  IMP | Base functionality and abstract base classes for representation, scoring and sampling |
 algebra | General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules |
  BoundedGridRangeD | |
| BoundingBoxD | An axis-aligned bounding box |
| Cone3D | Represent a cone in 3D |
| ConnollySurfacePoint | Represent a point on the Connolly surface |
| Cylinder3D | Represent a cylinder in 3D |
| DefaultEmbeddingD | Embed a grid as an evenly spaced axis aligned grid |
| DenseFloatLogGridKD | |
| DenseGrid3D | A dense grid of values |
| DenseGridStorageD | |
| DenseIntLogGrid3D | |
| DynamicNearestNeighbor3D | Provide an incremental nearest neighbor search function |
| Ellipsoid3D | Represent an ellipsoid in 3D |
| EuclideanVectorKDMetric | The l2 norm on the distance vector |
| ExtendedGridIndexD | An index in an infinite grid on space |
| FixedXYZ | A simple class for returning XYZ Euler angles |
| Gaussian3D | A Gaussian distribution in 3D |
| GeometricPrimitiveD | Base class for geometric types |
| GridD | A voxel grid in d-dimensional space |
| GridIndexD | Represent a real cell in a grid (one within the bounding box) |
| Line3D | Simple implementation of lines in 3D |
| LinearFit2D | Calculate line that fits best the input data points (Linear least squares) |
| LogEmbeddingD | |
| MaxVectorKDMetric | |
| NearestNeighborD | Build a structure for finding nearest neighbors |
| ParabolicFit2D | Calculate parabola that fits best the input data points |
| Plane3D | Represent a plane in 3D |
| PrincipalComponentAnalysisD | Represent an eigen analysis of some data |
| ReferenceFrame3D | A reference frame in 3D |
| Reflection3D | Reflect about a plane in 3D |
| Rotation2D | Represent a rotation in 2D space |
| Rotation3D | 3D rotation class |
| Segment3D | Simple implementation of segments in 3D |
| SparseGrid3D | A sparse grid of values |
| SparseGridStorageD | |
| SparseUnboundedGrid3D | A sparse, infinite grid of values |
| SparseUnboundedGridD | A sparse, infinite grid of values |
| SphereD | Represent a sphere in D-dimensions |
| SpherePatch3D | A sphere patch is defined as all points above the plane and on the sphere |
| SphericalVector3D | Class to represent a 3D point in spherical coordinates |
| Torus3D | Represent a torus in 3D |
| Transformation2D | Simple 2D transformation class |
| Transformation3D | Simple 3D transformation class |
| Triangle3D | Represent a triangle in 3D |
| UnboundedGridRangeD | |
| VectorBaseD | A Cartesian vector in D-dimensions |
| VectorD | A Cartesian vector in D-dimensions |
 VectorKDMetric | The base class for a metric on VectorKDs |
| atom | Functionality for loading, creating, manipulating and scoring atomic structures |
| AllMol2Selector | Read all atoms |
| AllPDBSelector | Defines a selector that will pick every ATOM and HETATM record |
| AndPDBSelector | Select atoms which are selected by both selectors |
| Angle | A particle that describes an angle between three particles |
| AngleSingletonScore | Score the angle based on a UnaryFunction, |
| AngularVelocity | A particle with angular velocity |
| Atom | A decorator for a particle representing an atom |
| ATOMPDBSelector | Select all non-alternative ATOM records |
| AtomType | The type of an atom |
| AtomTypePDBSelector | Select all atoms of the given types |
| BackbonePDBSelector | Select all backbone (N,CA,C,O) ATOM records |
| BerendsenThermostatOptimizerState | Maintains temperature during molecular dynamics |
| Bond | A decorator for wrapping a particle representing a molecular bond |
| Bonded | A decorator for a particle which has bonds |
| BondedPairFilter | A filter for bonds |
| BondEndpointsRefiner | Return the endpoints of a bond |
| BondGeometry | Display a Bond particle as a segment |
| BondGraph | Represent a bond graph as a boost graph |
| BondPairContainer | A container that returns pairs of the endpoints of the bonds |
| BondsGeometry | Display an IMP::SingletonContainer of Bond particles as segments |
| BondSingletonScore | Score the bond based on a UnaryFunction, |
| BrownianDynamics | Simple Brownian dynamics simulator |
| BrownianDynamicsTAMD | Simple Brownian dynamics simulator |
| CAAngleRestraint | Angle restraint between three residues in CA-only representation |
| CADihedralRestraint | Dihedral restraint between five residues in CA-only representation |
| CAlphaPDBSelector | Select all CA ATOM records |
| CBetaPDBSelector | Select all CB ATOM records |
| CenterOfMass | A particle that is the center of mass of other particles |
| Chain | Store info for a chain of a protein |
| ChainPDBSelector | Select all ATOM and HETATM records with the given chain ids |
| Charged | A decorator for a point particle that has an electrostatic charge |
| CHARMMAtom | A decorator for an atom that has a defined CHARMM type |
| CHARMMAtomTopology | A single atom in a CHARMM topology |
| CHARMMBondEndpoint | The end of a bond, angle, dihedral, improper, or internal coordinate |
| CHARMMBondParameters | The parameters for a CHARMM bond or angle |
| CHARMMConnection | A connection (bond, angle, dihedral) between some number of endpoints |
| CHARMMDihedralParameters | The parameters for a CHARMM dihedral or improper |
| CHARMMIdealResidueTopology | The ideal topology of a single residue |
| CHARMMInternalCoordinate | A geometric relationship between four atoms |
| CHARMMParameters | CHARMM force field parameters |
| CHARMMPatch | A CHARMM patch residue |
| CHARMMResidueTopology | The topology of a single residue in a model |
| CHARMMResidueTopologyBase | Base class for all CHARMM residue-based topology |
| CHARMMSegmentTopology | The topology of a single CHARMM segment in a model |
| CHARMMStereochemistryRestraint | Enforce CHARMM stereochemistry on the given Hierarchy |
| CHARMMTopology | The topology of a complete CHARMM model |
| Copy | A decorator for keeping track of copies of a molecule |
| CoulombPairScore | Coulomb (electrostatic) score between a pair of particles |
| CoverBond | Cover a bond with a sphere |
| CPDBSelector | Select all C (not CA or CB) ATOM records |
| Diffusion | A decorator for a diffusing particle with a diffusion coefficient |
| Dihedral | A particle that describes a dihedral angle between four particles |
| DihedralSingletonScore | Score the dihedral angle |
| Domain | A decorator to associate a particle with a part of a protein |
| DopePairScore | |
| ElementTable | |
| EzRestraint | Ez Potential restraint |
| ForceFieldParameters | Storage and access to force field |
| Bond | |
| ForceSwitch | Smooth interaction scores by switching the derivatives (force switch) |
| Fragment | A decorator to associate a particle with a part of a protein/DNA/RNA |
| HelixRestraint | Restraint a set of residues to use ideal helix dihedrals and bonds |
| HierarchiesGeometry | Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls |
| Hierarchy | The standard decorator for manipulating molecular structures |
| HierarchyGeometry | Display an IMP::atom::Hierarchy particle as balls |
| HydrogenPDBSelector | Select all hydrogen ATOM and HETATM records |
| ImproperSingletonScore | Score the improper dihedral based on a UnaryFunction, |
| LangevinThermostatOptimizerState | Maintains temperature during molecular dynamics |
| LennardJones | A decorator for a particle that has a Lennard-Jones potential well |
| LennardJonesPairScore | Lennard-Jones score between a pair of particles |
| LinearVelocity | A particle with linear (XYZ) velocity |
| Mass | Add mass to a particle |
| Mol2Selector | A base class for choosing which Mol2 atoms to read |
| MolecularDynamics | Simple molecular dynamics optimizer |
| Molecule | A decorator for a molecule |
| NonAlternativePDBSelector | Select all ATOM and HETATM records which are not alternatives |
| NonHydrogenMol2Selector | Defines a selector that will pick only non-hydrogen atoms |
| NonHydrogenPDBSelector | Select non hydrogen atoms |
| NonWaterNonHydrogenPDBSelector | Select non water and non hydrogen atoms |
| NonWaterPDBSelector | Select all non-water non-alternative ATOM and HETATM records |
| NotPDBSelector | Select atoms which are not selected by a given selector |
| NPDBSelector | Select all N ATOM records |
| OrientedSoapPairScore | Score a pair of atoms using an orientation-dependent SOAP score |
| OrPDBSelector | Select atoms which are selected by either or both selectors |
| PDBSelector | Select which atoms to read from a PDB file |
| PPDBSelector | Select all P (= phosphate) ATOM records |
| ProteinLigandAtomPairScore | |
| ProteinLigandRestraint | Score a pair of molecules |
