  IMP.isd.AbstractGrid.AbstractGrid | Grid main functionality: manage services |
| IMP.isd.AbstractGrid.AbstractService | Wrapper around Grid services, facilitating non parameter-specific usage of the remote objects |
| IMP::base::AddBoolFlag | |
| IMP::base::AddFloatFlag | |
| IMP::base::AddIntFlag | |
| IMP::base::AddStringFlag | |
| IMP.multifit.cluster.AlignmentClustering | Clusters assembly models |
| IMP::cnmultifit::AlignSymmetric | A class for fast alignment of a cyclic model to its density |
| 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::atom::AtomType | The type of an atom |
| IMP::modeller::BinormalTerm | A single binormal term in a MultipleBinormalRestraint |
| IMP::atom::BondGraph | Represent a bond graph as a boost graph |
 IMP::algebra::BoundedGridRangeD< D > | |
 IMP::algebra::DenseGridStorageD< 3, VT > | |
 IMP::algebra::GridD< 3, DenseGridStorageD< 3, VT >, VT, DefaultEmbeddingD< 3 > > | |
  IMP::algebra::DenseGrid3D< VT > | |
| IMP::algebra::DenseGridStorageD< D, VT > | |
| 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 > | |
| IMP::algebra::BoundingBoxD< D > | An axis-aligned bounding box |
| IMP::algebra::BoundingBoxD< 3 > | |
| 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.em2d.solutions_io.ClusterRecord | Simple named tuple class |
| IMP::em::CoarseConvolution | Convolutes two grids |
| IMP.kernel.CommandDispatcher | Allow applications to easily implement commmands |
| IMP.parallel.Context | A collection of tasks that run in the same environment |
| IMP.isd.TuneRex.CvEstimator | When created, estimates the heat capacity from the energies or from the indicator functions using the specified method |
| IMP.em2d.Database.Database2 | Class to manage a SQL database built with sqlite3 |
| IMP.em2d.solutions_io.ResultsDB | Class for managing the results of the experiments |
| IMP::multifit::DataPointsAssignment | |
| IMP::algebra::DefaultEmbeddingD< D > | |
| IMP::algebra::GridD< D, SparseGridStorageD< D, VT, UnboundedGridRangeD< D > >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::SparseUnboundedGridD< D, VT > | |
| 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 > | |
| IMP::multifit::DensityDataPoints | Stores density voxels as a vector of Array1D |
| IMP::em::DensityHeader | |
| IMP::kernel::DerivativeAccumulator | Class for adding derivatives from restraints to the model |
| IMP::core::DerivativesFromRefined | Accumulate the derivatives of the refined particles |
| IMP::core::DerivativesToRefined | Copy the derivatives from the particle to its refined particles |
| IMP.test.DirectorObjectChecker | Check to make sure the number of director references is as expected |
| IMP.restrainer._display.Display | Store Display |
| IMP.restrainer.Display | A class to display the configuration |
| IMP::em::DistanceMask | Calculates and stores a distance mask |
| IMP.em2d.buildxlinks.DockOrder | Compute the order of the docking experiments |
| IMP.em2d.DominoModel.DominoModel | Management of a model using DOMINO |
| IMP::atom::ElementTable | |
| IMP.isd.Entry.Entry | The entry class represents a column in the statistics file |
| 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::kernel::EvaluationState | |
| IMP::example::ExampleTemplateClassD< D > | A line segment templated on the dimension |
| IMP::base::Exception | The general base class for IMP exceptions |
| IMP::base::EventException | An exception that signifies some event occurred |
| IMP::base::IndexException | An exception for a request for an invalid member of a container |
| IMP::base::IOException | An input/output exception |
| IMP::base::ModelException | An exception which is thrown when the Model has attributes with invalid values |
| IMP::base::ValueException | An exception for an invalid value being passed to IMP |
| IMP.isd.FIFOBasedGrid.FIFOBasedRemoteObject | Filebased proxy instance |
| IMP.isd.FileBasedGrid.FileBasedRemoteObject | Filebased proxy instance |
| IMP::multifit::FittingSolutionRecord | A fitting solution record |
| IMP::em::FittingSolutions | A simple list of fitting solutions |
| IMP::saxs::FormFactorTable | |
| IMP::algebra::GeometricPrimitiveD< D > | |
| 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, SparseGridStorageD< D, VT, UnboundedGridRangeD< D > >, VT, DefaultEmbeddingD< D > > | |
