| IMP::container::AllBipartitePairContainer | Return all bipartite pairs between two containers |
| IMP::atom::AllMol2Selector | Read all atoms |
| IMP::container::AllPairContainer | Return all unordered pairs of particles taken from the SingletonContainer |
| IMP::atom::AllPDBSelector | Defines a selector that will pick every ATOM and HETATM record |
| IMP::atom::Angle | A particle that describes an angle between three particles |
| IMP::core::AngleRestraint | Angle restraint between three particles |
| IMP::atom::AngleSingletonScore | Score the angle based on a UnaryFunction, |
| IMP::core::AngleTripletScore | Apply a function to the angle between three particles |
| IMP::test::ApplicationTestCase | Super class for simple IMP application test cases |
| IMP::atom::Atom | A decorator for a particle representing an atom |
| IMP::atom::ATOMPDBSelector | Select all non-alternative ATOM records |
| IMP::atom::Atoms | |
| IMP::atom::AtomsTemp | |
| IMP::atom::AtomType | The type of an atom |
| IMP::core::AttributeSingletonScore | Apply a function to an attribute |
| IMP::core::BallMover | Modify a set of continuous variables by perturbing them within a ball |
| IMP::display::BildWriter | Write a Bild file with the geometry |
| IMP::modeller::BinormalTerm | A single binormal term in a MultipleBinormalRestraint |
| 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::BondedPairFilter | A filter for bonds |
| IMP::atom::Bondeds | |
| IMP::atom::BondedsTemp | |
| IMP::atom::BondEndpointsRefiner | Return the endpoints of a bond |
| IMP::atom::BondGraph | Represent a bond graph as a boost graph |
| IMP::atom::BondPairContainer | A container that returns pairs of the endpoints of the bonds |
| IMP::atom::Bonds | |
| IMP::atom::BondSingletonScore | Score the bond based on a UnaryFunction, |
| IMP::atom::BondsTemp | |
| IMP::core::BoundingBox3DSingletonScore | Score particles based on how far outside a box they are |
| IMP::algebra::BoundingBoxD< D > | An axis-aligned bounding box |
| IMP::atom::BrownianDynamics | Simple Brownian dynamics optimizer |
| IMP::atom::CAlphaPDBSelector | Select all CA ATOM records |
| IMP::domino::CartesianProductSampler | CartesianProductSampler |
| IMP::atom::CBetaPDBSelector | Select all CB ATOM records |
| IMP::core::Centroid | A particle that is the centroid of other particles |
| IMP::core::CentroidOfRefined | Set the coordinates of the particle to be the centoid of the particles |
| IMP::core::Centroids | |
| IMP::core::CentroidsTemp | |
| IMP::atom::Chain | Store info for a chain of a protein |
| IMP::atom::ChainPDBSelector | Select all ATOM and HETATMrecords with the given chain ids |
| IMP::atom::Chains | |
| IMP::atom::ChainsTemp | |
| IMP::atom::Charged | A decorator for a point particle that has an electrostatic charge |
| IMP::atom::CHARMMAtom | A decorator for an atom that has a defined CHARMM type |
| IMP::atom::CHARMMAtomTopology | A single atom in a CHARMM topology |
| IMP::atom::CHARMMBond< D > | A bond, angle, dihedral or improper between some number of endpoints |
| IMP::atom::CHARMMBondEndpoint | The end of a bond, angle, dihedral, or improper |
| IMP::atom::CHARMMBondParameters | The parameters for a CHARMM bond or angle |
| IMP::atom::CHARMMDihedralParameters | The parameters for a CHARMM dihedral or improper |
| IMP::atom::CHARMMIdealResidueTopology | The ideal topology of a single residue as read from a CHARMM topology file |
| IMP::atom::CHARMMParameters | CHARMM force field parameters |
| IMP::atom::CHARMMPatch | A CHARMM patch residue |
| IMP::atom::CHARMMResidueTopology | The topology of a single residue in a model |
| IMP::atom::CHARMMResidueTopologyBase | Base class for all CHARMM residue-based topology |
| IMP::atom::CHARMMSegmentTopology | The topology of a single CHARMM segment in a model |