| RemoveRigidMotionOptimizerState | Removes rigid translation and rotation from the particles |
| RemoveTranslationOptimizerState | Removes rigid translation from the particles |
| Representation | A decorator for a representation |
| Residue | A decorator for a residue |
| ResidueType | The type for a residue |
| ResidueTypePDBSelector | Select all atoms in residues of the given types |
| RigidBodyDiffusion | |
| SameResiduePairFilter | |
| SecondaryStructureResidue | A decorator for a residue with probability of secondary structure |
| Selection | Select hierarchy particles identified by the biological name |
| SelectionGeometry | Display a Selection |
| Simulator | The base class for simulators |
| SmoothingFunction | Base class for smoothing nonbonded interactions as a function of distance |
| SoapPairFilter | Filter atom pairs for SOAP |
| State | Associate an integer "state" index with a hierarchy node |
| StereochemistryPairFilter | A filter that excludes bonds, angles and dihedrals |
| StructureSource | Store strings describing the source of this structure fragment |
| TAMDCentroid | |
| TAMDParticle | |
| VelocityScalingOptimizerState | Maintains temperature during molecular dynamics by velocity scaling |
| WaterPDBSelector | Select all non-water ATOM and HETATM records |
| WritePDBOptimizerState | |
| XorPDBSelector | Select atoms which are selected by either selector but not both |
| benchmark | Support for developing and analyzing benchmarks of IMP code |
| Profiler | |
| cgal | Make CGAL functionality available to IMP |
| cnmultifit | Generate cyclic atomic structures using cryo-electron microscopy data |
| AlignSymmetric | A class for fast alignment of a cyclic model to its density |
| CnSymmAxisDetector | Detect cn symmetry in proteins and density maps |
| MolCnSymmAxisDetector | Molecule symmetry detector |
| container | Various classes to hold sets of particles |
| AllBipartitePairContainer | |
| AllPairContainer | Return all unordered pairs of particles taken from the SingletonContainer |
| CloseBipartitePairContainer | Return all spatially-proximals pairs of particles (a,b) from the two SingletonContainers A and B, where a is in A and b is in B |
| ClosePairContainer | Return all close unordered pairs of particles taken from the SingletonContainer |
| ConnectingPairContainer | A container which keeps a set of pairs that connect a set of spheres |
| ConsecutivePairContainer | A container which contains all consecutive particle pairs from an input list |
| ConsecutivePairFilter | |
| DistributePairsScoreState | Distribute contents of one container into several based on predicates |
| DistributeQuadsScoreState | Distribute contents of one container into several based on predicates |
| DistributeSingletonsScoreState | Distribute contents of one container into several based on predicates |
| DistributeTripletsScoreState | Distribute contents of one container into several based on predicates |
| DynamicListPairContainer | Store a ParticleIndexPairs |
| DynamicListQuadContainer | Store a ParticleIndexQuads |
| DynamicListSingletonContainer | Store a ParticleIndexes |
| DynamicListTripletContainer | Store a ParticleIndexTriplets |
| EventPairsOptimizerState | |
| EventQuadsOptimizerState | |
| EventSingletonsOptimizerState | |
| EventTripletsOptimizerState | |
| ExclusiveConsecutivePairContainer | |
| ExclusiveConsecutivePairFilter | |
| InContainerPairFilter | A filter which returns true if a container containers the Pair |
| InContainerQuadFilter | A filter which returns true if a container containers the Quad |
| InContainerSingletonFilter | A filter which returns true if a container containers the Singleton |
| InContainerTripletFilter | A filter which returns true if a container containers the Triplet |
| ListPairContainer | Store a list of ParticleIndexPairs |
| ListQuadContainer | Store a list of ParticleIndexQuads |
| ListSingletonContainer | Store a list of ParticleIndexes |
| ListTripletContainer | Store a list of ParticleIndexTriplets |
| MinimumPairRestraint | Score based on the min or max PairScore over a set |
| MinimumPairScore | Evaluate the min or max n particle_pair scores of the passed set |
| MinimumQuadRestraint | Score based on the min or max QuadScore over a set |
| MinimumQuadScore | Evaluate the min or max n particle_quad scores of the passed set |
| MinimumSingletonRestraint | Score based on the min or max SingletonScore over a set |
| MinimumSingletonScore | Evaluate the min or max n particle scores of the passed set |
| MinimumTripletRestraint | Score based on the min or max TripletScore over a set |
| MinimumTripletScore | Evaluate the min or max n particle_triplet scores of the passed set |
| PairContainerSet | Stores a set of PairContainers |
| PairContainerStatistics | Track statistics on a PairContainer |
| PairsConstraint | Apply a PairFunction to a PairContainer to maintain an invariant |
| PairsOptimizerState | Apply a PairFunction to a PairContainer to maintain an invariant |
| PairsRestraint | Applies a PairScore to each Pair in a list |
| PredicatePairsRestraint | Applies a PairScore to each Pair in a list based on a predicate |
| PredicateQuadsRestraint | Applies a QuadScore to each Quad in a list based on a predicate |
| PredicateSingletonsRestraint | Applies a SingletonScore to each Singleton in a list based on a predicate |
| PredicateTripletsRestraint | Applies a TripletScore to each Triplet in a list based on a predicate |
| QuadContainerSet | Stores a set of QuadContainers |
| QuadContainerStatistics | Track statistics on a QuadContainer |
| QuadsConstraint | Apply a QuadFunction to a QuadContainer to maintain an invariant |
| QuadsOptimizerState | Apply a QuadFunction to a QuadContainer to maintain an invariant |
| QuadsRestraint | Applies a QuadScore to each Quad in a list |
| SingletonContainerSet | Stores a set of SingletonContainers |
| SingletonContainerStatistics | Track statistics on a SingletonContainer |
| SingletonsConstraint | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
| SingletonsOptimizerState | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
| SingletonsRestraint | Applies a SingletonScore to each Singleton in a list |
| TripletContainerSet | Stores a set of TripletContainers |
| TripletContainerStatistics | Track statistics on a TripletContainer |
| TripletsConstraint | Apply a TripletFunction to a TripletContainer to maintain an invariant |
| TripletsOptimizerState | Apply a TripletFunction to a TripletContainer to maintain an invariant |
| TripletsRestraint | Applies a TripletScore to each Triplet in a list |
| core | Basic functionality that is expected to be used by a wide variety of IMP users |
| AllSamePairPredicate | |
| AllSameQuadPredicate | |
| AllSameSingletonPredicate | |
| AllSameTripletPredicate | |
| AngleRestraint | Angle restraint between three particles |
| AngleTripletScore | Apply a function to the angle between three particles |
| AttributeSingletonPredicate | Return the value of an int attribute as the predicate value |
| BallMover | Move continuous particle variables by perturbing them within a ball |
| BinormalTerm | A single binormal term in a MultipleBinormalRestraint |
| BoxSweepClosePairsFinder | Find all nearby pairs by sweeping the bounding boxes |
| Centroid | A particle that is the geometric centroid of other particles |
| CentroidOfRefined | |
| ChecksScoreState | |
| ChildrenRefiner | Return the hierarchy children of a particle |
| ClosedCubicSpline | Closed cubic spline function |
| ClosePairsFinder | A base class for algorithms to find spatial proximities |
| ClosePairsPairScore | Apply the score to all pairs whose spheres are within a distance threshold |
| CoinFlipPairPredicate | |
| CoinFlipQuadPredicate | |
| CoinFlipSingletonPredicate | |
| CoinFlipTripletPredicate | |
| ConjugateGradients | Simple conjugate gradients optimizer |
| ConnectivityRestraint | Ensure that a set of particles remains connected with one another |
| ConstantPairPredicate | |
| ConstantQuadPredicate | |
| ConstantRestraint | Return a constant value |
| ConstantSingletonPredicate | |
| ConstantTripletPredicate | |
| Cosine | Cosine function |
| Cover | A particle which covers a set of other particles |
| CoverRefined | Set the position and radius of a particle to enclose the refined |
| DataObject | |
| DerivativesFromRefined | Accumulate the derivatives of the refined particles |
| DerivativesToRefined | Copy the derivatives from a coarse particle to its refined particles |
| DiameterRestraint | Restrain the diameter of a set of points |