| IMP::algebra::GridD< D, Storage, Value, EmbeddingT > | A voxel grid in d-dimensional space space |
| IMP::algebra::PrincipalComponentAnalysisD< D > | |
| IMP::algebra::SphereD< D > | |
| IMP::algebra::VectorD< D > | A Cartesian vector in D-dimensions |
| IMP::algebra::VectorInputD< D > | |
| IMP::statistics::HistogramD< D, Grid > | |
| IMP::algebra::SphereD< 3 > | |
| IMP::algebra::VectorD< 1 > | |
| IMP::algebra::VectorInputD< 1 > | |
| IMP::algebra::VectorD< 2 > | |
| IMP::algebra::VectorD< 3 > | |
| IMP::algebra::VectorD< 4 > | |
| 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 | |
| IMP::algebra::Cylinder3D | |
| IMP::algebra::Ellipsoid3D | |
| IMP::algebra::FixedXYZ | A simple class for returning XYZ Euler angles |
| IMP::algebra::FixedZXZ | A simple class for returning ZXZ Euler angles |
| IMP::algebra::FixedZYZ | A simple class for returning ZYZ Euler angles |
| IMP::algebra::Plane3D | |
| IMP::algebra::Reflection3D | Reflect about a plane in 3D |
| IMP::algebra::Rotation3D | 3D rotation class |
| IMP::algebra::Segment3D | |
| IMP::algebra::SpherePatch3D | |
| IMP::algebra::SphericalVector3D | Class to represent a 3D point in spherical coordinates |
| IMP::algebra::Transformation3D | Simple 3D transformation class |
| IMP::algebra::Triangle3D | |
| 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::BildWriter | Write a Bild file with the geometry |
| IMP::display::ChimeraWriter | Write geometry to a python file for Chimera to read |
| IMP::display::CMMWriter | Write a CMM file with the geometry |
| IMP::display::PymolWriter | Write a CGO file with the geometry |
| IMP::em2d::HasHigherCCC< T > | Comparison by value of the ccc |
| IMP::em2d::HasLowerScore< T > | Compare two classes that return a score |
| IMP.em2d.solutions_io.HeapRecord | The heapq algorithm is a min-heap |
| 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 which applies a singleton modifier to each Particle in a hierarchy |
| IMP::statistics::Histogram | Histogram |
| 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 Microsocopy images in IMP |
| IMP.modeller.IMPRestraints | A Modeller restraint which evaluates all defined IMP restraints |
| IMP.em2d.buildxlinks.InitialDockingFromXlinks | Puts two subunits together using the Xlinkins restraints |
| IMP::base::InputAdaptor | |
| IMP::algebra::VectorInputD< D > | |
| IMP::algebra::VectorInputD< 1 > | |
| IMP::atom::Selection | |
| IMP::base::TextInput | |
| IMP::base::TextOutput | |
| IMP::display::WriterAdaptor | |
| IMP::domino::ParticlesAdaptor | |
| IMP::kernel::PairContainerAdaptor | |
| IMP::kernel::QuadContainerAdaptor | |
| IMP::kernel::ScoringFunctionAdaptor | |
| IMP::kernel::SingletonContainerAdaptor | |
| IMP::kernel::TripletContainerAdaptor | |
| IMP::base::InternalException | A general exception for an intenal error in IMP |
| IMP::em2d::JPGImageReaderWriter | Class to read and write EM images in JPG format |
| IMP::em::KernelParameters | |
| IMP::em2d::LessPairBySecond< T > | Comparison of pairs by checking the second element |
| IMP::algebra::LogEmbeddingD< D > | |
| IMP::base::LRUCache< Generator, Checker > | |
| IMP::base::LRUCache< Generator, ApproximatelyEqual > | |
| IMP.parallel.Manager | Manages slaves and contexts |
| IMP::base::map< Key, Data > | |
| IMP::base::map< base::Object *, Statistics > | |
| IMP::base::map< const IMP::kernel::Particle *, int > | |
| IMP::base::map< core::RigidBody, Particles > | |
| IMP::base::map< DGVertex, Particle * > | |
| IMP::base::map< Element, std::string > | |
| IMP::base::map< GridIndexD< D >, Ints > | |
| IMP::base::map< GridIndexD< D >, VT > | |
| IMP::base::map< IMP::base::Array, unsigned int > | |
| IMP::base::map< IMP::base::Array, Vector< IntPair > > | |
| IMP::base::map< IMP::domino::Subset, IMP::OwnerPointer< IMP::domino::AssignmentContainer > > | |
| IMP::base::map< IMP::kernel::Key, FloatRange > | |
| IMP::base::map< IMP::kernel::ModelObject *, ScoreStatesTemp > | |
| IMP::base::map< IMP::kernel::Particle *, ConstData > | |
| IMP::base::map< IMP::kernel::Particle *, Data > | |
| IMP::base::map< IMP::kernel::Particle *, Particles > | |
| IMP::base::map< IMP::kernel::Particle *, Pointer< display::Geometry > > | |
| IMP::base::map< IMP::kernel::Particle *, Pointer< Geometry > > | |