| IMP::atom::CHARMMTopology | The topology of a complete CHARMM model |
| IMP::core::ChecksScoreState | |
| IMP::core::ChildrenRefiner | Return the hierarchy children of a particle |
| IMP::display::ChimeraWriter | Write geometry to a python file for Chimera to read |
| IMP::container::CloseBipartitePairContainer | Return all close unordered pairs of particles taken from the SingletonContainer |
| IMP::core::ClosedCubicSpline | Closed cubic spline function |
| IMP::container::ClosePairContainer | Return all close unordered pairs of particles taken from the SingletonContainer |
| IMP::core::ClosePairsFinder | A base class for algorithms to find spatial proximities |
| IMP::core::ClosePairsPairScore | Traverse the Refiner hierarchy to find all pairs which are close |
| IMP::display::CMMWriter | Write a CMM file with the geometry |
| IMP::em::CoarseCC | Responsible for performing coarse fitting between two density objects |
| IMP::em::CoarseCCatIntervals | Cross correlation coefficient calculator |
| IMP::em::CoarseConvolution | Convolutes two grids |
| IMP::display::Color | Represent an RGB color |
| IMP::display::Colored | A particle with a color |
| IMP::domino::CombState | Holds a combination of states for each particle in the restraint graph |
| IMP::misc::CommonEndpointPairFilter | Return true for any pair of bonds sharing an endpoint |
| IMP::algebra::Cone3D | |
| IMP::ConfigurationSet | A class to store a set of configurations of a model |
| IMP::statistics::ConfigurationSetXYZEmbedding | Embed a configuration using the XYZ coordinates of a set of particles |
| IMP::core::ConjugateGradients | Simple conjugate gradients optimizer |
| IMP::gsl::ConjugateGradients | A conjugate gradients optimizer taken from GSL |
| IMP::core::ConnectingPairContainer | A container which keeps a set of pairs that connect a set of spheres |
| IMP::core::ConnectivityRestraint | Ensure that a set of particles remains connected with one another |
| IMP::core::ConstantRestraint | Return a constant value |
| IMP::test::ConstPairScore | An IMP::PairScore which always returns a constant value |
| IMP::test::ConstQuadScore | An IMP::PairScore which always returns a constant value |
| IMP::Constraint | Implement a constraint on the Model |
| IMP::test::ConstSingletonScore | An IMP::SingletonScore which always returns a constant value |
| IMP::test::ConstTripletScore | An IMP::TripletScore which always returns a constant value |
| IMP::test::ConstUnaryFunction | An IMP::UnaryFunction which always returns a constant value |
| IMP::Container | Abstract class for containers of particles |
| IMP::Containers | |
| IMP::ContainersTemp | |
| IMP::core::Cosine | Cosine function |
| IMP::atom::CoulombPairScore | Coulomb (electrostatic) score between a pair of particles |
| IMP::core::Cover | A particle which covers a set of other particles |
| IMP::atom::CoverBond | Cover a bond with a sphere |
| IMP::core::CoverRefined | This class sets the position and radius of each particle to enclose the refined |
| IMP::core::Covers | |
| IMP::core::CoversTemp | |
| IMP::atom::CPDBSelector | Select all C (not CA or CB) ATOM records |
| IMP::algebra::Cylinder3D | |
| IMP::Decorator | |
| IMP::saxs::DeltaDistributionFunction | |
| IMP::em::DensityHeader | |
| IMP::em::DensityMap | Class for handling density maps |
| IMP::em::DensityMaps | |
| IMP::em::DensityMapsTemp | Rotate a grid |
| IMP::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::core::DiameterRestraint | Restrain the diameter of a set of points |
| IMP::atom::Diffusion | A decorator for a diffusing particle |
| IMP::atom::Diffusions | |
| IMP::atom::DiffusionsTemp | |
| IMP::atom::Dihedral | A particle that describes a dihedral angle between four particles |
| IMP::core::DihedralRestraint | Dihedral restraint between four particles |