| DihedralRestraint | Dihedral restraint between four particles |
| DistancePairScore | |
| DistanceRestraint | Distance restraint between two particles |
| EdgePairGeometry | Display a segment connecting a pair of particles |
| EdgePairsGeometry | Display a segment for each pair in a IMP::PairContainer |
| ExcludedVolumeRestraint | Prevent a set of particles and rigid bodies from inter-penetrating |
| FixedRefiner | The refiner can refine any particle by returning a fixed set |
| Gaussian | |
| GenericAttributeSingletonScore | Apply a function to an attribute |
| GenericBoundingBox3DSingletonScore | Score particles based on how far outside a box they are |
| GenericDistanceToSingletonScore | Apply a function to the distance to a fixed point |
| GridClosePairsFinder | Find all nearby pairs by testing all pairs |
| Harmonic | Harmonic function (symmetric about the mean) |
| HarmonicDistancePairScore | |
| HarmonicLowerBound | Lower bound harmonic function (non-zero when feature < mean) |
| HarmonicSphereDistancePairScore | A harmonic score on the distance between two spheres |
| HarmonicSurfaceDepthPairScore | |
| HarmonicSurfaceDistancePairScore | A harmonic score on the distance between a surface and a sphere |
| HarmonicSurfaceHeightPairScore | |
| HarmonicUpperBound | Upper bound harmonic function (non-zero when feature > mean) |
| HarmonicUpperBoundSphereDiameterPairScore | A harmonic upper bound on the diameter of the span of two spheres |
| HarmonicUpperBoundSphereDistancePairScore | A harmonic upper bound on the distance between two spheres |
| HarmonicWell | A well with harmonic barriers |
| Hierarchy | A decorator for helping deal with a generalized hierarchy |
| HierarchyCounter | A simple functor to count the number of particles in a hierarchy |
| HierarchyTraits | Define the type for a type of hierarchy |
| HierarchyVisitor | A visitor for traversal of a hierarchy |
| InBoundingBox3DSingletonPredicate | Return 1 if the XYZ is in the bounding box, 0 otherwise |
| IncrementalScoringFunction | Score the model efficiently when a small number of particles are changed |
| IsCollisionPairPredicate | Return 1 if two XYZRs collide |
| KClosePairsPairScore | Apply a score to a fixed number of close pairs from the two sets |
| LateralSurfaceConstraint | Constrain the center of a Surface for visualization |
| LeavesRefiner | Return the hierarchy leaves under a particle |
| Linear | Linear function |
| MCCGSampler | A simple sampler |
| MinimumRestraint | Score based on the minimum scoring members of a set of restraints |
| ModifierVisitor | A visitor which applies a modifier to each Particle in a hierarchy |
| MonteCarlo | A Monte Carlo optimizer |
| MonteCarloMover | A base class for classes which perturb particles |
| MonteCarloMoverResult | Return value of the MonteCarloMover::propose() function |
| MonteCarloWithBasinHopping | This variant of Monte Carlo uses basis hopping |
| MonteCarloWithLocalOptimization | This variant of Monte Carlo that relaxes after each move |
| MoveStatisticsScoreState | Keep track of statistics about how particles move |
| MSConnectivityRestraint | Ensure that a set of particles remains connected with one another |
| MultipleBinormalRestraint | Modeller-style multiple binormal (phi/psi) restraint |
| NearestNeighborsClosePairsFinder | Find all nearby pairs using the algebra::NearestNeighbor code |
| NeighborsTable | |
| NonRigidMember | A decorator for a particle that is part of a rigid body but not rigid |
| NormalizedSphereDistancePairScore | A score on the normalized distance between the surfaces of two spheres |
| NormalMover | Modify a set of continuous variables using a normal distribution |
| OpenCubicSpline | An OpenCubicSpline |
| OrderedTypePairPredicate | |
| OrderedTypeQuadPredicate | |
| OrderedTypeSingletonPredicate | |
| OrderedTypeTripletPredicate | |
| PairConstraint | Apply a PairFunction to a Pair |
| PairRestraint | Applies a PairScore to a Pair |
| PredicateSingletonScore | |
| QuadConstraint | Apply a QuadFunction to a Quad |
| QuadraticClosePairsFinder | Find all nearby pairs by testing all pairs |
| QuadRestraint | Applies a QuadScore to a Quad |
| Reference | A particle that has an associated reference particle |
| RefinedPairsPairScore | Generate pairs to score by applying a Refiner |
| RestraintsScoringFunction | |
| RigidBody | A decorator for a rigid body |
| RigidBodyAnglePairScore | Score on the crossing angle between two rigid bodies |
| RigidBodyDerivativeGeometry | |
| RigidBodyDerivativesGeometry | |
| RigidBodyDistancePairScore | Accelerated computation of the distance between two rigid bodies |
| RigidBodyFrameGeometry | |
| RigidBodyFramesGeometry | |
| RigidBodyHierarchyGeometry | |
| RigidBodyMember | A member of a rigid body, it has internal (local) coordinates |
| RigidBodyMover | Modify the transformation of a rigid body |
| RigidBodyTorque | |
| RigidBodyTunneler | Modify the transformation of a rigid body |
| RigidBodyUmbrella | Umbrella-like restraint for rigid bodies |
| RigidClosePairsFinder | Perform more efficient close pair finding when rigid bodies are involved |
| RigidMember | |
| SerialMover | Applies a list of movers one at a time |
| SingletonConstraint | Apply a SingletonFunction to a Singleton |
| SingletonRestraint | Applies a SingletonScore to a Singleton |
| SoftSpherePairScore | |
| SoftSubSurfacePairScore | A harmonic score that keeps a sphere below a surface |
| SoftSuperSurfacePairScore | A harmonic score that keeps a sphere above a surface |
| SphereDistancePairScore | A score on the distance between the surfaces of two spheres |
| SphereDistanceToSingletonScore | Apply a function to the distance to a fixed point |
| StatisticalPairScore | |
| SteepestDescent | A simple steepest descent optimizer |
| SubsetMover | Applies a subset of a list of movers |
| Surface | A decorator for a particle that represents a surface, its coordinates, and orientation |
| SurfaceDepthPairScore | A score on the depth of a sphere below a surface |
| SurfaceDistancePairScore | A score on the distance between a surface and a sphere |
| SurfaceGeometry | Display a Surface particle as a cylindrical disk |
| SurfaceGeometryConstraint | Constrain a SurfaceGeometry to a Surface |
| SurfaceHeightPairScore | A score on the height of a sphere above a surface |
| SurfaceMover | Modify a surface orientation |
| SurfaceSymmetryConstraint | Constrain orientation of surfaces with respect to rigid bodies |
| SurfaceTetheredChain | Score on surface-to-end distance of chain tethered to impenetrable surface |
| TableRefiner | A lookup based particle refiner |
| Transform | Apply a transformation to a passed particle |
| TransformationAndReflectionSymmetry | Set the coordinates of a particle to be a transformed version of a reference |
| TransformationSymmetry | Set the coordinates of a particle to be a transformed version of a reference |
| TransformationSymmetryMover | Modify the given TransformationSymmetry |
| TransformedDistancePairScore | Apply a function to the distance between two particles after transforming the first |
| TripletConstraint | Apply a TripletFunction to a Triplet |
| TripletRestraint | Applies a TripletScore to a Triplet |
| TruncatedHarmonic | A function that is harmonic over an interval |
| Typed | A decorator for classifying particles in your system |
| TypedPairScore | Delegate to another PairScore depending on particle types |
| UnorderedTypePairPredicate | |
| UnorderedTypeQuadPredicate | |
| UnorderedTypeSingletonPredicate | |
| UnorderedTypeTripletPredicate | |
| VolumeRestraint | A restraint that prevents spheres from inter-penetrating |
| WeightedDerivativesToRefined | Copy the derivatives from a coarse particle to its refined particles |
| WeightedSphereDistancePairScore | A score on a weighted distance between the surfaces of two spheres |
| WeightedSum | Weighted sum of unary functions |
| WeightedSumOfExponential | Negative logarithm of weighted sum of negative exponential of unary functions |
| WriteRestraintScoresOptimizerState | Write the scores of the passed restraints to a file during optimization |
| XYZ | A decorator for a particle with x,y,z coordinates |
| XYZDerivativeGeometry | |
| XYZDerivativesGeometry | |
| XYZR | A decorator for a particle with x,y,z coordinates and a radius |
| XYZRGeometry | Display an IMP::core::XYZR particle as a ball |
| XYZRsGeometry | Display an IMP::SingletonContainer of IMP::core::XYZR particles as balls |
| display | Output IMP model data in various file formats |
