IMP
2.0.1
The Integrative Modeling Platform
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IMP | All IMP::kernel code is brought into the IMP namespace |
algebra | See IMP.algebra Overview for more information |
BoundedGridRangeD | |
BoundingBoxD | An axis-aligned bounding box |
Cone3D | |
Cylinder3D | |
DefaultEmbeddingD | |
DenseGrid3D | |
DenseGridStorageD | |
DynamicNearestNeighbor3D | |
Ellipsoid3D | |
EuclideanVectorKDMetric | |
ExtendedGridIndexD | An index in an infinite grid on space |
FixedXYZ | A simple class for returning XYZ Euler angles |
FixedZXZ | A simple class for returning ZXZ Euler angles |
FixedZYZ | A simple class for returning ZYZ Euler angles |
GeometricPrimitiveD | |
GridD | A voxel grid in d-dimensional space space |
GridIndexD | Represent a real cell in a grid (one within the bounding box) |
LinearFit2D | Calculate line that fits best the input data points (Linear least squares) |
LogEmbeddingD | |
MaxVectorKDMetric | |
NearestNeighborD | |
ParabolicFit2D | Calculate parabola that fits best the input data points |
Plane3D | |
PrincipalComponentAnalysisD | |
ReferenceFrame3D | A reference frame in 3D |
Reflection3D | Reflect about a plane in 3D |
Rotation2D | Stores a 2D rotation matrix |
Rotation3D | 3D rotation class |
Segment3D | |
SparseGrid3D | |
SparseGridStorageD | |
SparseUnboundedGrid3D | |
SparseUnboundedGridD | |
SphereD | |
SpherePatch3D | |
SphericalVector3D | Class to represent a 3D point in spherical coordinates |
Transformation2D | Simple 2D transformation class |
Transformation3D | Simple 3D transformation class |
Triangle3D | |
UnboundedGridRangeD | |
VectorD | A Cartesian vector in D-dimensions |
VectorInputD | |
VectorInputD< 1 > | |
VectorKDMetric | |
atom | See IMP.atom Overview for more information |
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, |
Atom | A decorator for a particle representing an atom |
ATOMPDBSelector | Select all non-alternative ATOM records |
AtomType | The type of an atom |
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 an 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 optimizer |
CAlphaPDBSelector | Select all CA ATOM records |
CBetaPDBSelector | Select all CB ATOM records |
Chain | Store info for a chain of a protein |
ChainPDBSelector | Select all ATOM and HETATMrecords 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 |
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 | |
ForceFieldParameters | Storage and access to force field |
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 |
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 |
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 |
NonWaterNonHydrogenPDBSelector | Select non water and non hydrogen atoms |
NonWaterPDBSelector | Select all non-water non-alternative ATOM and HETATM records |
NotPDBSelector | Select atoms which not selected by a given selector |
NPDBSelector | Select all N ATOM records |
OrPDBSelector | Select atoms which are selected by either selector |
PDBSelector | Select which atoms to read from a PDB file |
PPDBSelector | Select all P ATOM records |
ProteinLigandAtomPairScore | |
ProteinLigandRestraint | |
RemoveRigidMotionOptimizerState | Removes rigid translation and rotation from the particles |
RemoveTranslationOptimizerState | Removes rigid translation from the particles |
Residue | A decorator for a residue |
ResidueType | The type for a residue |
RigidBodyDiffusion | |
RMSDCalculator | Used to calculate rmsd between multiple transformation that operate on the same particles |
SameResiduePairFilter | |
SecondaryStructureResidue | A decorator for a residue with probability of secondary structure |
Selection | |
SelectionGeometry | Display a Selection |
Simulator | The base class for simulators |
SmoothingFunction | Base class for smoothing nonbonded interactions as a function of distance |
StereochemistryPairFilter | A filter that excludes bonds, angles and dihedrals |
VelocityScalingOptimizerState | Maintains temperature during molecular dynamics by velocity scaling |
WaterPDBSelector | Select all non-water ATOM and HETATMrecords |
WritePDBOptimizerState | |
base | See IMP.base Overview for more information |
AddBoolFlag | |
AddFloatFlag | |
AddIntFlag | |
AddStringFlag | |
Array | A class to store an fixed array of same-typed values |
ConstVector | Store an array of values of the same type |
CreateLogContext | Create a new log context |
EventException | An exception that signifies some event occurred |
Exception | The general base class for IMP exceptions |
Index | |
IndexException | An exception for a request for an invalid member of a container |
IndexVector | |
InputAdaptor | |
InternalException | A general exception for an intenal error in IMP |
IOException | An input/output exception |
LRUCache | |
map | |
Memoizer | |
ModelException | An exception which is thrown when the Model has attributes with invalid values |