| IMP::base::map< IMP::kernel::Particle *, unsigned int > | |
| IMP::base::map< Index< ParticleIndexTag >, Vector< ParticleIndex > > | |
| IMP::base::map< Particle *, DGVertex > | |
| IMP::base::map< Particle *, IMP::OwnerPointer< ParticleStates > > | |
| IMP::base::map< ParticleIndex, base::OwnerPointer< internal::SingleParticleScoringFunction > > | |
| IMP::base::map< Pointer< Restraint >, int > | |
| IMP::base::map< Pointer< Restraint >, Subset > | |
| IMP::base::map< Restraint *, RestraintData > | |
| IMP::base::map< Restraint *, SetData > | |
| IMP::base::map< std::string, Element > | |
| IMP::base::map< Tracked *, std::string > | |
| IMP::base::map< unsigned int, ParticlesTemp > | |
| IMP::em2d::MasksManager | Manage of projection masks |
| IMP::em2d::MatchTemplateResult | |
| IMP::base::Memoizer< Generator, Checker > | |
| IMP.modeller.ModelLoader | Read a Modeller model into IMP |
| IMP.em2d.MonteCarloRelativeMoves.MonteCarloRelativeMoves | Class to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies |
| IMP::base::NonCopyable | |
| IMP::base::RAII | |
| IMP::base::CreateLogContext | Create a new log context |
| IMP::base::SetCheckState | A class to change and restore check state |
| IMP::base::SetLogState | A class to change and restore log state |
| IMP::base::SetLogTarget | |
| IMP::base::SetNumberOfThreads | |
| IMP::benchmark::Profiler | |
| IMP::kernel::GenericScopedRemoveRestraint< SS > | Removes the Restraint until RAII object is destroyed |
| IMP::kernel::GenericScopedRemoveScoreState< SS > | Removes the ScoreState until RAII object is destroyed |
| IMP::kernel::GenericScopedRestraint< SS > | Removes the Restraint when the RAII object is destroyed |
| IMP::kernel::GenericScopedScoreState< SS > | Removes the ScoreState when the RAII object is destroyed |
| IMP::kernel::ScopedAddCacheAttribute< Key, Value > | |
| IMP::kernel::ScopedSetAttribute< Key, Value > | |
| IMP::base::RefCounted | Common base class for ref counted objects |
| IMP::base::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::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 HETATMrecords 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::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 ATOM records |
| IMP::atom::WaterPDBSelector | Select all non-water ATOM and HETATMrecords |
| IMP::atom::NotPDBSelector | Select atoms which not selected by a given selector |
| IMP::atom::OrPDBSelector | Select atoms which are selected by either selector |
| 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::base::TrackedObject< Type, Tracker > | |
| 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 | Peform more efficient close pair finding when rigid bodies are involved |
| 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 an IMP::atom::Bond particle as a segment |
| IMP::display::PairsGeometry | A base class for geometry from a set of particles |
| IMP::core::EdgePairsGeometry | Display an IMP::SingletonContainer of IMP::atom::Bond particles as segments |
| 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 an 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 triangule |
| 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::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::Image | 2D Electron Microscopy images in IMP |
| IMP::em2d::ProjectionFinder | Class to perform registration of model projections to images images |
| IMP::em2d::ScoreFunction | Base class for all scoring functions related to em2d |
| IMP::em2d::ChiSquaredScore | Score based on Chi^2 = ((pixels_iamge - pixels_projection)/stddev_image)^2 |
| IMP::em2d::EM2DScore | |
| 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 repersents 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::MRCReaderWriter | |
| IMP::em::SpiderMapReaderWriter | Class to read EM maps (3D) in Spider and Xmipp formats |
| IMP::em::PCAAligner | |
| IMP::isd::BivariateFunction | Base class for functions of two variables |
| IMP::isd::Covariance1DFunction | Covariance function |
| IMP::isd::FNormal | FNormal |
| 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::kernel::Configuration | A class to store a configuration of a model |
| IMP::kernel::ConfigurationSet | A class to store a set of configurations of a model |