| BoundingBoxGeometry | Display a bounding box |
| Color | Represent an RGB color |
| Colored | A particle with a color |
| CylinderGeometry | Display a cylinder |
| EllipsoidGeometry | Display a ellipsoid |
| FilterGeometry | Remove geometry which is not above a plane |
| Geometry | The base class for geometry |
| GeometryProcessor | Provide a standard geometry processing framework |
| GeometrySet | Group of set of geometric elements |
| IsosurfaceGeometry | Display an isosurface of a density map |
| LabelGeometry | A text label for a ball in space |
| PairGeometry | A base class for geometry contained in particles |
| PairsGeometry | A base class for geometry from a set of particles |
| PivyWriter | |
| PlaneGeometry | Display a plane as truncated to a bounding box |
| PointGeometry | Display a point |
| PolygonGeometry | |
| PymolWriter | Write a CGO file with the geometry |
| ReferenceFrameGeometry | Display a reference frame |
| RestraintGeometry | Try to draw some stuff for a generic restraint |
| RestraintSetGeometry | Geometry for a whole set of restraints |
| SegmentGeometry | Display a segment |
| SingletonGeometry | A base class for geometry contained in particles |
| SingletonsGeometry | A base class for geometry from a set of particles |
| SkinSurfaceGeometry | Display an isosurface of a density map |
| SphereGeometry | Display a sphere |
| SurfaceMeshGeometry | Display a surface mesh |
| TextWriter | |
| TriangleGeometry | Display a triangle |
| WriteOptimizerState | |
| Writer | Base class for writing geometry to a file |
| WriterAdaptor | |
| domino | Divide-and-conquer inferential optimization in discrete space |
| Assignment | Store a configuration of a subset |
| AssignmentContainer | The base class for containers of assignments |
| AssignmentsTable | |
| BranchAndBoundAssignmentsTable | |
| BranchAndBoundSampler | Sample best solutions using BranchAndBound |
| CappedAssignmentContainer | Store no more than a max number of states |
| CompoundStates | |
| DependencyScoreState | Add a dependency to the dependency graph |
| DiscreteSampler | A base class for discrete samplers in Domino2 |
| DisjointSetsSubsetFilterTable | A base class |
| DominoSampler | Sample best solutions using Domino |
| EqualitySubsetFilterTable | Do not allow two particles to be in the same state |
| EquivalenceAndExclusionSubsetFilterTable | Define sets of equivalent and exclusive particles |
| EquivalenceSubsetFilterTable | Define sets of equivalent particles |
| ExclusionSubsetFilterTable | Do not allow two particles to be in the same state |
| HeapAssignmentContainer | Store a set of k top scoring assignments |
| IndexStates | |
| ListAssignmentContainer | Simple storage of a set of Assignments |
| ListAssignmentsTable | |
| ListSubsetFilterTable | Maintain an explicit list of what states each particle is allowed to have |
| MinimumRestraintScoreSubsetFilterTable | Filter a configuration of the subset using the Model thresholds |
| NestedRigidBodyStates | |
| Order | Store a persistent ordering for a subset based on the list |
| PackedAssignmentContainer | Store assignments in a compact form in memory |
| PairListSubsetFilterTable | |
| ParticlesAdaptor | |
| ParticleStates | |
| ParticleStatesTable | |
| PermutationStates | |
| ProbabilisticSubsetFilterTable | |
| RangeViewAssignmentContainer | Expose a range [begin, end) of an inner assignment container to consumers |
| ReadAssignmentContainer | Read the assignments from binary data on disk |
| ReadHDF5AssignmentContainer | Store the assignments in an HDF5DataSet |
| RecursiveAssignmentsTable | |
| RecursiveStates | |
| RestraintCache | |
| RestraintScoreSubsetFilterTable | Filter a configuration of the subset using the Model thresholds |
| RigidBodyStates | |
| SampleAssignmentContainer | Store a list of k assignments chosen from all those added to this table |
| SimpleAssignmentsTable | |
| Slice | Store a subset of a subset or assignment |
| Subset | Represent a subset of the particles being optimized |
| SubsetFilter | |
| SubsetFilterTable | |
| WriteAssignmentContainer | Store the assignments on disk as binary data |
| WriteHDF5AssignmentContainer | Store the assignments in an HDF5DataSet |
| XYZStates | |
| em | Basic utilities for handling cryo-electron microscopy 3D density maps |
| CoarseCC | Responsible for performing coarse fitting between two density objects |
| CoarseCCatIntervals | Cross correlation coefficient calculator |
| CoarseConvolution | Convolutes two grids |
| DensityFillingRestraint | Calculate score based on fit to EM map |
| DensityHeader | |
| DensityMap | Class for handling density maps |
| DistanceMask | Calculates and stores a distance mask |
| EMReaderWriter | |
| EnvelopeFitRestraint | A restraint for envelope-based scoring of particles in the density map |
| EnvelopePenetrationRestraint | Calculate score based on fit to EM map |
| EnvelopeScore | Class for envelope based scoring using MapDistanceTransform |
| FitRestraint | Calculate score based on fit to EM map |
| FittingSolutions | A simple list of fitting solutions |
| HighDensityEmbedding | |
| ImageHeader | Class to deal with the header of Electron Microscopy images in IMP |
| KernelParameters | Calculates and stores Gaussian kernel parameters |
| MapDistanceTransform | Class for getting the distance from the map envelope |
| MapReaderWriter | The base class to handle reading and writing of density maps |
| MRCReaderWriter | |
| PCAAligner | Fast alignment of points to a density map using principal components |
| PCAFitRestraint | Calculate score based on fit to EM map |
| RadiusDependentDistanceMask | |
| SampledDensityMap | Class for sampling a density map from particles |
| SpiderHeader | Header for Spider images. IMP-EM is designed to be compatible with it |
| SpiderMapReaderWriter | Class to read EM maps (3D) in Spider and Xmipp formats |
| SurfaceShellDensityMap | The class represents a molecule as shells of distance from the surface |
| Voxel | |
| XplorReaderWriter | |
| em2d | Restraints using electron microscopy 2D images (class averages) |
| AverageDistanceLinkage | Functor for hierarchical clustering based on average-linkage |
| CenteredMat | |
| ChiSquaredScore | Score based on Chi^2 = ((pixels_image - pixels_projection)/stddev_image)^2 |
| ClusterSet | A class to store the clusters generated during hierarchical clustering |
| CollisionCrossSection | Determine the collision cross section for some projections of particles |
| CompleteLinkage | Functor for hierarchical clustering based on complete linkage |
| DistanceFilter | SubsetFilter for checking overlap between projections and images |
| DistanceFilterTable | |
| DummyRestraint | Dummy restraint between two particles |
| Em2DRestraint | |
| Em2DRestraintParameters | Parameters used by Em2DRestraint and ProjectionFinder |
| EM2DScore | |
| Fine2DRegistrationRestraint | |
| GridStates | |
| HasHigherCCC | Comparison by value of the ccc |
| HasLowerScore | Compare two classes that return a score |
| Image | 2D Electron Microscopy images in IMP |
| ImageReaderWriter | Virtual class for reader/writers of images |
| IntsOrder | |
| JPGImageReaderWriter | Class to read and write EM images in JPG format |
| LessPairBySecond | Comparison of pairs by checking the second element |
| MasksManager | Management of projection masks |
| MatchTemplateResult | |
| MeanAbsoluteDifference | Score based on the mean of the absolute difference |
| ParticlesDummyRestraint | Dummy restraint for a set of particles. Same use as DummyRestraint |
| PCAFitRestraint | Fast scoring of Particles against electron microscopy class averages |
| PolarResamplingParameters | |
| ProjectingOptions | Parameters given as options to the get_projections() functions |
| ProjectingParameters | Parameters needed for the core projection routine |
| ProjectionFinder | Class to perform registration of model projections to images |
| ProjectionMask | |
| ProjectionParameters | |
| ProjectionParametersScoreState | |
| ProjectionStates | |
| RegistrationResult | Class to manage registration results |
| RelativePositionMover | |
| RigidBodiesImageFitRestraint | Fit rigid bodies to an image |
| ScoreFunction | Base class for all scoring functions related to em2d |
| SegmentationParameters | Class to provide all the parameters to the segmentation function |
| SingleLinkage | Functor for hierarchical clustering based on single linkage |
| SpiderImageReaderWriter | |
| TIFFImageReaderWriter | Management of reading/writing TIFF images |
| EMageFit | Build assembly models consistent with EM images (class averages) |
