IMP Reference Guide
2.21.0
The Integrative Modeling Platform
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IMP | Base functionality and abstract base classes for representation, scoring and sampling |
algebra | General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules |
BoundedGridRangeD | |
BoundingBoxD | An axis-aligned bounding box |
Cone3D | Represent a cone in 3D |
ConnollySurfacePoint | Represent a point on the Connolly surface |
Cylinder3D | Represent a cylinder in 3D |
DefaultEmbeddingD | Embed a grid as an evenly spaced axis aligned grid |
DenseFloatLogGridKD | |
DenseGrid3D | A dense grid of values |
DenseGridStorageD | |
DenseIntLogGrid3D | |
DynamicNearestNeighbor3D | Provide an incremental nearest neighbor search function |
Ellipsoid3D | Represent an ellipsoid in 3D |
EuclideanVectorKDMetric | The l2 norm on the distance vector |
ExtendedGridIndexD | An index in an infinite grid on space |
FixedXYZ | A simple class for returning XYZ Euler angles |
Gaussian3D | A Gaussian distribution in 3D |
GeometricPrimitiveD | Base class for geometric types |
GridD | A voxel grid in d-dimensional space |
GridIndexD | Represent a real cell in a grid (one within the bounding box) |
Line3D | Simple implementation of lines in 3D |
LinearFit2D | Calculate line that fits best the input data points (Linear least squares) |
LogEmbeddingD | |
MaxVectorKDMetric | |
NearestNeighborD | Build a structure for finding nearest neighbors |
ParabolicFit2D | Calculate parabola that fits best the input data points |
Plane3D | Represent a plane in 3D |
PrincipalComponentAnalysisD | Represent an eigen analysis of some data |
ReferenceFrame3D | A reference frame in 3D |
Reflection3D | Reflect about a plane in 3D |
Rotation2D | Represent a rotation in 2D space |
Rotation3D | 3D rotation class |
Segment3D | Simple implementation of segments in 3D |
SparseGrid3D | A sparse grid of values |
SparseGridStorageD | |
SparseUnboundedGrid3D | A sparse, infinite grid of values |
SparseUnboundedGridD | A sparse, infinite grid of values |
SphereD | Represent a sphere in D-dimensions |
SpherePatch3D | A sphere patch is defined as all points above the plane and on the sphere |
SphericalVector3D | Class to represent a 3D point in spherical coordinates |
Torus3D | Represent a torus in 3D |
Transformation2D | Simple 2D transformation class |
Transformation3D | Simple 3D transformation class |
Triangle3D | Represent a triangle in 3D |
UnboundedGridRangeD | |
UnitSimplexBaseD | Base class for a unit simplex embedded in D-dimensional real space |
UnitSimplexD | Represent a unit simplex embedded in D-dimensional real space |
UnitSimplexD<-1 > | Represent a unit simplex embedded in d-dimensional real space |
VectorBaseD | A Cartesian vector in D-dimensions |
VectorD | A Cartesian vector in D-dimensions |
VectorKDMetric | The base class for a metric on VectorKDs |
atom | Functionality for loading, creating, manipulating and scoring atomic structures |
AllMol2Selector | Read all atoms |
AllPDBSelector | Defines a selector that will pick every ATOM and HETATM record |
AndPDBSelector | Select atoms which are selected by both selectors |
Angle | A particle that describes an angle between three particles |
AngleSingletonScore | Score the angle based on a UnaryFunction, |
AngularVelocity | A particle with angular velocity |
Atom | A decorator for a particle representing an atom |
ATOMPDBSelector | Select all non-alternative ATOM records |
AtomType | The type of an atom |
AtomTypePDBSelector | Select all atoms of the given types |
BackbonePDBSelector | Select all backbone (N,CA,C,O) ATOM records |
BerendsenThermostatOptimizerState | Maintains temperature during molecular dynamics |
Bond | A decorator for wrapping a particle representing a molecular bond |
Bonded | A decorator for a particle which has bonds |
BondedPairFilter | A filter for bonds |
BondEndpointsRefiner | Return the endpoints of a bond |
BondGeometry | Display a Bond particle as a segment |
BondGraph | Represent a bond graph as a boost graph |
BondPairContainer | A container that returns pairs of the endpoints of the bonds |
BondsGeometry | Display an IMP::SingletonContainer of Bond particles as segments |