| IMP::kernel::Model | Class for storing model, its restraints, constraints, and particles |
| IMP::kernel::ModelObject | |
| 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::Mover | A base class for classes which perturb particles |
| IMP::core::MoverBase | A class to help implement movers |
| IMP::isd::MolecularDynamicsMover | Modify a set of continuous variables using a MD simulation |
| IMP::core::NormalMover | Modify a set of continuous variables using a normal distribution |
| IMP::core::RigidBodyMover | Modify the transformation of a rigid body |
| IMP::core::SerialMover | Apply a list of movers one at a time |
| IMP::kernel::Particle | Class to handle individual model particles |
| IMP::kernel::Restraint | A restraint is a term in an IMP ScoringFunction |
| IMP::atom::CHARMMStereochemistryRestraint | Enforce CHARMM stereochemistry on the given Hierarchy |
| 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 | |
| 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::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 | Restraint the volume of a set of spheres |
| 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::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::isd::ISDRestraint | Apply an NOE distance restraint between two particles |
| 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::GaussianProcessInterpolationRestraint | Gaussian process restraint |
| IMP::isd::GaussianRestraint | Normal probability distribution as a restraint |
| IMP::isd::JeffreysRestraint | |
| IMP::isd::LognormalRestraint | Normal probability distribution as a restraint |
| 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::SlidingPriorRestraint | Score a Scale particle with unnormalized probability |
| IMP::isd::vonMisesKappaConjugateRestraint | Conjugate prior for the concentration parameter of a von Mises distribution |
| IMP::isd::vonMisesKappaJeffreysRestraint | |
| IMP::isd::LogicalORRestraint | Apply an NOE distance restraint between two particles |
| IMP::isd::TALOSRestraint | Phi/psi dihedral restraint between four particles, using data from TALOS |
| IMP::kernel::RestraintSet | Object used to hold a set of restraints |
| 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::RadiusOfGyrationRestraint | Ensure the radius of gyration of particles fits the predicted one |
| IMP::multifit::WeightedExcludedVolumeRestraint | Calculate score based on fit to EM map |
| IMP::saxs::RadiusOfGyrationRestraint | Calculate score based on radius of gyration, taken from saxs profile |
| IMP::saxs::Restraint | Calculate score based on fit to SAXS profile |
| IMP::kernel::ScoreState | ScoreStates maintian invariants in the Model |
| 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::domino::DependencyScoreState | Add a dependency to the dependency graph |
| IMP::em2d::ProjectionParametersScoreState | |
| IMP::kernel::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::isd::MaintainScaleOrderConstraint | Constrain scales to be ordered and positive |
| IMP::kernel::Container | Abstract class for containers of particles |
| IMP::kernel::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 pairs from an input list |
| IMP::container::DynamicListPairContainer | Store a list of ParticlePairsTemp |
| IMP::container::ExclusiveConsecutivePairContainer | |
| IMP::container::ListPairContainer | Store a list of ParticlePairsTemp |
| IMP::container::PairContainerSet | Stores a set of PairContainers |
| IMP::kernel::QuadContainer | A shared container for Quads |
| IMP::container::DynamicListQuadContainer | Store a list of ParticleQuadsTemp |
| IMP::container::ListQuadContainer | Store a list of ParticleQuadsTemp |
| IMP::container::QuadContainerSet | Stores a set of QuadContainers |
| IMP::kernel::SingletonContainer | A shared container for Singletons |
| IMP::container::DynamicListSingletonContainer | Store a list of ParticlesTemp |
| IMP::container::ListSingletonContainer | Store a list of ParticlesTemp |
| IMP::container::SingletonContainerSet | Stores a set of SingletonContainers |
| IMP::kernel::TripletContainer | A shared container for Triplets |
| IMP::container::DynamicListTripletContainer | Store a list of ParticleTripletsTemp |
| IMP::container::ListTripletContainer | Store a list of ParticleTripletsTemp |