| IMP::atom::DihedralSingletonScore | Score the dihedral angle |
| IMP::test::DirectorObjectChecker | Check to make sure the number of director references is as expected |
| IMP::domino::DiscreteSampler | |
| IMP::restrainer::Display | A class to display the configuration |
| IMP::display::DisplayModelOnFailure | Dump the state of the model to a file on an error and then go on the the other handlers |
| IMP::core::DistancePairScore | Apply a function to the distance between two particles |
| IMP::core::DistanceRestraint | Distance restraint between two particles |
| IMP::core::DistanceToSingletonScore | Apply a function to the distance to a fixed point |
| IMP::saxs::Distribution< ValueT > | |
| IMP::atom::Domain | A decorator to associate a particle with a part of a protein |
| IMP::atom::Domains | |
| IMP::atom::DomainsTemp | |
| IMP::domino::DominoOptimizer | An exact inference optimizer |
| IMP::DumpModelOnFailure | Dump the state of the model to a file on an error and then go on the the other handlers |
| IMP::core::EditGuard< Container > | RAII class for objects with batch editing modes |
| IMP::atom::ElementTable | |
| IMP::algebra::Ellipsoid3D | |
| IMP::statistics::Embedding | Map clustering data to spatial positions |
| IMP::example::ExampleComplexRestraint | Restrain the diameter of a set of points |
| IMP::example::ExampleDecorator | A simple decorator which adds a name to a particle |
| IMP::example::ExampleRefCounted | An example simple object which is reference counted |
| IMP::example::ExampleRestraint | Apply a PairScore to a list of particle pairs |
| IMP::example::ExampleSingletonModifier | An example singleton modifer |
| IMP::example::ExampleTemplateClass< D > | A line segment templated on the dimension |
| IMP::example::ExampleUnaryFunction | A simple unary function |
| IMP::Exception | The general base class for IMP exceptions |
| IMP::core::ExcludedVolumeRestraint | Prevent a set of particles and rigid bodies from inter-penetrating |
| IMP::FailureHandler | |
| IMP::FailureHandlerBase | A base class for setting up failure handlers |
| IMP::em::FilterByThreshold< T, D > | |
| IMP::display::FilterGeometry | Remove geometry which is not above a plane |
| IMP::em::FitRestraint | Calculate score based on fit to EM map |
| IMP::core::FixedRefiner | The refiner can refine any particle by returning a fixed set |
| IMP::algebra::FixedXYZ | A simple class for returning XYZ Euler angles |
| IMP::algebra::FixedZYZ | A simple class for returning ZYZ Euler angles |
| IMP::FloatKey | The type used to identify float attributes in the Particles |
| IMP::atom::ForceFieldParameters | Storage and access to force field |
| IMP::atom::ForceSwitch | Smooth interaction scores by switching the derivatives (force switch) |
| IMP::saxs::FormFactorTable | |
| IMP::atom::Fragment | A decorator to associate a particle with a part of a protein/DNA/RNA |
| IMP::atom::Fragments | |
| IMP::atom::FragmentsTemp | |
| IMP::core::GenericHierarchies | |
| IMP::core::GenericHierarchiesTemp | |
| IMP::display::Geometry | The base class for geometry |
| IMP::display::GeometryProcessor | Provide a standard geometry processing framework |
| IMP::algebra::Grid3D< VT > | A voxel grid in 3D space |
| IMP::core::GridClosePairsFinder | Find all nearby pairs by testing all pairs |
| IMP::algebra::GridRangeD< D > | A Boost.Range over the vertices of a grid |
| IMP::gsl::GSLOptimizer | A base class for GSL-based optimizers |
| 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::atom::Hierarchies | |
| IMP::atom::HierarchiesTemp | |
| IMP::core::Hierarchy | A decorator for helping deal with a hierarchy |
| IMP::atom::Hierarchy | The standard decorator for manipulating molecular structures |
| IMP::core::HierarchyCounter | A simple functor to count the number of particles in a hierarchy |