BondSingletonScore | Score the bond based on a UnaryFunction, |
BrownianDynamics | Simple Brownian dynamics simulator |
BrownianDynamicsTAMD | Simple Brownian dynamics simulator |
CAAngleRestraint | Angle restraint between three residues in CA-only representation |
CADihedralRestraint | Dihedral restraint between five residues in CA-only representation |
CAlphaPDBSelector | Select all CA ATOM records |
CBetaPDBSelector | Select all CB ATOM records |
CenterOfMass | A particle that is the center of mass of other particles |
Chain | Store info for a chain of a protein |
ChainPDBSelector | Select all ATOM and HETATM records with the given chain ids |
ChainType | The type for a chain |
Charged | A decorator for a point particle that has an electrostatic charge |
CHARMMAtom | A decorator for an atom that has a defined CHARMM type |
CHARMMAtomTopology | A single atom in a CHARMM topology |
CHARMMBondEndpoint | The end of a bond, angle, dihedral, improper, or internal coordinate |
CHARMMBondParameters | The parameters for a CHARMM bond or angle |
CHARMMConnection | A connection (bond, angle, dihedral) between some number of endpoints |
CHARMMDihedralParameters | The parameters for a CHARMM dihedral or improper |
CHARMMIdealResidueTopology | The ideal topology of a single residue |
CHARMMInternalCoordinate | A geometric relationship between four atoms |
CHARMMParameters | CHARMM force field parameters |
CHARMMPatch | A CHARMM patch residue |
CHARMMResidueTopology | The topology of a single residue in a model |
CHARMMResidueTopologyBase | Base class for all CHARMM residue-based topology |
CHARMMSegmentTopology | The topology of a single CHARMM segment in a model |
CHARMMStereochemistryRestraint | Enforce CHARMM stereochemistry on the given Hierarchy |
CHARMMTopology | The topology of a complete CHARMM model |
Copy | A decorator for keeping track of copies of a molecule |
CoulombPairScore | Coulomb (electrostatic) score between a pair of particles |
CoverBond | Cover a bond with a sphere |
CPDBSelector | Select all C (not CA or CB) ATOM records |
Diffusion | A decorator for a diffusing particle with a diffusion coefficient |
Dihedral | A particle that describes a dihedral angle between four particles |
DihedralSingletonScore | Score the dihedral angle |
Domain | A decorator to associate a particle with a part of a protein |
DopePairScore | Score pair of atoms based on DOPE |
ElementTable | |
EzRestraint | Ez Potential restraint |
ForceFieldParameters | Storage and access to force field |
Bond | |
ForceSwitch | Smooth interaction scores by switching the derivatives (force switch) |
Fragment | A decorator to associate a particle with a part of a protein/DNA/RNA |
HelixRestraint | Restraint a set of residues to use ideal helix dihedrals and bonds |
HierarchiesGeometry | Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls |
Hierarchy | The standard decorator for manipulating molecular structures |
HierarchyGeometry | Display an IMP::atom::Hierarchy particle as balls |
HydrogenPDBSelector | Select all hydrogen ATOM and HETATM records |
ImproperSingletonScore | Score the improper dihedral based on a UnaryFunction, |
LangevinThermostatOptimizerState | Maintains temperature during molecular dynamics |
LennardJones | A decorator for a particle that has a Lennard-Jones potential well |
LennardJonesPairScore | Lennard-Jones score between a pair of particles |
LinearVelocity | A particle with linear (XYZ) velocity |
LoopStatisticalPairScore | Score atoms based on the Fiser/Melo loop modeling statistical potential |
Mass | Add mass to a particle |
Mol2Selector | A base class for choosing which Mol2 atoms to read |
MolecularDynamics | Simple molecular dynamics simulator |
Molecule | A decorator for a molecule |
NonAlternativePDBSelector | Select all ATOM and HETATM records which are not alternatives |
NonHydrogenMol2Selector | Defines a selector that will pick only non-hydrogen atoms |
NonHydrogenPDBSelector | Select non hydrogen atoms |
NonWaterNonHydrogenPDBSelector | Select non water and non hydrogen atoms |
NonWaterPDBSelector | Select all non-water non-alternative ATOM and HETATM records |