| IMP::container::TripletContainerSet | Stores a set of TripletContainers |
| IMP::misc::StateAdaptor | Allow OptimizerStates to be used as ScoreStates |
| IMP::kernel::ScoringFunction | |
| IMP::core::IncrementalScoringFunction | |
| IMP::core::RestraintsScoringFunction | |
| IMP::kernel::Optimizer | Base class for all optimizers |
| IMP::atom::Simulator | The base class for simulators |
| IMP::atom::BrownianDynamics | Simple Brownian dynamics optimizer |
| IMP::atom::MolecularDynamics | Simple molecular dynamics optimizer |
| IMP::isd::MolecularDynamics | Molecular dynamics optimizer on 1-D and 3-D particles |
| IMP::core::ConjugateGradients | Simple conjugate gradients optimizer |
| 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::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::kernel::OptimizerState | Shared optimizer state |
| 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::PeriodicOptimizerState | |
| IMP::core::WriteRestraintScoresOptimizerState | |
| IMP::misc::DecayPairContainerOptimizerState | Maintain a pair container with a decaying list of pairs |
| IMP::rmf::SaveOptimizerState | |
| IMP::display::WriteOptimizerState | |
| IMP::kernel::PairModifier | A base class for modifiers of ParticlePairsTemp |
| IMP::kernel::PairPredicate | Abstract predicate function |
| IMP::atom::BondedPairFilter | A filter for bonds |
| IMP::atom::SameResiduePairFilter | |
| 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::OrderedTypePairPredicate | |
| IMP::core::UnorderedTypePairPredicate | |
| IMP::misc::CommonEndpointPairFilter | Return true for any pair of bonds sharing an endpoint |
| IMP::kernel::PairScore | Abstract score function |
| IMP::score_functor::DistancePairScore< score_functor::Dope > | |
| IMP::atom::DopePairScore | |
| 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::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::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::kernel::QuadModifier | A base class for modifiers of ParticleQuadsTemp |
| IMP::kernel::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::kernel::QuadScore | Abstract score function |
| IMP::container::MinimumQuadScore | Evaluate the min or max n particle_quad scores of the passed set |
| IMP::kernel::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::kernel::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::kernel::SingletonModifier | A base class for modifiers of ParticlesTemp |
| IMP::atom::CoverBond | Cover a bond with a sphere |
| IMP::core::CentroidOfRefined | Set the coordinates of the particle to be the centoid of the particles |
| IMP::core::CoverRefined | This class sets the position and radius of each particle to enclose the refined |
| 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::example::ExampleSingletonModifier | An example singleton modifer |
| IMP::kernel::SingletonPredicate | Abstract predicate function |
| IMP::container::InContainerSingletonFilter | A filter which returns true if a container containers the Singleton |
| IMP::core::AllSameSingletonPredicate | |
| IMP::core::AttributeSingletonPredicate | |
| IMP::core::CoinFlipSingletonPredicate | |
| IMP::core::ConstantSingletonPredicate | |
| IMP::core::InBoundingBox3DSingletonPredicate | |
| IMP::core::OrderedTypeSingletonPredicate | |
| IMP::core::UnorderedTypeSingletonPredicate | |
| IMP::kernel::SingletonScore | Abstract score function |
| 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::kernel::TripletModifier | A base class for modifiers of ParticleTripletsTemp |
| IMP::kernel::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::kernel::TripletScore | Abstract score function |
| 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::kernel::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::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::kernel::Undecorator | |
| IMP::kmeans::KMeans | |
| 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::SettingsData | Holds header data for optimization |
| IMP::rmf::LoadLink | |
| IMP::rmf::SaveLink | |
| 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::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::ConfigurationSetRMSDMetric | |
| IMP::statistics::RecursivePartitionalClusteringMetric | |