| IMP::core::HierarchyPrinter< PD > | A simple visitor which pretty-prints the hierarchy |
| IMP::core::HierarchyTraits | Define the type for a type of hierarchy |
| IMP::core::HierarchyVisitor | A visitor for traversal of a hierarchy |
| IMP::statistics::HighDensityEmbedding | |
| IMP::atom::HydrogenPDBSelector | Select all hydrogen ATOM and HETATM records |
| IMP::em::Image< T > | Template class for managing 2D Electron Microscopy images in IMP |
| IMP::em::ImageHeader | |
| IMP::modeller::IMPRestraints | A Modeller restraint which evaluates all defined IMP restraints |
| IMP::atom::ImproperSingletonScore | Score the improper dihedral based on a UnaryFunction, |
| IMP::IncreaseIndent | Increase the current indent in the log by one level |
| IMP::core::IncrementalBallMover | Modify a set of continuous variables by perturbing them within a ball |
| IMP::IndexException | An exception for a request for an invalid member of a container |
| IMP::InternalException | A general exception for an intenal error in IMP |
| IMP::IntKey | The type used to identify int attributes in the Particles |
| IMP::IOException | An input/output exception |
| IMP::domino::JNode | Handles all functionalities of a junction tree node |
| IMP::domino::JunctionTree | Stores a junction tree |
| IMP::em::KernelParameters | |
| IMP::KeyBase< ID, LazyAdd > | A base class for Keys |
| IMP::statistics::KMeansClustering | |
| IMP::statistics::KMLProxy | Proxy to apply k-means clustering on a set of Particles |
| IMP::core::LeavesRefiner | Return the hierarchy leaves under a particle |
| IMP::atom::LennardJones | A decorator for a particle that has a Lennard-Jones potential well |
| IMP::atom::LennardJonesPairScore | Lennard-Jones score between a pair of particles |
| IMP::core::Linear | Linear function |
| IMP::algebra::LinearFit | Calculate line that fits best the input data points |
| IMP::container::ListPairContainer | Store a list of ParticlePairs |
| IMP::container::ListQuadContainer | Store a list of ParticleQuads |
| IMP::container::ListSingletonContainer | Store a list of Particles |
| IMP::container::ListTripletContainer | Store a list of ParticleTriplets |
| IMP::display::LogOptimizerState | Write geometry to a container periodically |
| IMP::test::LogPairScore | An IMP::PairScore which logs which Particles it is called with |
| 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::em::MapFilterByThreshold | Class to filter by threshold (only DensityMap) |
| IMP::domino::MappedDiscreteSet | MappedDiscreteSet |
| IMP::atom::Mass | Add mass to a particle |
| IMP::algebra::Matrix2D< T > | |
| IMP::algebra::Matrix3D< T > | |
| IMP::container::MaximumPairRestraint | Score based on the maximum pair over a set of Pairs |
| IMP::container::MaximumPairScore | Evaluate the maximum n pair scores of the passed set of PairScores |
| IMP::container::MaximumQuadRestraint | Score based on the maximum quad over a set of Quads |
| IMP::container::MaximumQuadScore | Evaluate the maximum n quad scores of the passed set of QuadScores |
| IMP::container::MaximumSingletonRestraint | Score based on the maximum singleton over a set of Singletons |
| IMP::container::MaximumSingletonScore | Evaluate the maximum n singleton scores of the passed set of SingletonScores |
| IMP::container::MaximumTripletRestraint | Score based on the maximum triplet over a set of Triplets |
| IMP::container::MaximumTripletScore | Evaluate the maximum n triplet scores of the passed set of TripletScores |
| IMP::core::MCCGSampler | A simple sampler |
| IMP::container::MinimumPairRestraint | Score based on the minimum pair over a set of Pairs |
| IMP::container::MinimumPairScore | Evaluate the minimum n pair scores of the passed set of PairScores |
| IMP::container::MinimumQuadRestraint | Score based on the minimum quad over a set of Quads |