NonCopyable | |
Object | Common base class for heavy weight IMP objects |
OwnerPointer | A reference counted pointer to an Object |
piecewise_linear_distribution | |
Pointer | A reference counted pointer to an object |
RAII | |
RefCounted | Common base class for ref counted objects |
set | |
SetCheckState | A class to change and restore check state |
SetLogState | A class to change and restore log state |
SetLogTarget | |
SetNumberOfThreads | |
Showable | |
SparseSymmetricPairMemoizer | |
TextInput | |
TextOutput | |
TrackedObject | |
Tracker | |
UncheckedWeakPointer | A weak pointer to an IMP::Object or IMP::RefCountedObject |
UsageException | An exception for an invalid usage of IMP |
Value | |
ValueException | An exception for an invalid value being passed to IMP |
Vector | |
VersionInfo | Version and module information for Objects |
WarningContext | |
WeakPointer | |
benchmark | See IMP.benchmark Overview for more information |
Profiler | |
cgal | See IMP.cgal Overview for more information |
cnmultifit | See IMP.cnmultifit Overview for more information |
AlignSymmetric | A class for fast alignment of a cyclic model to its density |
container | See IMP.container Overview for more information |
AllBipartitePairContainer | Return all bipartite pairs between two containers |
AllPairContainer | Return all unordered pairs of particles taken from the SingletonContainer |
CloseBipartitePairContainer | Return all close ordered pairs of particles taken from the two SingletonContainers |
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 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 list of ParticlePairsTemp |
DynamicListQuadContainer | Store a list of ParticleQuadsTemp |
DynamicListSingletonContainer | Store a list of ParticlesTemp |
DynamicListTripletContainer | Store a list of ParticleTripletsTemp |
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 ParticlePairsTemp |
ListQuadContainer | Store a list of ParticleQuadsTemp |
ListSingletonContainer | Store a list of ParticlesTemp |
ListTripletContainer | Store a list of ParticleTripletsTemp |
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 | See IMP.core Overview for more information |
AllSamePairPredicate | |
AllSameQuadPredicate | |
AllSameSingletonPredicate | |
AllSameTripletPredicate | |
AngleRestraint | Angle restraint between three particles |
AngleTripletScore | Apply a function to the angle between three particles |
AttributeSingletonPredicate | |
BallMover | Modify a set of continuous variables by perturbing them within a ball |
BoxSweepClosePairsFinder | Find all nearby pairs by sweeping the bounding boxes |
Centroid | A particle that is the centroid of other particles |
CentroidOfRefined | Set the coordinates of the particle to be the centoid of the particles |
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 | |
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 | This class sets the position and radius of each particle to enclose the refined |
DataObject | |
DerivativesFromRefined | Accumulate the derivatives of the refined particles |
DerivativesToRefined | Copy the derivatives from the 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 an IMP::atom::Bond particle as a segment |
EdgePairsGeometry | Display an IMP::SingletonContainer of IMP::atom::Bond particles as segments |
ExcludedVolumeRestraint | Prevent a set of particles and rigid bodies from inter-penetrating |
FixedRefiner | The refiner can refine any particle by returning a fixed set |
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 |
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 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 | |
IncrementalScoringFunction | |
KClosePairsPairScore | |
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 which applies a singleton modifier to each Particle in a hierarchy |
MonteCarlo | A Monte Carlo optimizer |
MonteCarloMover | A base class for classes which perturb particles |
MonteCarloMoverResult | |
MonteCarloWithBasinHopping | This variant of Monte Carlo uses basis hopping |
MonteCarloWithLocalOptimization | This variant of Monte Carlo that relaxes after each move |
Mover | A base class for classes which perturb particles |
MoverBase | A class to help implement movers |
MoveStatisticsScoreState | Keep track of statistics about how particles move |
MSConnectivityRestraint | Ensure that a set of particles remains connected with one another |
NearestNeighborsClosePairsFinder | Find all nearby pairs using the algebra::NearestNeighbor code |
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 |
PeriodicOptimizerState | |
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 a decorator for a particle with an associated reference particle |
RefinedPairsPairScore | Generate pairs to score by applying a Refiner |
RestraintsScoringFunction | |