| write_a_metric.MyMetric | Define a metric on a list of floating point numbers based on their difference |
| write_a_metric.MyMetric | Define a metric on a list of floating point numbers based on their difference |
| IMP::statistics::PartitionalClustering | A base class for clustering results where each item is in one cluster |
| IMP::statistics::PartitionalClusteringWithCenter | |
| IMP::example::ExampleRefCounted | An example simple object which is reference counted |
| IMP.kernel.OptionParser | IMP-specific subclass of optparse.OptionParser |
| IMP::base::OwnerPointer< O > | A reference counted pointer to an Object |
| IMP::base::OwnerPointer< algebra::NearestNeighbor3D > | |
| IMP::base::OwnerPointer< algebra::NearestNeighbor6D > | |
| IMP::base::OwnerPointer< IMP::container::ConsecutivePairContainer > | |
| IMP::base::OwnerPointer< IMP::core::SoftSpherePairScore > | |
| IMP::base::OwnerPointer< IMP::display::Writer > | |
| IMP::base::OwnerPointer< IMP::IMP::kernel::UnaryFunction > | |
| IMP::base::OwnerPointer< IMP::kernel::PairContainer > | |
| IMP::base::OwnerPointer< IMP::kernel::PairPredicate > | |
| IMP::base::OwnerPointer< IMP::kernel::PairScore > | |
| IMP::base::OwnerPointer< IMP::kernel::QuadContainer > | |
| IMP::base::OwnerPointer< IMP::kernel::QuadPredicate > | |
| IMP::base::OwnerPointer< IMP::kernel::QuadScore > | |
| IMP::base::OwnerPointer< IMP::kernel::Restraint > | |
| IMP::base::OwnerPointer< IMP::kernel::ScoringFunction > | |
| IMP::base::OwnerPointer< IMP::kernel::SingletonContainer > | |
| IMP::base::OwnerPointer< IMP::kernel::SingletonPredicate > | |
| IMP::base::OwnerPointer< IMP::kernel::SingletonScore > | |
| IMP::base::OwnerPointer< IMP::kernel::TripletContainer > | |
| IMP::base::OwnerPointer< IMP::kernel::TripletPredicate > | |
| IMP::base::OwnerPointer< IMP::kernel::TripletScore > | |
| IMP::base::OwnerPointer< IMP::kernel::UnaryFunction > | |
| IMP::base::OwnerPointer< IMP::statistics::Embedding > | |
| IMP::base::OwnerPointer< internal::PairContainerIndex > | |
| IMP::base::OwnerPointer< internal::QuadContainerIndex > | |
| IMP::base::OwnerPointer< internal::SingletonContainerIndex > | |
| IMP::base::OwnerPointer< internal::TripletContainerIndex > | |
| IMP::base::OwnerPointer< multifit::ProteomicsData > | |
| IMP::base::OwnerPointer< PairScore > | |
| IMP::base::piecewise_linear_distribution< T > | |
| IMP.isd.utils.Pipe | Implements a FIFO pipe that merges lists (see self.put) |
| IMP::base::Pointer< O > | A reference counted pointer to an object |
| IMP::base::Pointer< IMP::internal::InternalDynamicListPairContainer > | |
| IMP::base::Pointer< IMP::kernel::Model > | |
| IMP::base::Pointer< IMP::kernel::PairContainer > | |
| IMP::base::Pointer< IMP::kernel::Particle > | |
| IMP::base::Pointer< IMP::kernel::QuadContainer > | |
| IMP::base::Pointer< IMP::kernel::RestraintSet > | |
| IMP::base::Pointer< IMP::kernel::ScoringFunction > | |
| IMP::base::Pointer< IMP::kernel::SingletonContainer > | |
| IMP::base::Pointer< IMP::kernel::TripletContainer > | |
| IMP::base::Pointer< List > | |
| IMP::base::Pointer< SS > | |
| IMP::em2d::PolarResamplingParameters | |
| IMP::saxs::Profile | |
| IMP::em2d::ProjectionMask | |
| IMP::multifit::ProteinsAnchorsSamplingSpace | Stores the anchors sampling space for each protein |
| IMP.isd.PyroGrid.PyroHandler | Runs on remote side, non-specific object |
| IMP.isd.PyroGrid.PyroProxy | This is high level wrapper of Pyro proxy objects, returns immediately with an empty Result object |
| IMP::kernel::PythonDirectedGraph | |
| IMP::em::RadiusDependentKernelParameters | Calculates kernel parameters as a function of a specific radius |
| 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.restrainer._representation.Representation | Store Representation |
| IMP.restrainer.Representation | Store Representation |
| IMP::rotamer::ResidueRotamer | A class storing the rotated coordinates of the atoms in the residue |
| IMP::atom::ResidueType | The type for a residue |
| IMP.restrainer._restraint.Restraint | Store Restraint |
| IMP.restrainer.Restraint | Store Restraint |
| IMP.isd.AbstractGrid.Result | A Result object is returned by a Proxy object, when some remote function invoked |
| IMP::atom::RMSDCalculator | Used to calculate rmsd between multiple transformation that operate on the same particles |