| IMP::container::MinimumQuadScore | Evaluate the minimum n quad scores of the passed set of QuadScores |
| IMP::container::MinimumSingletonRestraint | Score based on the minimum singleton over a set of Singletons |
| IMP::container::MinimumSingletonScore | Evaluate the minimum n singleton scores of the passed set of SingletonScores |
| IMP::container::MinimumTripletRestraint | Score based on the minimum triplet over a set of Triplets |
| IMP::container::MinimumTripletScore | Evaluate the minimum n triplet scores of the passed set of TripletScores |
| IMP::Model | Class for storing model, its restraints, constraints, and particles |
| IMP::ModelException | An exception which is thrown when the Model has attributes with invalid values |
| IMP::modeller::ModellerRestraints | An IMP restraint using all defined Modeller restraints |
| IMP::modeller::ModelLoader | Read a Modeller model into IMP |
| IMP::core::ModifierVisitor | A which applies a singleton modifier to each Particle in a hierarchy |
| IMP::atom::Mol2Selector | A base class for choosing which Mol2 atoms to read |
| IMP::atom::MolecularDynamics | Simple molecular dynamics optimizer |
| IMP::core::MonteCarlo | A Monte Carlo optimizer |
| IMP::core::Mover | A base class for classes which pertub particles |
| IMP::core::MoverBase | A class to help implement movers |
| IMP::core::Movers | |
| IMP::core::MoversTemp | |
| IMP::em::MRCHeader | Class to deal with the header of MRC files |
| IMP::em::MRCReaderWriter | |
| IMP::algebra::MultiArray< T, D > | |
| IMP::modeller::MultipleBinormalRestraint | Modeller-style multiple binormal (phi/psi) restraint |
| IMP::algebra::NearestNeighborD< D > | |
| IMP::atom::NonAlternativePDBSelector | Select all ATOM and HETATM records which are not alternatives |
| IMP::atom::NonhydrogenMol2Selector | Defines a selector that will pick only non-hydrogen atoms |
| IMP::atom::NonWaterNonHydrogenPDBSelector | Select non water and non hydrogen atoms |
| IMP::atom::NonWaterPDBSelector | Select all non-water non-alternative ATOM and HETATM records |
| IMP::core::NormalizedSphereDistancePairScore | A score on the normalized distance between the surfaces of two spheres |
| IMP::core::NormalMover | Modify a set of continuous variables using a normal distribution |
| IMP::atom::NPDBSelector | Select all N ATOM records |
| IMP::Object | Common base class for heavy weight IMP objects |
| IMP::ObjectKey | The type used to identify a particle attribute in the Particles |
| IMP::core::OpenCubicSpline | Open cubic spline function |
| IMP::Optimizer | Base class for all optimizers |
| IMP::OptimizerState | Shared optimizer state |
| IMP::OptimizerStates | |
| IMP::OptimizerStatesTemp | |
| IMP::core::PairConstraint | Apply a PairFunction to a Pair |
| IMP::PairContainer | A shared container for particle_pairs |
| IMP::PairContainers | |
| IMP::container::PairContainerSet | Stores a set of PairContainers |
| IMP::PairContainersTemp | A collection of containers |
| IMP::PairFilter | A shared filter for particle_pairs |
| IMP::PairFunctor | Create a functor which can be used with build in C++ and python commands |
| IMP::display::PairGeometry | A base class for geometry contained in particles |
| IMP::PairModifier | A base class for modifiers of ParticlePairs |
| IMP::core::PairRestraint | Applies a PairScore to a ParticlePair |
| IMP::container::PairsConstraint | Apply a PairFunction to a PairContainer to maintain an invariant |
| IMP::PairScore | Abstract score function |
| IMP::PairScores | |
| IMP::PairScoresTemp | |
| IMP::display::PairsGeometry | A base class for geometry from a set of particles |
| IMP::container::PairsOptimizerState | Apply a PairFunction to a PairContainer to maintain an invariant |
| IMP::container::PairsRestraint | Applies a PairScore to each ParticlePair in a list |