RigidBody | A decorator for a rigid body |
RigidBodyDerivativeGeometry | |
RigidBodyDerivativesGeometry | |
RigidBodyDistancePairScore | Accelerated computation of the distance between two rigid bodies |
RigidBodyFrameGeometry | |
RigidBodyFramesGeometry | |
RigidBodyHierarchyGeometry | |
RigidBodyMover | Modify the transformation of a rigid body |
RigidBodyTorque | |
RigidClosePairsFinder | Peform more efficient close pair finding when rigid bodies are involved |
RigidMember | A decorator for a particle that is part of a rigid body |
SerialMover | Apply a list of movers one at a time |
SingletonConstraint | Apply a SingletonFunction to a Singleton |
SingletonRestraint | Applies a SingletonScore to a Singleton |
SoftSpherePairScore | |
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 |
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 |
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 | Restraint the volume of a set of spheres |
WeightedSphereDistancePairScore | A score on a weighted distance between the surfaces of two spheres |
WriteRestraintScoresOptimizerState | |
XYZ | A 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 | See IMP.display Overview for more information |
BildWriter | Write a Bild file with the geometry |
BoundingBoxGeometry | Display a bounding box |
ChimeraWriter | Write geometry to a python file for Chimera to read |
CMMWriter | Write a CMM file with the geometry |
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 triangule |
WriteOptimizerState | |
Writer | Base class for writing geometry to a file |
WriterAdaptor | |
domino | See IMP.domino Overview for more information |
Assignment | Store a configuration of a subset |
AssignmentContainer | |
AssignmentsTable | |
BranchAndBoundAssignmentsTable | |
BranchAndBoundSampler | Sample best solutions using BranchAndBound |
CappedAssignmentContainer | |
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 | |
IndexStates | |
ListAssignmentContainer | |
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 | |
PairListSubsetFilterTable | |
ParticlesAdaptor | |
ParticleStates | |
ParticleStatesTable | |
PermutationStates | |
ProbabilisticSubsetFilterTable | |
RangeViewAssignmentContainer | |
ReadAssignmentContainer | |
ReadHDF5AssignmentContainer | |
RecursiveAssignmentsTable | |
RecursiveStates | |
RestraintCache | |
RestraintScoreSubsetFilterTable | Filter a configuration of the subset using the Model thresholds |
RigidBodyStates | |
SampleAssignmentContainer | |
SimpleAssignmentsTable | |
Slice | Store a subset of a subset or assignment |
Subset | Represent a subset of the particles being optimized |
SubsetFilter | |
SubsetFilterTable | |
WriteAssignmentContainer | |
WriteHDF5AssignmentContainer | |
XYZStates | |
em | See IMP.em Overview for more information |
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 |
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 Microsocopy images in IMP |
KernelParameters | |
MapDistanceTransform | Class for getting the distance from the map envelope |
MapReaderWriter | The base class to handle reading and writing of density maps |
MRCReaderWriter | |
PCAAligner | |
PCAFitRestraint | Calculate score based on fit to EM map |
RadiusDependentKernelParameters | Calculates kernel parameters as a function of a specific radius |
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 repersents a molecule as shells of distance from the surface |
Voxel | |
em2d | See IMP.em2d Overview for more information |
buildxlinks | |
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 |
Database | |
Database2 | Class to manage a SQL database built with sqlite3 |
DominoModel | |
DominoModel | Management of a model using DOMINO |
MonteCarloRelativeMoves | |
MonteCarloRelativeMoves | Class to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies |
solutions_io | |
ClusterRecord | Simple named tuple class |
HeapRecord | The heapq algorithm is a min-heap |
ResultsDB | Class for managing the results of the experiments |
CenteredMat | |
ChiSquaredScore | Score based on Chi^2 = ((pixels_iamge - pixels_projection)/stddev_image)^2 |
DistanceFilterTable | |
DummyRestraint | Dummy restraint between two particles |
Em2DRestraint | |
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 |
JPGImageReaderWriter | Class to read and write EM images in JPG format |
LessPairBySecond | Comparison of pairs by checking the second element |
MasksManager | Manage of projection masks |
MatchTemplateResult | |
ParticlesDummyRestraint | Dummy restraint for a set of particles. Same use as DummyRestraint |
PolarResamplingParameters | |
ProjectionFinder | Class to perform registration of model projections to images images |
ProjectionMask | |
ProjectionParameters | |
ProjectionParametersScoreState | |
ProjectionStates | |
RegistrationResult | Class to manage registration results |