| argminmax | Utility functions to extract min/max from the inputs |
| buildxlinks | Utility functions to handle cross links |
| DockOrder | Compute the order of the docking experiments |
| InitialDockingFromXlinks | Puts two subunits together using the Xlinkins restraints |
| Xlink | Class defining a cross-link |
| XlinksDict | Description of crosslinking restraints as a python dictionary |
| csv_related | Utility functions to handle CSV files |
| database | Utility functions to manage SQL databases with sqlite3 |
| Database2 | Class to manage a SQL database built with sqlite3 |
| domino_model | Classes to manage a model using DOMINO |
| DominoModel | Management of a model using DOMINO |
| imp_general | Utility functions that are supposedly not EMageFit-specific |
| alignments | Utility functions to handle alignments |
| comparisons | Utility functions for comparisons |
| io | Utility functions to handle IO |
| ReferenceFrameToText | Transform a IMP reference frame into parseable output |
| Transformation3DToText | Parseable output for a IMP Transformation3D |
| movement | Utility functions to handle movement |
| representation | Utility functions to handle representation |
| monte_carlo | Classes for Monte Carlo sampling using rigid body relative moves |
| MonteCarloRelativeMoves | Class to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies |
| restraints | Utility functions to handle restraints |
| sampling | Utility functions to handle sampling |
| solutions_io | Utility functions to store and retrieve solution information |
| HeapRecord | The heapq algorithm is a min-heap |
| ResultsDB | Class for managing the results of the experiments |
| utility | Utility functions |
| example | Example module |
| ExampleComplexRestraint | Restrain the diameter of a set of points |
| ExampleConstraint | A trivial constraint that just increments a counter |
| ExampleDecorator | A simple decorator which adds a name to a particle |
| ExampleObject | An example simple object which is reference counted |
| ExamplePairScore | Apply a harmonic to the distance between two particles |
| ExampleRestraint | Restrain a particle to be in the x,y plane |
| ExampleSingletonModifier | An example singleton modifier |
| ExampleSubsetFilterTable | |
| ExampleTemplateClassD | A line segment templated on the dimension |
| ExampleUnaryFunction | A simple unary function |
| PythonExampleConstraint | An example Constraint written in Python |
| PythonExamplePairScore | An example PairScore written in Python |
| PythonExampleRestraint | An example restraint written in Python |
| PythonExampleSingletonModifier | An example SingletonModifier written in Python |
| PythonExampleUnaryFunction | An example UnaryFunction written in Python |
| foxs | Determine small angle X-ray (SAXS) profiles |
| gsl | Several general purpose optimizers from the GNU Scientific Library (GSL) |
| ConjugateGradients | A conjugate gradients optimizer taken from GSL |
| GSLOptimizer | A base class for GSL-based optimizers |
| QuasiNewton | A quasi-Newton optimizer taken from GSL |
| Simplex | A simplex optimizer taken from GSL |
| integrative_docking | Pairwise docking incorporating additional data |
| isd | Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD) |
| Analysis | |
| Analysis | Class that produces analysis-related output, and is able to parse the output of a file produced by the Statistics class |
| demux_trajs | |
| Demuxer | Uses column to demux a replica trajectory |
| LogHolder | Manages information on a given simulation |
| Entry | Classes to handle ISD statistics files |
| Entry | The entry class represents a column in the statistics file |
| gmm_tools | Tools for handling Gaussian Mixture Models |
| History | Classes to store output from replicas |
| History | Class that contains the output of one replica, used by the Analysis class |
| shared_functions | |
| sfo_common | Nonspecific methods used across all shared function objects |
| Statistics | |
| Statistics | Statistics gathering and printing class for ISD gibbs sampling |
| TALOSReader | Classes to handle TALOS files or folders |
| TALOSReader | Reads a TALOS file, or a TALOS folder, and stores the data |
| TBLReader | Classes to handle TBL files |
| TuneRex | |
| CvEstimator | When created, estimates the heat capacity from the energies or from the indicator functions using the specified method |
| utils | Miscellaneous utilities |
| Pipe | Implements a FIFO pipe that merges lists (see self.put) |
| AmbiguousNOERestraint | Ambiguous NOE distance restraint between a number of pairs of particles |
| AmbiguousRestraint | Apply an ambiguous restraint by computing the d-norm |
| AtomicCrossLinkMSRestraint | Restrain atom pairs based on a set of crosslinks |
| BivariateFunction | Base class for functions of two variables |
| Covariance1DFunction | Covariance function |
| CrossLinkData | CrossLinkData |
| CrossLinkMSRestraint | A restraint for ambiguous cross-linking MS data and multiple state approach |
| CysteineCrossLinkData | CysteineCrossLinkData |
| CysteineCrossLinkRestraint | A restraint for cysteine cross-linking data |
| FNormal | FNormal |
| FretData | Auxiliary class for FRET_R restraint |
| FretRestraint | |
| GaussianAnchorEMRestraint | Restraint between two sets of anchor points "model" and "EM density" |
| GaussianEMRestraint | Restraint between two Gaussian Mixture Models, "model" and "density" |
| GaussianProcessInterpolation | GaussianProcessInterpolation |
| GaussianProcessInterpolationRestraint | Gaussian process restraint |
| GaussianRestraint | Normal probability distribution as a restraint |
| GeneralizedGuinierPorodFunction | 1D mean function for SAS data |
| HybridMonteCarlo | Hybrid Monte Carlo optimizer |
| ISDRestraint | A base class for ISD Restraints |
| JeffreysRestraint | |
| Linear1DFunction | Linear one-dimensional function |
| LognormalAmbiguousRestraint | |
| LognormalRestraint | Normal probability distribution as a restraint |
| LogWrapper | Calculate the -Log of a list of restraints |
| MarginalHBondRestraint | Apply a lognormal distance restraint between two particles |
| MarginalNOERestraint | Apply an NOE distance restraint between two particles |
| MolecularDynamics | Molecular dynamics optimizer on 1-D and 3-D particles |
| MolecularDynamicsMover | Modify a set of continuous variables using a MD simulation |
| MultivariateFNormalSufficient | MultivariateFNormalSufficient |
| NOERestraint | Apply an NOE distance restraint between two particles |
| Nuisance | Add nuisance parameter to particle |
| RepulsiveDistancePairScore | A repulsive potential on the distance between two atoms |
| Scale | Add scale parameter to particle |
| Switching | Add switching parameter to particle |
| TALOSRestraint | Phi/psi dihedral restraint between four particles, using data from TALOS |
| UniformPrior | Uniform distribution with harmonic boundaries |
| UnivariateFunction | Base class for functions of one variable |
| vonMises | VonMises |
| vonMisesKappaConjugateRestraint | Conjugate prior for the concentration parameter of a von Mises distribution |
| vonMisesKappaJeffreysRestraint | Jeffreys prior for the \(\kappa\) concentration parameter of a von Mises distribution |
| vonMisesSufficient | VonMisesSufficient |
| Weight | Add weights for a set of states to a particle |
| WeightMover | A mover that perturbs a Weight particle |
| WeightRestraint | |
| kinematics | Functionality for dealing with kinematic mechanical structures |
| BondAngleRevoluteJoint | Joint that is parameterized as a bond angle between three particles |
| CCDLoopClosure | CCD loop closure |
| CompositeJoint | Joint that combines several inner joints, acting on the same rigid body pair |
| DihedralAngleRevoluteJoint | Joint that is parameterized as a dihedral angle between two planes |
| DirectionalDOF | |
| DOF | Represention of one degree of freedom (DOF) |
| DOFsSampler | Base class for sampling certain combinations of degrees of freedom |
| DOFValues | A class that holds DOF values for DOFs |
| Joint | Base class for joints between rigid bodies in a kinematic tree |
| KinematicForest | Define and manipulate a kinematic structure over a model |
| KinematicForestScoreState | |
| KinematicNode | A rigid body that is connected by a joint to other rigid bodies |
| LocalPlanner | |
| PathLocalPlanner | Local planner that samples conformations on a path between two nodes |
| PrismaticJoint | Joint in which two rigid bodies may slide along a line |
| ProteinKinematics | Kinematic structure over a protein, with backbone and side chain dihedrals |