| IMP::algebra::ParabolicFit | Calculate parabola that fits best the input data points |
| IMP::Particle | Class to handle individual model particles |
| IMP::statistics::ParticleEmbedding | |
| IMP::ParticleKey | The type used to identify a particle attribute in the Particles |
| IMP::Particles | |
| IMP::ParticlesTemp | |
| IMP::ParticleTuple< D > | A class to store a tuple of particles |
| IMP::statistics::PartitionalClustering | The base class for clusterings of data sets |
| IMP::display::PDBOptimizerState | Write molecules in pdb format periodically |
| IMP::atom::PDBSelector | Select which atoms to read from a PDB file |
| IMP::domino::PermutationSampler | Permutation sampler |
| IMP::algebra::Plane3D | |
| IMP::Pointer< O > | A reference counted pointer to an object |
| IMP::atom::PPDBSelector | Select all P ATOM records |
| IMP::saxs::Profile | |
| IMP::atom::ProteinLigandAtomPairScore | |
| IMP::atom::ProteinLigandRestraint | |
| IMP::display::PymolWriter | Write a CGO file with the geometry |
| IMP::core::QuadConstraint | Apply a QuadFunction to a Quad |
| IMP::QuadContainer | A shared container for particle_quads |
| IMP::QuadContainers | |
| IMP::container::QuadContainerSet | Stores a set of QuadContainers |
| IMP::QuadContainersTemp | A collection of containers |
| IMP::QuadFilter | A shared filter for particle_quads |
| IMP::QuadFunctor | Create a functor which can be used with build in C++ and python commands |
| IMP::QuadModifier | A base class for modifiers of ParticleQuads |
| IMP::core::QuadraticClosePairsFinder | Find all nearby pairs by testing all pairs |
| IMP::core::QuadRestraint | Applies a QuadScore to a ParticleQuad |
| IMP::container::QuadsConstraint | Apply a QuadFunction to a QuadContainer to maintain an invariant |
| IMP::QuadScore | Abstract score function |
| IMP::QuadScores | |
| IMP::QuadScoresTemp | |
| IMP::container::QuadsOptimizerState | Apply a QuadFunction to a QuadContainer to maintain an invariant |
| IMP::container::QuadsRestraint | Applies a QuadScore to each ParticleQuad in a list |
| IMP::gsl::QuasiNewton | A quasi-Newton optimizer taken from GSL |
| IMP::saxs::RadialDistributionFunction | |
| IMP::em::RadiusDependentKernelParameters | Calculates kernel parameters as a function of a specific radius |
| IMP::RAII | RAII-style objects |
| IMP::test::RefCountChecker | Check to make sure the number of C++ object references is as expected |
| IMP::RefCounted | Common base class for ref counted objects |
| IMP::core::RefinedPairsPairScore | Generate pairs to score by applying a Refiner |
| IMP::Refiner | Abstract class to implement hierarchical methods |
| IMP::restrainer::Representation | Store Representation |
| IMP::atom::Residue | A decorator for a residue |
| IMP::atom::Residues | |
| IMP::atom::ResiduesTemp | |
| IMP::atom::ResidueType | The type for a residue |
| IMP::Restraint | Abstract class for representing restraints |
| IMP::saxs::Restraint | Calculate score based on fit to SAXS profile |
| IMP::restrainer::Restraint | Store Restraint |
| IMP::domino::RestraintEvaluator | A direct restraint evaluator |
| IMP::domino::RestraintEvaluatorFromFile | A read restraint values from precalculated files |
| IMP::domino::RestraintEvaluatorI | Restraint Evaluator interface class |
| IMP::domino::RestraintGraph | RestraintGraph |
| IMP::Restraints | |
| IMP::RestraintSet | Container used to hold a set of restraints |
| IMP::RestraintsTemp | |
| IMP::core::RigidBody | A decorator for a rigid body |
| IMP::core::RigidBodyDistancePairScore | Accelerated computation of the distance between two rigid bodies |
| IMP::core::RigidBodyMover | Modify the transformation of a rigid body |
| IMP::core::RigidClosePairsFinder | Peform more efficient close pair finding when rigid bodies are involved |
