > | |
| IMP::Vector< core::RigidBody > | |
| IMP::Vector< Data > | |
| IMP::Vector< double > | |
| IMP::Vector< FittingSolutionRecord > | |
| IMP::Vector< Float > | |
| IMP::Vector< FloatIndex > | |
| IMP::Vector< FloatKey > | |
| IMP::Vector< FloatRange > | |
| IMP::Vector< Floats > | |
| IMP::Vector< Hierarchy > | |
| IMP::Vector< IMP::algebra::VectorD< D > > | |
| IMP::Vector< IMP::atom::CHARMMAtomTopology > | |
| IMP::Vector< IMP::atom::CHARMMBondEndpoint > | |
| IMP::Vector< IMP::atom::ForceFieldParameters::Bond > | |
| IMP::Vector< IMP::Index > | |
| IMP::Vector< IMP::multi_state::MultiStateModelScore * > | |
| IMP::Vector< IMP::Pointer< DihedralAngleRevoluteJoint > > | |
| IMP::Vector< IMP::Pointer< DOF > > | |
| IMP::Vector< IMP::Pointer< Geometry > > | |
| IMP::Vector< IMP::Pointer< Image > > | |
| IMP::Vector< IMP::Pointer< IMP::Configuration > > | |
| IMP::Vector< IMP::Pointer< IMP::Particle > > | |
| IMP::IndexVector< ParticleIndexTag, IMP::Pointer< IMP::Particle > > | |
| IMP::Vector< IMP::Pointer< Joint > > | |
| IMP::Vector< IMP::Pointer< MonteCarloMover > > | |
| IMP::Vector< IMP::Pointer< O > > | |
| IMP::Vector< IMP::Pointer< PairContainer > > | |
| IMP::Vector< IMP::Pointer< PairScore > > | |
| IMP::Vector< IMP::Pointer< Particle > > | |
| IMP::Vector< IMP::Pointer< Profile > > | |
| IMP::Vector< IMP::Pointer< QuadScore > > | |
| IMP::Vector< IMP::Pointer< Restraint > > | |
| IMP::Vector< IMP::Pointer< RevoluteJoint > > | |
| IMP::Vector< IMP::Pointer< SampledDensityMap > > | |
| IMP::Vector< IMP::Pointer< SingletonScore > > | |
| IMP::Vector< IMP::Pointer< SubsetFilterTable > > | |
| IMP::Vector< IMP::Pointer< SurfaceShellDensityMap > > | |
| IMP::Vector< IMP::Pointer< TripletScore > > | |
| IMP::Vector< IMP::Pointer< UnaryFunction > > | |
| IMP::Vector< IMP::PointerMember< IMP::Object > > | |
| IMP::Vector< IMP::PointerMember< Score > > | |
| IMP::Vector< IMP::Vector > | |
| IMP::IndexVector< ParticleIndexTag, IMP::Vector > | |
| IMP::Vector< IMP::Vector< double > > | |
| IMP::Vector< IMP::WeakPointer< Container > > | |
| IMP::Vector< IMP::WeakPointer< Restraint > > | |
| IMP::Vector< Index > | |
| IMP::Vector< Int > | |
| IMP::Vector< int > | |
| IMP::Vector< internal::NBLScoring * > | |
| IMP::Vector< IntPair > | |
| IMP::Vector< Ints > | |
| IMP::Vector< IntsList > | |
| IMP::Vector< Key > | |
| IMP::Vector< ModelObject * > | |
| IMP::Vector< ParticleIndex > | |
| IMP::Vector< ParticleIndexPair > | |
| IMP::Vector< ParticleIndexQuad > | |
| IMP::Vector< ParticleIndexTriplet > | |
| IMP::Vector< ParticlePair > | |
| IMP::Vector< Pointer< Particle > > | |
| IMP::Vector< ReferenceFrame3D > | |
| IMP::Vector< RegistrationResult > | |
| IMP::Vector< RestraintSetData > | |
| IMP::Vector< RigidBody > | |
| IMP::Vector< Rotation3D > | |
| IMP::Vector< Slice > | |
| IMP::Vector< Sphere3D > | |
| IMP::Vector< std::pair< internal::CHARMMDihedralNames, CHARMMDihedralParameters > > | |
| IMP::Vector< std::string > | |
| IMP::Vector< String > | |
| IMP::Vector< Transformation3D > | |
| IMP::Vector< unsigned int > | |
| IMP::Vector< VectorD< 2 > > | |
| IMP::Vector< VectorD< 3 > > | |
| IMP::Vector< VectorD<-1 > > | |
| IMP::Vector< WeakPointer< Particle > > | |
| IMP::domino::ParticlesAdaptor | |
| IMP::Vector< XYZ > | |
| IMP::Vector< XYZR > | |
| std::vector< T > | STL class |
| IMP::saxs::Distribution< algebra::Vector3D > | |
| IMP::saxs::DeltaDistributionFunction | |
| IMP::saxs::Distribution< double > | |
| IMP::saxs::RadialDistributionFunction | |
| IMP::saxs::Distribution< ValueT > | |
| IMP::WarningContext | |
| IMP::WeakPointer< O > | Smart pointer to Object-derived classes that does not refcount |
| IMP::WeakPointer< atom::Simulator > | |
| IMP::WeakPointer< IMP::Model > | |
| IMP::WeakPointer< IMP::Particle > | |
| IMP::WeakPointer< IMP::Restraint > | |
| IMP::score_functor::WeightScore< BaseDistanceScore > | |
| IMP.EMageFit.buildxlinks.Xlink | Class defining a cross-link |
| IMP.EMageFit.buildxlinks.XlinksDict | Description of crosslinking restraints as a python dictionary |
| IMP.pmi.io.xltable.XLTable | Class 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 |