| RevoluteJoint | Abstract class for all revolute joints |
| RevoluteJointMover | Modify a set of joints using a normal distribution |
| RRT | Simple implementation of the Rapidly-exploring Random Trees algorithm |
| RRTNode | Simple RRT node implementation |
| TransformationJoint | |
| UniformBackboneSampler | Sample uniformly over a set of backbone dihedral joints |
| kmeans | Interface to the GPL k-means clustering library |
| KMeans | |
| misc | Miscellaneous functionality that is not expected to be used by many IMP users |
| CommonEndpointPairFilter | Return true for any pair of bonds sharing an endpoint |
| CustomXYZR | A decorator for a particle with x,y,z coordinates and a radius |
| DecayPairContainerOptimizerState | Maintain a pair container with a decaying list of pairs |
| FreelyJointedChain | Score on end-to-end distance of freely jointed chain |
| LogPairScore | Track the pairs of particles passed |
| LowestRefinedPairScore | Refine both particles with the refiner and score on the lowest pair |
| MetricClosePairsFinder | |
| SoftCylinderPairScore | Apply a function to the distance between the cylinders defined by two bonds |
| StateAdaptor | Allow OptimizerStates to be used as ScoreStates |
| WormLikeChain | Worm-like-chain energy for polymer chains |
| modeller | Interface to the Modeller comparative modeling package |
| BinormalTerm | A single binormal term in a MultipleBinormalRestraint |
| IMPRestraints | A Modeller restraint which evaluates an IMP scoring function |
| ModellerRestraints | An IMP restraint using all defined Modeller restraints |
| ModelLoader | Read a Modeller model into IMP |
| MultipleBinormalRestraint | Modeller-style multiple binormal (phi/psi) restraint |
| mpi | Code that uses the MPI parallel library |
| ReplicaExchange | A class to implement Hamiltonian Replica Exchange |
| multi_state | Functionality for handling multi-state models |
| CompareMultiStateModels | Utility class to help sort MultiStateModel objects |
| EnsembleGenerator | Enumeration of an ensemble of good scoring MultiStateModels |
| MultiStateModel | Keep track of multiple states |
| MultiStateModelScore | Base class for MultiStateModel scoring classes |
| SAXSMultiStateModelScore | |
| multifit | Fitting atomic structures into a cryo-electron microscopy density map |
| cluster | |
| AlignmentClustering | Clusters assembly models |
| AnchorsData | Storage of anchors (points and edges) |
| AssemblyHeader | Holds data about the assembly density needed for optimization |
| ComplementarityRestraint | Compute the complementarity between two molecules |
| ComponentHeader | Holds data about a component needed for optimization |
| DataPointsAssignment | |
| DensityDataPoints | Stores density voxels as a vector of Array1D |
| DummyRestraint | A simple Restraint that always returns a score of zero |
| Ensemble | An ensemble of fitting solutions |
| FFTFitting | Fit a molecule inside its density by local or global FFT |
| FFTFittingOutput | Storage of the results from an FFT fit |
| FittingSolutionRecord | A fitting solution record |
| FittingStates | |
| GeometricHash | Geometric Hash table |
| MergeTreeBuilder | Utility class for building merge trees |
| ProbabilisticAnchorGraph | Probabilistic anchor graph |
| ProteinsAnchorsSamplingSpace | Stores the anchors sampling space for each protein |
| ProteomicsData | Storage of proteomics data |
| ProteomicsEMAlignmentAtomic | Align proteomics graph to EM density map |
| RadiusOfGyrationRestraint | Ensure the radius of gyration of particles fits the predicted one |
| RigidLeavesRefiner | Return all rigid body members that are also hierarchy leaves |
| SettingsData | Holds header data for optimization |
| WeightedExcludedVolumeRestraint | Calculate score based on fit to EM map |
| parallel | Distribute IMP tasks to multiple processors or machines |
| master_communicator | Classes for communicating from the master to slaves |
| MasterCommunicator | For communicating from the master to slaves |
| subproc | Subprocess handling |
| util | Utilities for the IMP.parallel module |
| Context | A collection of tasks that run in the same environment |
| Error | Base class for all errors specific to the parallel module |
| LocalSlave | A slave running on the same machine as the master |
| Manager | Manages slaves and contexts |
| NetworkError | Error raised if a problem occurs with the network |
| NoMoreSlavesError | Error raised if all slaves failed, so tasks cannot be run |
| RemoteError | Error raised if a slave has an unhandled exception |
| SGEPESlaveArray | An array of slaves in a Sun Grid Engine system parallel environment |
| SGEQsubSlaveArray | An array of slaves on a Sun Grid Engine system, started with 'qsub' |
| Slave | Representation of a single slave |
| SlaveArray | Representation of an array of slaves |
| pepdock | Initial peptide docking |
| pmi | Python classes to represent, score, sample and analyze models |
| analysis | Tools for clustering and cluster analysis |
| Alignment | Performs alignment and RMSD calculation for two sets of coordinates |
| Clustering | A class to cluster structures |
| CrossLinkTable | Visualization of crosslinks |
| GetModelDensity | Compute mean density maps from structures |
| GetRMSD | This object can be added to output_objects in (for example in the ReplicaExchange0 macro) |
| Precision | A class to evaluate the precision of an ensemble |
| dof | Create movers and setup constraints for PMI objects |
| DegreesOfFreedom | A class to simplify create of constraints and movers for an IMP Hierarchy |
| io | Utility classes and functions for reading and storing PMI files |
| crosslink | Handles cross-link data sets |
| CrossLinkDataBaseFromStructure | This class generates a CrossLinkDataBase from a given structure |
| CrossLinkDataBaseKeywordsConverter | This class is needed to convert the keywords from a generic database to the standard ones |
| FilterOperator | This class allows to create filter functions that can be passed to the CrossLinkDataBase in this way: |
| FixedFormatParser | A class to handle different XL format with fixed format currently support ProXL |
| ResiduePairListParser | A class to handle different styles of site pairs parsers |
| utilities | Utility classes and functions for IO |
| xltable | Tools to plot a contact map overlaid with cross-links |
| XLTable | Class to read, analyze, and plot xlink data on contact maps Canonical way to read the data: 1) load sequences and name them 2) load coordinates for those sequences from PDB file 3) add crosslinks 4) create contact map 5) plot |
| RMSDOutput | A helper output based on dist to initial coordinates |
| TotalScoreOutput | A helper output for model evaluation |
| macros | Protocols for sampling structures and analyzing them |
| AnalysisReplicaExchange0 | A macro for running all the basic operations of analysis |
| BuildModel | A macro to build a Representation based on a Topology and lists of movers DEPRECATED - Use BuildSystem instead |
| BuildModel1 | Deprecated building macro - use BuildSystem() |
| BuildSystem | A macro to build a IMP::pmi::topology::System based on a TopologyReader object |
| ReplicaExchange0 | A macro to help setup and run replica exchange |
| metadata | Classes for attaching metadata to PMI objects |
| Citation | A publication that describes the modeling |
| ComparativeModelDataset | A 3D structure determined by comparative modeling |
| CXMSDataset | Processed crosslinks from a CX-MS experiment |
| DatabaseLocation | A dataset stored in an official database (PDB, EMDB, PRIDE, etc.) |
| Dataset | A set of input data, for example, a crystal structure or EM map |
| EM2DClassDataset | 2DEM class average |
| EMDBLocation | Something stored in the EMDB database |
| EMDensityDataset | A 3D electron microscopy dataset |
| EMMicrographsDataset | Raw 2D electron micrographs |
| FileLocation | An individual file or directory |
| Location | Identifies the location where a resource can be found |
| MassIVELocation | Something stored in the MassIVE database |
| MassSpecDataset | Raw mass spectrometry files such as peaklists |
| Metadata | Base class for all metadata |
| PDBDataset | An experimentally-determined 3D structure as a set of a coordinates, usually in a PDB file |
| PDBLocation | Something stored in the PDB database |
| PythonScript | A Python script used as part of the modeling |
| Repository | A repository containing modeling files |
| RootMetadata | Metadata that only makes sense for the top-level PMI object |