| IMP::multifit::RMSDClustering< TransT > | RMSD clustering |
| 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 | |
| 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::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > | |
| IMP::score_functor::UnaryFunctionEvaluate | |
| IMP::score_functor::Statistical< DopeType, false, true > | |
| IMP::score_functor::Dope | |
| IMP::score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > | |
| IMP::em2d::SegmentationParameters | Class to provide all the parameters to the segmentation function |
| IMP.isd.AbstractGrid.Server | Contains all the information that is required to use a remote object (alone and within a grid) |
| IMP::base::set< Key > | |
| IMP::base::set< IMP::kernel::Particle * > | |
| IMP::base::set< std::string > | |
| IMP::base::set< Tracked * > | |
| IMP.isd.shared_functions.sfo_common | Nonspecific methods used across all shared function objects |
| IMP::score_functor::Shift< BaseDistanceScore > | |
| IMP::base::Showable | |
| IMP::restrainer::SimpleConnectivity | Simple connectivity restraint |
| IMP::restrainer::SimpleDiameter | Simple diameter restraint |
| IMP::restrainer::SimpleDistance | Simple distance restraint between two particles |
| IMP::restrainer::SimpleEMFit | Simple EM fit restraint |
| IMP::restrainer::SimpleExcludedVolume | Simple excluded volume restraint |
| 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::base::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::em2d::SpiderImageReaderWriter | |
| IMP.isd.Statistics.Statistics | Statistics gathering and printing class for ISD gibbs sampling |
| IMP.isd.TALOSReader.TALOSReader | Reads a TALOS file, or a TALOS folder, and stores the data |
| IMP.test.TestCase | Super class for IMP test cases |
| IMP.test.ApplicationTestCase | Super class for simple IMP application test cases |
| IMP::base::Tracker< Tracked > | |
| 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::base::UncheckedWeakPointer< O > | A weak pointer to an IMP::Object or IMP::RefCountedObject |
| IMP::base::UncheckedWeakPointer< IMP::base::Tracker > | |
| IMP::base::UncheckedWeakPointer< Type > | |
| IMP::base::UsageException | An exception for an invalid usage of IMP |
| IMP::base::Value | |
| IMP::base::Array< 2, Key > | |
| IMP::base::ConstVector< base::WeakPointer< Particle >, Particle * > | |
| IMP::domino::Subset | Represent a subset of the particles being optimized |
| IMP::base::ConstVector< int > | |
| IMP::domino::Assignment | Store a configuration of a subset |
| IMP::base::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::base::Array< D, Data, SwigData > | A class to store an fixed array of same-typed values |
| IMP::base::ConstVector< Data, SwigData > | Store an array of values of the same type |
| IMP::base::Index< Tag > | |
| IMP::base::Vector< T > | |
| IMP::base::IndexVector< Tag, T > | |
| IMP::base::VersionInfo | Version and module information for Objects |
| IMP::core::MonteCarloMoverResult | |
| IMP::display::Color | Represent an RGB color |
| IMP::kernel::Decorator | |
| IMP::atom::Angle | A particle that describes an angle between three particles |
| 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::Dihedral | A particle that describes a dihedral angle between four particles |
| IMP::atom::Mass | Add mass to a particle |
| IMP::atom::SecondaryStructureResidue | A decorator for a residue with probability of secondary structure |
| IMP::core::Hierarchy | A decorator for helping deal with a 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::Residue | A decorator for a residue |
| IMP::core::Reference | A a decorator for a particle with an associated reference particle |
| IMP::core::Typed | A decorator for classifying particles in your system |
| IMP::core::XYZ | A 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 |
| IMP::atom::RigidBodyDiffusion | |
| IMP::core::Centroid | A particle that is the centroid of other particles |
| IMP::core::NonRigidMember | A decorator for a particle that is part of a rigid body but not rigid |
| IMP::core::RigidBody | A decorator for a rigid body |
| IMP::core::RigidMember | A decorator for a particle that is part of a rigid body |
| 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::kernel::FloatIndex | |
