IMP Reference Guide
2.7.0
The Integrative Modeling Platform

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 axisaligned 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 ddimensional 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 Ddimensions 
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 Ddimensions 
VectorD  A Cartesian vector in Ddimensions 
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 nonalternative 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 CAonly representation 
CADihedralRestraint  Dihedral restraint between five residues in CAonly 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 residuebased 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 LennardJones potential well 
LennardJonesPairScore  LennardJones 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 nonhydrogen atoms 
NonHydrogenPDBSelector  Select non hydrogen atoms 
NonWaterNonHydrogenPDBSelector  Select non water and non hydrogen atoms 
NonWaterPDBSelector  Select all nonwater nonalternative 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 orientationdependent 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 nonwater 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 cryoelectron 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 spatiallyproximals 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 interpenetrating 
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 (nonzero 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 (nonzero 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  Modellerstyle 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  Umbrellalike 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 surfacetoend 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 interpenetrating 
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  Divideandconquer 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 cryoelectron 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 envelopebased 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. IMPEM 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 averagelinkage 
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 crosslink 
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 EMageFitspecific 
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 minheap 
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 Xray (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 GSLbased optimizers 
QuasiNewton  A quasiNewton 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 analysisrelated 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 dnorm 
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 crosslinking MS data and multiple state approach 
CysteineCrossLinkData  CysteineCrossLinkData 
CysteineCrossLinkRestraint  A restraint for cysteine crosslinking 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 onedimensional 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 1D and 3D 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 Rapidlyexploring Random Trees algorithm 
RRTNode  Simple RRT node implementation 
TransformationJoint  
UniformBackboneSampler  Sample uniformly over a set of backbone dihedral joints 
kmeans  Interface to the GPL kmeans 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 endtoend 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  Wormlikechain 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  Modellerstyle 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 multistate 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 cryoelectron 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 crosslink 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 crosslinks 
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 CXMS 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 experimentallydetermined 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 toplevel 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 crosslink 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 crosslink 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 crosslinked aminoacids 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 crosslink 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 Gaussiandecorated 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 VelazquezMuriel 
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 xray (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 multistate, multiresolution IMP hierarchy 
Molecule  Stores a named protein chain 
PDBSequences  Data_structure for reading and storing sequence data from pdb 
Sequences  A dictionarylike 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 crosslinking 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 Xray scattering (SAXS) data 
ChiFreeScore  
ChiScore  
ChiScoreLog  
DeltaDistributionFunction  
DerivativeCalculator  
Distribution  
FitParameters  Parameters of a fit, from ProfileFitter 
FormFactorTable  
Profile  
ProfileClustering  
ProfileFitter  Fit two profiles with userdefined 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 compiletime composition 
AddScores  
DistancePairScore  Create efficient distancebased pair scores 
Dope  
Harmonic  
HarmonicLowerBound  
HarmonicUpperBound  
LinearLowerBound  
OpenCubicSpline  Open cubic spline function 
OrientedSoap  Orientationdependent 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 depthbased pair scores 
SurfaceDistancePairScore  Create efficient surface distancebased pair scores 
SurfaceHeightPairScore  Create efficient surface heightbased 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 Ddimensional 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 RAIIstyle class to run in a temporary directory 
TempDir  Simple RAIIstyle 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 sametyped 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  IMPspecific 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 refcounted 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 primitivelike type 
ValueException  An exception for an invalid value being passed to IMP 
Vector  A more IMPlike version of the std::vector 
VersionInfo  Version and module information for Objects 
WarningContext  
WeakPointer  Smart pointer to Objectderived classes that does not refcount 
write_a_metric  
MyMetric  
SurfacesGeometry  Display an IMP::SingletonContainer of Surface particles as cylindrical disks 