| IMP::core::RigidMember | A decorator for a particle that is part of a rigid body |
| IMP::core::RigidMembers | |
| IMP::core::RigidMembersTemp | |
| IMP::algebra::Rotation2D | Stores a 2D rotation matrix |
| IMP::algebra::Rotation3D | 3D rotation class |
| IMP::em::SampledDensityMap | Class for sampling a density map from particles |
| IMP::Sampler | Base class for all samplers |
| IMP::SaveOptimizeds | Save and restore the set of optimized attributes for a set of particles |
| IMP::ScopedFailureHandler | Control a scope-dependent failure handler |
| IMP::saxs::Score | |
| IMP::ScoreState | Shared score state |
| IMP::ScoreStatePointer | Removes the ScoreState when the RAII object is destroyed |
| IMP::ScoreStates | |
| IMP::ScoreStatesTemp | |
| IMP::algebra::Segment3D | |
| IMP::SetLogState | A class to change and restore log state |
| IMP::SetLogTarget | |
| IMP::helper::SimpleConnectivity | Simple connectivity restraint |
| IMP::helper::SimpleDiameter | Simple diameter restraint |
| IMP::helper::SimpleDistance | Simple distance restraint between two particles |
| IMP::helper::SimpleEMFit | Simple EM fit restraint |
| IMP::helper::SimpleExcludedVolume | Simple excluded volume restraint |
| IMP::gsl::Simplex | A simplex optimizer taken from GSL |
| IMP::atom::SimulationParameters | A decorator for a particle storing parameters of the current simulation |
| IMP::core::SingletonConstraint | Apply a SingletonFunction to a Singleton |
| IMP::SingletonContainer | A shared container for particles |
| IMP::SingletonContainers | |
| IMP::container::SingletonContainerSet | Stores a set of SingletonContainers |
| IMP::SingletonContainersTemp | A collection of containers |
| IMP::SingletonFilter | A shared filter for particles |
| IMP::SingletonFunctor | Create a functor which can be used with build in C++ and python commands |
| IMP::display::SingletonGeometry | A base class for geometry contained in particles |
| IMP::SingletonModifier | A base class for modifiers of Particles |
| IMP::core::SingletonRestraint | Applies a SingletonScore to a Particle |
| IMP::container::SingletonsConstraint | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
| IMP::SingletonScore | Abstract score function |
| IMP::SingletonScores | |
| IMP::SingletonScoresTemp | |
| IMP::display::SingletonsGeometry | A base class for geometry from a set of particles |
| IMP::container::SingletonsOptimizerState | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
| IMP::container::SingletonsRestraint | Applies a SingletonScore to each Particle in a list |
| IMP::atom::SmoothingFunction | Base class for smoothing nonbonded interactions as a function of distance |
| IMP::saxs::SolventAccessibleSurface | |
| IMP::algebra::SphereD< D > | |
| IMP::core::SphereDistancePairScore | A score on the distance between the surfaces of two spheres |
| IMP::core::SphereDistanceToSingletonScore | Apply a function to the distance to a fixed point |
| IMP::algebra::SpherePatch3D | |
| IMP::algebra::SphericalVector3D | Class to represent a 3D point in spherical coordinates |
| IMP::em::SpiderHeader | Header for Spider images. IMP-EM is designed to be compatible with it |
| IMP::em::SpiderImageReaderWriter< T > | |
| IMP::em::SpiderMapReaderWriter | Class to read EM maps (3D) in Spider and Xmipp formats |
| IMP::misc::StateAdaptor | Allow OptimizerStates to be used as ScoreStates |
| IMP::core::SteepestDescent | A simple steepest descent optimizer |
| IMP::atom::StereochemistryPairFilter | A filter that excludes bonds, angles and dihedrals |
| IMP::StringKey | The type used to identify string attributes in the Particles |
| IMP::em::SurfaceShellDensityMap | The class repersents a molecule as shells of distance from the surface |
| IMP::domino::SymmetrySampler | SymmetrySampler |
| IMP::core::TableRefiner | A lookup based particle refiner |