| Software | Software (other than IMP) used as part of the modeling protocol |
| mmcif | Support for the mmCIF file format |
| ProtocolOutput | Class to encode a modeling protocol as mmCIF |
| nonmaintained | Nonmaintained code |
| nonmantained | |
| CrossLinkMS | This class initializes a CrossLinkMS restraint and contains all useful information, such as the cross-link database, contained in self.pairs If restraint_file=None, it will proceed creating simulated data |
| output | Classes for writing output files and processing them |
| Output | Class for easy writing of PDBs, RMFs, and stat files |
| ProcessOutput | A class for reading stat files |
| ProtocolOutput | Base class for capturing a modeling protocol |
| plotting | |
 topology | |
 TopologyPlot | A class to read RMF files and make a network contact map |
| representation | Representation of the system |
| Representation | Set up the representation of all proteins and nucleic acid macromolecules |
| restraints | Classes to handle different kinds of restraints |
| basic | Some miscellaneous simple restraints |
| BiStableDistanceRestraint | Python restraint with bistable potential Authors: G |
| CylinderRestraint | PMI2 python restraint |
| DistanceRestraint | A simple distance restraint |
| DistanceToPointRestraint | Restraint for anchoring a particle to a specific coordinate |
| ExternalBarrier | Restraint to keep all structures inside sphere |
| crosslinking | Restraints for handling crosslinking data |
| AtomicCrossLinkMSRestraint | Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes' theory of probability |
| ConnectivityCrossLinkMS | This restraint allows ambiguous crosslinking between multiple copies it is a variant of the SimplifiedCrossLinkMS |
| CrossLinkingMassSpectrometryRestraint | Setup cross-link distance restraints from mass spectrometry data |
| crosslinking_new | Restraints for handling crosslinking data |
| em | Restraints for handling electron microscopy maps |
| CrossCorrelationRestraint | Fit particles to an EM map |
| GaussianEMRestraint | Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) |
| em2d | Restraints for handling electron microscopy images |
| ElectronMicroscopy2D | Fit particles against a set of class averages by principal components |
| ElectronMicroscopy2D_FFT | FFT based image alignment, developed by Javier Velazquez-Muriel |
| parameters | Restraints for parameters |
| JeffreysPrior | Wrapper for IMP.isd.JeffreysRestraint |
| WeightRestraint | Wrapper for an IMP.isd.WeightRestraint |
| proteomics | Restraints for handling various kinds of proteomics data |
| AmbiguousCompositeRestraint | This restraint allows ambiguous crosslinking between multiple copies excluding between symmetric copies It allows name ambiguity |
| CompositeRestraint | Handleparticles is a selection tuple compositeparticles is a list of selection tuples |
| ConnectivityNetworkRestraint | Python restraint that computes the score for a composite of proteins Authors: G |
| ConnectivityRestraint | Generate a connectivity restraint between domains setting up the restraint example: cr=restraints.ConnectivityRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")]) cr.add_to_model() cr.set_label("CR1") Multistate support =No Selection type=selection tuple Resolution=Yes |
| FuzzyBoolean | Fully Ambiguous Restraint that can be built using boolean logic R |
| FuzzyRestraint | Fully Ambiguous Restraint that can be built using boolean logic R |
| SetupConnectivityNetworkRestraint | Generates and wraps a IMP.pmi.ConnectivityRestraint between domains example: cr=restraints.ConnectivityNetworkRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")]) cr.add_to_model() cr.set_label("CR1") |
| SetupMembraneRestraint | |
| saxs | Restraints for handling small angle x-ray (SAXS) data |
| SAXSISDRestraint | Basic SAXS restraint using ISD |
| SAXSRestraint | Basic SAXS restraint |
| stereochemistry | Restraints for keeping correct stereochemistry |
| CharmmForceFieldRestraint | Enable CHARMM force field |
| ConnectivityRestraint | This class creates a restraint between consecutive TempResidue objects OR an entire PMI MOlecule object |
| ElasticNetworkRestraint | Add harmonic restraints between all pairs |
| ExcludedVolumeSphere | A class to create an excluded volume restraint for a set of particles at a given resolution |
| FusionRestraint | This class creates a restraint between the termini two polypeptides, to simulate the sequence connectivity |
| HelixRestraint | Enforce ideal Helix dihedrals and bonds for a selection at resolution 0 |
| PlaneDihedralRestraint | Restrain the dihedral between planes defined by three particles |
| PseudoAtomicRestraint | Add bonds and improper dihedral restraints for the CBs |
| ResidueAngleRestraint | Add angular restraint between triplets of consecutive residues/beads to enforce the stereochemistry |
| ResidueBondRestraint | Add bond restraint between pair of consecutive residues/beads to enforce the stereochemistry |
| ResidueDihedralRestraint | Add dihedral restraints between quadruplet of consecutive residues/beads to enforce the stereochemistry |
| SecondaryStructure | Experimental, requires isd_emxl for now |
| SymmetryRestraint | Create harmonic restraints between the reference and (transformed) clones |
| RestraintBase | Base class for PMI restraints, which wrap IMP.Restraint(s) |
| samplers | Sampling of the system |
| ConjugateGradients | Sample using conjugate gradients |
| MolecularDynamics | Sample using molecular dynamics |
| MonteCarlo | Sample using Monte Carlo |
| ReplicaExchange | Sample using replica exchange |
| tools | Miscellaneous utilities |
| ColorChange | Change color code to hexadecimal to rgb |
| HierarchyDatabase | Store the representations for a system |
| OrderedDefaultDict | Store objects in order they were added, but with default type |
| Segments | This class stores integers in ordered compact lists eg: [[1,2,3],[6,7,8]] the methods help splitting and merging the internal lists Example: s=Segments([1,2,3]) is [[1,2,3]] s.add(4) is [[1,2,3,4]] (add right) s.add(3) is [[1,2,3,4]] (item already existing) s.add(7) is [[1,2,3,4],[7]] (new list) s.add([8,9]) is [[1,2,3,4],[7,8,9]] (add item right) s.add([5,6]) is [[1,2,3,4,5,6,7,8,9]] (merge) s.remove(3) is [[1,2],[4,5,6,7,8,9]] (split) etc |
| topology | Set of python classes to create a multi-state, multi-resolution IMP hierarchy |
| Molecule | Stores a named protein chain |
| PDBSequences | Data_structure for reading and storing sequence data from pdb |
| Sequences | A dictionary-like wrapper for reading and storing sequence data |
| State | Stores a list of Molecules all with the same State index |
| System | This class initializes the root node of the global IMP.atom.Hierarchy |
| TempResidue | Temporarily stores residue information, even without structure available |
| TopologyReader | Automatically setup Sytem and Degrees of Freedom with a formatted text file |
| CompositeRestraint | A restraint for ambiguous cross-linking MS data and multiple state approach |
| MembraneRestraint | Membrane Restraint |
| Resolution | Add resolution to a particle |
| SigmoidRestraintSphere | Simple sigmoidal score calculated between sphere surfaces |
| Symmetric | Add symmetric attribute to a particle |
| TransformMover | Modify the transformation of a rigid body |
| Uncertainty | Add uncertainty to a particle |
| rmf | Support for the RMF file format for storing hierarchical molecular data and markup |
| HierarchyLoadLink | |
| HierarchySaveLink | |
| LoadLink | |
| SaveLink | |
| SaveOptimizerState | Periodically dump the state of all associated objects into the RMF file |
| SimpleLoadLink | |
| SimpleSaveLink | |
| rotamer | Sampling of sidechain rotamers |
| ResidueRotamer | A class storing the rotated coordinates of the atoms in the residue |
| RotamerAngleTuple | A simple class storing chi angles and their probability |
| RotamerCalculator | A class performing the rotations of atoms in the residues |
| RotamerLibrary | A class storing a whole rotamer library read from a file |
| saxs | Support for small angle X-ray scattering (SAXS) data |
| ChiFreeScore | |
| ChiScore | |
| ChiScoreLog | |
| DeltaDistributionFunction | |
| DerivativeCalculator | |
| Distribution | |
| FitParameters | Parameters of a fit, from ProfileFitter |
| FormFactorTable | |
| Profile | |
| ProfileClustering | |
| ProfileFitter | Fit two profiles with user-defined scoring function as a template parameter |
| RadialDistributionFunction | |
| RadiusOfGyrationRestraint | Calculate score based on radius of gyration, taken from saxs profile |