ScoreFunction | Base class for all scoring functions related to em2d |
SegmentationParameters | Class to provide all the parameters to the segmentation function |
SpiderImageReaderWriter | |
example | See IMP.example Overview for more information |
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 |
ExamplePairScore | Apply a harmonic to the distance between two particles |
ExampleRefCounted | An example simple object which is reference counted |
ExampleRestraint | Restrain a particle to be in the x,y plane |
ExampleSingletonModifier | An example singleton modifer |
ExampleSubsetFilterTable | |
ExampleTemplateClassD | A line segment templated on the dimension |
ExampleUnaryFunction | A simple unary function |
gsl | See IMP.gsl Overview for more information |
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 |
isd | See IMP.isd Overview for more information |
AbstractGrid | |
AbstractGrid | Grid main functionality: manage services |
AbstractService | Wrapper around Grid services, facilitating non parameter-specific usage of the remote objects |
Result | A Result object is returned by a Proxy object, when some remote function invoked |
Server | Contains all the information that is required to use a remote object (alone and within a grid) |
Analysis | |
Analysis | Class that produces analysis-related output, and is able to parse the output of a file produced by the Statistics class |
Entry | |
Entry | The entry class represents a column in the statistics file |
FIFOBasedGrid | |
FIFOBasedRemoteObject | Filebased proxy instance |
FileBasedGrid | |
FileBasedRemoteObject | Filebased proxy instance |
History | |
History | Class that contains the output of one replica, used by the Analysis class |
PyroGrid | |
PyroHandler | Runs on remote side, non-specific object |
PyroProxy | This is high level wrapper of Pyro proxy objects, returns immediately with an empty Result object |
shared_functions | |
sfo_common | Nonspecific methods used across all shared function objects |
Statistics | |
Statistics | Statistics gathering and printing class for ISD gibbs sampling |
TALOSReader | |
TALOSReader | Reads a TALOS file, or a TALOS folder, and stores the data |
TuneRex | |
CvEstimator | When created, estimates the heat capacity from the energies or from the indicator functions using the specified method |
utils | |
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 |
BivariateFunction | Base class for functions of two variables |
Covariance1DFunction | Covariance function |
FNormal | FNormal |
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 | Apply an NOE distance restraint between two particles |
JeffreysRestraint | |
Linear1DFunction | Linear one-dimensional function |
LogicalORRestraint | Apply an NOE distance restraint between two particles |
LognormalRestraint | Normal probability distribution as a restraint |
MaintainScaleOrderConstraint | Constrain scales to be ordered and positive |
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 |
SlidingPriorRestraint | Score a Scale particle with unnormalized probability |
Switching | Add switching parameter to particle |
TALOSRestraint | Phi/psi dihedral restraint between four particles, using data from TALOS |
UnivariateFunction | Base class for functions of one variable |
vonMises | VonMises |
vonMisesKappaConjugateRestraint | Conjugate prior for the concentration parameter of a von Mises distribution |
vonMisesKappaJeffreysRestraint | |
vonMisesSufficient | VonMisesSufficient |
kernel | See IMP.kernel Overview for more information |
CommandDispatcher | Allow applications to easily implement commmands |
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 |
Container | Abstract class for containers of particles |
Decorator | |
DerivativeAccumulator | Class for adding derivatives from restraints to the model |
EvaluationState | |
FloatIndex | |
GenericScopedRemoveRestraint | Removes the Restraint until RAII object is destroyed |
GenericScopedRemoveScoreState | Removes the ScoreState until RAII object is destroyed |
GenericScopedRestraint | Removes the Restraint when the RAII object is destroyed |
GenericScopedScoreState | Removes the ScoreState when the RAII object is destroyed |
Key | A base class for Keys |
Model | Class for storing model, its restraints, constraints, and particles |
ModelObject | |
Optimizer | Base class for all optimizers |
OptimizerState | Shared optimizer state |
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 score function |
Particle | Class to handle individual model particles |
PythonDirectedGraph | |
QuadContainer | A shared container for Quads |
QuadContainerAdaptor | |
QuadModifier | A base class for modifiers of ParticleQuadsTemp |
QuadPredicate | Abstract predicate function |
QuadScore | Abstract score function |
Refiner | Abstract class to implement hierarchical methods |