| IMP::kernel::Key< ID, LazyAdd > | A base class for Keys |
| IMP::kernel::RestraintStatistics | |
| IMP::kernel::ScoreAccumulator | Class for adding up scores during ScoringFunction evaluation |
| IMP::base::Index< ParticleIndexTag > | |
| IMP::kernel::Key< 0, true > | |
| IMP::base::Vector< algebra::Vector3D > | |
| IMP::base::Vector< algebra::VectorKD > | |
| IMP::base::Vector< AP > | |
| IMP::base::Vector< Assignment > | |
| IMP::base::Vector< AtomType > | |
| IMP::base::Vector< base::OwnerPointer< base::Object > > | |
| IMP::base::Vector< base::Pointer< IMP::kernel::Particle > > | |
| IMP::base::IndexVector< ParticleIndexTag, base::Pointer< IMP::kernel::Particle > > | |
| IMP::base::Vector< base::Pointer< O > > | |
| IMP::base::Vector< base::Pointer< Particle > > | |
| IMP::base::Vector< Bond > | |
| IMP::base::Vector< CHARMMAngle > | |
| IMP::base::Vector< CHARMMBond > | |
| IMP::base::Vector< CHARMMDihedral > | |
| IMP::base::Vector< CHARMMInternalCoordinate > | |
| IMP::base::Vector< Data > | |
| IMP::base::Vector< FittingSolutionRecord > | |
| IMP::base::Vector< Float > | |
| IMP::base::Vector< FloatRange > | |
| IMP::base::Vector< Floats > | |
| IMP::base::Vector< IMP::algebra::VectorD< D > > | |
| IMP::base::Vector< IMP::atom::CHARMMAtomTopology > | |
| IMP::base::Vector< IMP::atom::CHARMMBondEndpoint > | |
| IMP::base::Vector< IMP::base::Pointer< Geometry > > | |
| IMP::base::Vector< IMP::base::Pointer< Image > > | |
| IMP::base::Vector< IMP::base::Pointer< MonteCarloMover > > | |
| IMP::base::Vector< IMP::base::Pointer< SampledDensityMap > > | |
| IMP::base::Vector< IMP::base::Pointer< SubsetFilterTable > > | |
| IMP::base::Vector< IMP::base::Pointer< SurfaceShellDensityMap > > | |
| IMP::base::Vector< IMP::base::Vector > | |
| IMP::base::IndexVector< ParticleIndexTag, IMP::base::Vector > | |
| IMP::base::Vector< IMP::kernel::Key > | |
| IMP::base::Vector< Index > | |
| IMP::base::Vector< Int > | |
| IMP::base::Vector< int > | |
| IMP::base::Vector< internal::NBLScoring * > | |
| IMP::base::Vector< IntPair > | |
| IMP::base::Vector< Ints > | |
| IMP::base::Vector< IntsList > | |
| IMP::base::Vector< Key > | |
| IMP::base::Vector< Node > | |
| IMP::base::Vector< OwnerPointer< Score > > | |
| IMP::base::Vector< ParticleData > | |
| IMP::base::Vector< ParticleIndex > | |
| IMP::base::Vector< ParticlesTemp > | |
| IMP::base::Vector< ParticleType > | |
| IMP::base::Vector< Pointer< IMP::kernel::Configuration > > | |
| IMP::base::Vector< ReferenceFrame3D > | |
| IMP::base::Vector< RegistrationResult > | |
| IMP::base::Vector< ResidueType > | |
| IMP::base::Vector< RestraintSetData > | |
| IMP::base::Vector< Rotation3D > | |
| IMP::base::Vector< Slice > | |
| IMP::base::Vector< std::pair< internal::CHARMMDihedralNames, CHARMMDihedralParameters > > | |
| IMP::base::Vector< std::pair< unsigned int, int > > | |
| IMP::base::Vector< std::string > | |
| IMP::base::Vector< String > | |
| IMP::base::Vector< Transformation3D > | |
| IMP::base::Vector< unsigned int > | |
| IMP::base::Vector< Vector< Float > > | |
| IMP::base::Vector< VectorD< 2 > > | |
| IMP::base::Vector< VectorD< 3 > > | |
| IMP::base::Vector< VectorD<-1 > > | |
| std::vector< T > | STL class |
| IMP::saxs::Distribution< algebra::Vector3D > | |
| IMP::saxs::DeltaDistributionFunction | |
| IMP::saxs::Distribution< Float > | |
| IMP::saxs::RadialDistributionFunction | |
| IMP::saxs::Distribution< ValueT > | |
| IMP::base::WarningContext | |
| IMP::base::WeakPointer< O > | |
| IMP::base::WeakPointer< atom::Simulator > | |
| IMP::base::WeakPointer< IMP::kernel::Particle > | |
| IMP::score_functor::WeightScore< BaseDistanceScore > | |
| IMP.em2d.buildxlinks.Xlink | Class defining a cross-link |
| IMP.em2d.buildxlinks.XlinksDict | Description of crosslinking restraints as a python dictionary |
| IMP.restrainer._xml_parser.XMLDisplay | Construct Display from XML file |
| IMP.restrainer.XMLDisplay | Construct Display from XML file |
| IMP.restrainer._xml_parser.XMLRepresentation | Construct Representation from XML file |
| IMP.restrainer.XMLRepresentation | Construct Representation from XML file |
| IMP.restrainer._xml_parser.XMLRestraint | Construct Restraint from XML file |
| IMP.restrainer.XMLRestraint | Construct Restraint from XML file |