| RatioVolatilityScore | |
| Restraint | Calculate score based on fit to SAXS profile |
| RigidBodiesProfileHandler | Handle the profile for a set of particles, which may include rigid bodies |
| SolventAccessibleSurface | |
| WeightedFitParameters | Parameters of a weighted fit, from WeightedProfileFitter |
| WeightedProfileFitter | Fitting of multiple profiles to the experimental one |
| saxs_merge | A method for merging SAXS profiles using Gaussian processes |
| score_functor | Composable functors to implement scores via compile-time composition |
| AddScores | |
| DistancePairScore | Create efficient distance-based pair scores |
| Dope | |
| Harmonic | |
| HarmonicLowerBound | |
| HarmonicUpperBound | |
| LinearLowerBound | |
| OpenCubicSpline | Open cubic spline function |
| OrientedSoap | Orientation-dependent SOAP score |
| PointToSphereDistance | |
| Score | A functor for computing a distance based score for two particles |
| ScoreUnaryFunction | |
| Shift | |
| SingletonStatistical | |
| Soap | |
| SphereDistance | |
| Statistical | |
| SurfaceDepthPairScore | Create efficient surface depth-based pair scores |
| SurfaceDistancePairScore | Create efficient surface distance-based pair scores |
| SurfaceHeightPairScore | Create efficient surface height-based pair scores |
| UnaryFunctionEvaluate | |
| WeightScore | |
| scratch | A space to add temporary classes while experimenting without forcing you to create your own module |
| statistics | Code to compute statistical measures |
| ChiSquareMetric | Compute the distance between two configurations using chi2 |
| ConfigurationSetRMSDMetric | |
| ConfigurationSetXYZEmbedding | Embed a configuration using the XYZ coordinates of a set of particles |
| Embedding | Store data to be clustered for embedding based algorithms |
| EuclideanMetric | |
| HistogramD | Dynamically build a histogram embedded in D-dimensional space |
| Metric | Store data to be clustered for distance metric based algorithms |
| ParticleEmbedding | |
| PartitionalClustering | A base class for clustering results where each item is in one cluster |
| PartitionalClusteringWithCenter | |
| RecursivePartitionalClusteringEmbedding | |
| RecursivePartitionalClusteringMetric | Represent a metric for clustering data that has already been clustered once |
| VectorDEmbedding | Simply return the coordinates of a VectorD |
| symmetry | Support for basic symmetry, such as periodic boundary conditions (PBC) |
| BallMover | Move a particle and keep it in the primitive cell of a periodic lattice |
| RigidBodyMover | Move a rigid body and keep it in the primitive cell of a periodic lattice |
| test | Support for running tests of IMP functionality |
| ApplicationTestCase | Super class for simple IMP application test cases |
| DirectorObjectChecker | Check to make sure the number of director references is as expected |
| RefCountChecker | Check to make sure the number of C++ object references is as expected |
| RunInTempDir | Simple RAII-style class to run in a temporary directory |
| TempDir | Simple RAII-style class to make a temporary directory |
| TestCase | Super class for IMP test cases |
| AddBoolFlag | |
| AddFloatFlag | |
| AddIntFlag | |
| AddStringFlag | |
| AdvancedFlag | Use this to add an advanced flag to the program |
| Array | A class to store an fixed array of same-typed values |
| AttributeOptimizer | Base class for optimizers that act on individual attributes |
| CommandDispatcher | Allow command line tools to easily implement multiple commands |
| Configuration | A class to store a configuration of a model |
| ConfigurationSet | A class to store a set of configurations of a model |
| Constraint | Implement a constraint on the Model |
| ConstVector | Store an array of values of the same type |
| Container | Abstract class for containers of particles |
| CreateLogContext | Create a new log context |
| Decorator | Interface to specialized Particle types (e.g. atoms) |
| DerivativeAccumulator | Class for adding derivatives from restraints to the model |
| EvaluationState | |
| EventException | An exception that signifies some event occurred |
| Exception | The general base class for IMP exceptions |
| Flag | |
| FloatIndex | |
| Index | A typed index |
| IndexException | An exception for a request for an invalid member of a container |
| IndexVector | |
| InputAdaptor | |
| InternalException | A general exception for an internal error in IMP |
| IOException | An input/output exception |
| Key | A base class for Keys |
| LRUCache | |
| Memoizer | |
| Model | Class for storing model, its restraints, constraints, and particles |
| ModelException | An exception which is thrown when the Model has attributes with invalid values |
| ModelObject | |
| NonCopyable | |
| Object | Common base class for heavy weight IMP objects |
| Optimizer | Base class for all optimizers |
| OptimizerState | Shared optimizer state that is invoked upon commitment of new coordinates |
| OptionParser | IMP-specific subclass of optparse.OptionParser |
| PairContainer | A shared container for Pairs |
| PairContainerAdaptor | |
| PairModifier | A base class for modifiers of ParticlePairsTemp |
| PairPredicate | Abstract predicate function |
| PairScore | Abstract class for scoring object(s) of type ParticleIndexPair |
| Particle | Class to handle individual particles of a Model object |
| ParticleAdaptor | |
| ParticleIndexAdaptor | |
| ParticleIndexesAdaptor | |
| ParticleIndexPairsAdaptor | |
| ParticleInputs | Base class for objects that take particle arguments and read from them |
| ParticleOutputs | Base class for objects that take particle arguments and modify them |
| piecewise_linear_distribution | |
| Pointer | A smart pointer to a reference counted object |
| PointerMember | A smart pointer to a ref-counted Object that is a class member |
| PythonDirectedGraph | |
| QuadContainer | A shared container for Quads |
| QuadContainerAdaptor | |
| QuadModifier | A base class for modifiers of ParticleQuadsTemp |
| QuadPredicate | Abstract predicate function |
| QuadScore | Abstract class for scoring object(s) of type ParticleIndexQuad |
| RAII | Temporarily change something; undo the change when this object is destroyed |
| Refiner | Abstract class to implement hierarchical methods |
| Restraint | A restraint is a term in an IMP ScoringFunction |
| RestraintsAdaptor | Provide a consistent interface for things that take Restraints as arguments |
| RestraintSet | Object used to hold a set of restraints |
| Sampler | Base class for all samplers |
| SaveToConfigurationSetOptimizerState | |
| ScopedAddCacheAttribute | |
| ScopedSetAttribute | |
| ScoreAccumulator | Class for adding up scores during ScoringFunction evaluation |
| ScoreState | ScoreStates maintain invariants in the Model |
| ScoringFunction | Represents a scoring function on the model |
| ScoringFunctionAdaptor | |
| SetCheckState | A class to change and restore check state |
| SetLogState | A class to change and restore log state |
| SetLogTarget | |
| SetNumberOfThreads | |
| Showable | |
| SingletonContainer | A shared container for Singletons |
| SingletonContainerAdaptor | |
| SingletonModifier | A base class for modifiers of ParticlesTemp |
| SingletonPredicate | Abstract predicate function |
| SingletonScore | Abstract class for scoring object(s) of type ParticleIndex |
| SparseSymmetricPairMemoizer | |
| TextInput | |
| TextOutput | |
| Timer | Time an operation and save the timings |
| TripletContainer | A shared container for Triplets |
| TripletContainerAdaptor | |
| TripletModifier | A base class for modifiers of ParticleTripletsTemp |
| TripletPredicate | Abstract predicate function |
| TripletScore | Abstract class for scoring object(s) of type ParticleIndexTriplet |
| TypeException | An exception for an invalid type being passed to IMP |
| UnaryFunction | Abstract single variable functor class for score functions |
| UncheckedWeakPointer | A weak pointer to an Object or RefCountedObject |
| Undecorator | |
| UsageException | An exception for an invalid usage of IMP |
| Value | Base for a simple primitive-like type |
| ValueException | An exception for an invalid value being passed to IMP |
| Vector | A more IMP-like version of the std::vector |
| VersionInfo | Version and module information for Objects |
| WarningContext | |
| WeakPointer | Smart pointer to Object-derived classes that does not refcount |
| write_a_metric | |
| MyMetric | |
| SurfacesGeometry | Display an IMP::SingletonContainer of Surface particles as cylindrical disks |