Restraint | A restraint is a term in an IMP ScoringFunction |
RestraintSet | Object used to hold a set of restraints |
RestraintStatistics | |
Sampler | Base class for all samplers |
ScopedAddCacheAttribute | |
ScopedSetAttribute | |
ScoreAccumulator | Class for adding up scores during ScoringFunction evaluation |
ScoreState | ScoreStates maintian invariants in the Model |
ScoringFunction | |
ScoringFunctionAdaptor | |
SingletonContainer | A shared container for Singletons |
SingletonContainerAdaptor | |
SingletonModifier | A base class for modifiers of ParticlesTemp |
SingletonPredicate | Abstract predicate function |
SingletonScore | Abstract score function |
TripletContainer | A shared container for Triplets |
TripletContainerAdaptor | |
TripletModifier | A base class for modifiers of ParticleTripletsTemp |
TripletPredicate | Abstract predicate function |
TripletScore | Abstract score function |
UnaryFunction | Abstract single variable functor class for score functions |
Undecorator | |
kmeans | See IMP.kmeans Overview for more information |
KMeans | |
misc | See IMP.misc Overview for more information |
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 |
LogPairScore | Track the pairs of particles passed |
LowestRefinedPairScore | Refine both particles with the refiner and score on the lowest pair |
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 | See IMP.modeller Overview for more information |
BinormalTerm | A single binormal term in a MultipleBinormalRestraint |
IMPRestraints | A Modeller restraint which evaluates all defined IMP restraints |
ModellerRestraints | An IMP restraint using all defined Modeller restraints |
ModelLoader | Read a Modeller model into IMP |
MultipleBinormalRestraint | Modeller-style multiple binormal (phi/psi) restraint |
multifit | See IMP.multifit Overview for more information |
cluster | |
AlignmentClustering | Clusters assembly models |
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 |
FittingSolutionRecord | A fitting solution record |
FittingStates | |
ProteinsAnchorsSamplingSpace | Stores the anchors sampling space for each protein |
RadiusOfGyrationRestraint | Ensure the radius of gyration of particles fits the predicted one |
RMSDClustering | RMSD clustering |
SettingsData | Holds header data for optimization |
WeightedExcludedVolumeRestraint | Calculate score based on fit to EM map |
parallel | See IMP.parallel Overview for more information |
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 | See IMP.pepdock Overview for more information |
restrainer | See IMP.restrainer Overview for more information |
Display | A class to display the configuration |
Representation | Store Representation |
Restraint | Store Restraint |
SimpleConnectivity | Simple connectivity restraint |
SimpleDiameter | Simple diameter restraint |
SimpleDistance | Simple distance restraint between two particles |
SimpleEMFit | Simple EM fit restraint |
SimpleExcludedVolume | Simple excluded volume restraint |
XMLDisplay | Construct Display from XML file |
XMLRepresentation | Construct Representation from XML file |
XMLRestraint | Construct Restraint from XML file |
rmf | See IMP.rmf Overview for more information |
LoadLink | |
SaveLink | |
SaveOptimizerState | |
rotamer | See IMP.rotamer Overview for more information |
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 | See IMP.saxs Overview for more information |
DeltaDistributionFunction | |
Distribution | |
FormFactorTable | |
Profile | |
RadialDistributionFunction | |
RadiusOfGyrationRestraint | Calculate score based on radius of gyration, taken from saxs profile |
Restraint | Calculate score based on fit to SAXS profile |
SolventAccessibleSurface | |
score_functor | See IMP.score_functor Overview for more information |
AddScores | |
DistancePairScore | Create efficient distance-based pair scores |
Dope | |
Harmonic | |
HarmonicLowerBound | |
HarmonicUpperBound | |
LinearLowerBound | |
OpenCubicSpline | Open cubic spline function |
Score | |
ScoreUnaryFunction | |
Shift | |
SphereDistance | |
Statistical | |
UnaryFunctionEvaluate | |
WeightScore | |
scratch | See IMP.scratch Overview for more information |
statistics | See IMP.statistics Overview for more information |
ConfigurationSetRMSDMetric | |
ConfigurationSetXYZEmbedding | Embed a configuration using the XYZ coordinates of a set of particles |
Embedding | Store data to be clustered for embedding based algorithms |
Histogram | Histogram |
HistogramD | |
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 | |
VectorDEmbedding | Simply return the coordinates of a VectorD |
system | See IMP.system Overview for more information |
test | |
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 |
TestCase | Super class for IMP test cases |
write_a_metric | |
MyMetric | Define a metric on a list of floating point numbers based on their difference |