| IMP::test::TestCase | Super class for IMP test cases |
| IMP::test::TestRefiner | A class which makes sure that the right particles are passed back |
| IMP::TextInput | |
| IMP::TextOutput | |
| IMP::core::Transform | Apply a transformation to a passed particle |
| IMP::domino::Transformation | |
| IMP::algebra::Transformation2D | Simple 2D transformation class |
| IMP::algebra::Transformation3D | Simple 3D transformation class |
| IMP::domino::TransformationDiscreteSet | Holds a set of transformations |
| IMP::domino::TransformationMappedDiscreteSet | TransformationMappedDiscreteSet |
| IMP::domino::TransformationPermutationSampler | Sample all permutations of transformations on particles |
| IMP::core::TransformedDistancePairScore | Apply a function to the distance between two particles after transforming the first |
| IMP::core::TripletConstraint | Apply a TripletFunction to a Triplet |
| IMP::TripletContainer | A shared container for particle_triplets |
| IMP::TripletContainers | |
| IMP::container::TripletContainerSet | Stores a set of TripletContainers |
| IMP::TripletContainersTemp | A collection of containers |
| IMP::TripletFilter | A shared filter for particle_triplets |
| IMP::TripletFunctor | Create a functor which can be used with build in C++ and python commands |
| IMP::TripletModifier | A base class for modifiers of ParticleTriplets |
| IMP::core::TripletRestraint | Applies a TripletScore to a ParticleTriplet |
| IMP::container::TripletsConstraint | Apply a TripletFunction to a TripletContainer to maintain an invariant |
| IMP::TripletScore | Abstract score function |
| IMP::TripletScores | |
| IMP::TripletScoresTemp | |
| IMP::container::TripletsOptimizerState | Apply a TripletFunction to a TripletContainer to maintain an invariant |
| IMP::container::TripletsRestraint | Applies a TripletScore to each ParticleTriplet in a list |
| IMP::core::TruncatedHarmonic< DIRECTION > | A function that is harmonic over an interval |
| IMP::core::TypedPairScore | Delegate to another PairScore depending on particle types |
| IMP::UnaryFunction | Abstract single variable functor class for score functions |
| IMP::UsageException | An exception for an invalid usage of IMP |
| IMP::ValueException | An exception for an invalid value being passed to IMP |
| IMP::algebra::VectorD< D > | A Cartesian vector in D-dimensions |
| IMP::statistics::VectorDEmbedding< D > | Simply return the coordinates of a VectorD |
| IMP::VectorOfRefCounted< RC, Policy > | A vector-like container for reference counted objects |
| IMP::atom::VelocityScalingOptimizerState | Maintains temperature during molecular dynamics by velocity scaling |
| IMP::VersionInfo | Version and module information for Objects |
| IMP::em::Volume< T > | Template class for managing 3D Electron Microscopy volumes in IMP |
| IMP::core::VolumeRestraint | Restraint the volume of a set of spheres |
| IMP::em::Voxel | |
| IMP::atom::WaterPDBSelector | Select all non-water ATOM and HETATMrecords |
| IMP::WeakPointer< O > | A weak pointer to an IMP::Object or IMP::RefCountedObject |
| IMP::core::WeightedSphereDistancePairScore | A score on a weighted distance between the surfaces of two spheres |
| IMP::misc::WormLikeChain | Worm-like-chain energy for polymer chains |
| IMP::display::Writer | Base class for writing geometry to a file |
| IMP::restrainer::XMLDisplay | Construct Display from XML file |
| IMP::restrainer::XMLRepresentation | Construct Representation from XML file |
| IMP::restrainer::XMLRestraint | Construct Restraint from XML file |
| IMP::core::XYZ | A a decorator for a particle with x,y,z coordinates |
| IMP::core::XYZR | A decorator for a particle with x,y,z coordinates and a radius |
| IMP::core::XYZRs | |
| IMP::core::XYZRsTemp | |
| IMP::core::XYZs | |
| IMP::core::XYZsTemp | |