NotPDBSelector | Select atoms which are not selected by a given selector |
NPDBSelector | Select all N ATOM records |
OrientedSoapPairScore | Score a pair of atoms using an orientation-dependent SOAP score |
OrPDBSelector | Select atoms which are selected by either or both selectors |
PDBRecord | Represent a single ATOM/HETATM "line" in PDB or mmCIF format |
PDBSelector | Select which atoms to read from a PDB file |
PPDBSelector | Select all P (= phosphate) ATOM records |
ProteinLigandAtomPairScore | |
ProteinLigandRestraint | Score a pair of molecules |
RemoveRigidMotionOptimizerState | Removes rigid translation and rotation from the particles |
RemoveTranslationOptimizerState | Removes rigid translation from the particles |
Representation | A decorator for a representation |
Residue | A decorator for a residue |
ResidueType | The type for a residue |
ResidueTypePDBSelector | Select all atoms in residues of the given types |
RigidBodyDiffusion | |
SameResiduePairFilter | |
SecondaryStructureResidue | A decorator for a residue with probability of secondary structure |
Selection | Select hierarchy particles identified by the biological name |
SelectionGeometry | Display a Selection |
Simulator | The base class for simulators |
SmoothingFunction | Base class for smoothing nonbonded interactions as a function of distance |
SoapPairFilter | Filter atom pairs for SOAP |
State | Associate an integer "state" index with a hierarchy node |
StereochemistryPairFilter | A filter that excludes bonds, angles and dihedrals |
StructureSource | Store strings describing the source of this structure fragment |
TAMDCentroid | |
TAMDParticle | |
VelocityScalingOptimizerState | Maintains temperature during molecular dynamics by velocity scaling |
WaterPDBSelector | Select all non-water ATOM and HETATM records |
WritePDBOptimizerState | |
XorPDBSelector | Select atoms which are selected by either selector but not both |
bayesianem | Restraints for handling electron microscopy maps |
restraint | |
GaussianEMRestraintWrapper | Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) |
GaussianEMRestraint | Creates a restraint between two Gaussian Mixture Models, "model" and "density" |
benchmark | Support for developing and analyzing benchmarks of IMP code |
Profiler | |
cgal | Make CGAL functionality available to IMP |
cnmultifit | Generate cyclic atomic structures using cryo-electron microscopy data |
AlignSymmetric | A class for fast alignment of a cyclic model to its density |
CnSymmAxisDetector | Detect cn symmetry in proteins and density maps |
MolCnSymmAxisDetector | Molecule symmetry detector |
container | Various classes to hold sets of particles |
AllBipartitePairContainer | |
AllPairContainer | Return all unordered pairs of particles taken from the SingletonContainer |
CloseBipartitePairContainer | Return all spatially-proximal 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 contains the Pair |
InContainerQuadFilter | A filter which returns true if a container contains the Quad |
InContainerSingletonFilter | A filter which returns true if a container contains the Singleton |
InContainerTripletFilter | A filter which returns true if a container contains 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 | Return true (1) if all members of the tuple are the same |
AllSameQuadPredicate | Return true (1) if all members of the tuple are the same |
AllSameSingletonPredicate | Return true (1) if all members of the tuple are the same |
AllSameTripletPredicate | Return true (1) if all members of the tuple are the same |
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 | Set a particle to be the centroid of the refined particles |
ChecksScoreState | Turn checks on with a given probability each evaluate call |
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 |
ClusterProvenance | Track creation of a system fragment from clustering |
CoinFlipPairPredicate | Return true (1) with a fixed probability |
CoinFlipQuadPredicate | Return true (1) with a fixed probability |
CoinFlipSingletonPredicate | Return true (1) with a fixed probability |
CoinFlipTripletPredicate | Return true (1) with a fixed probability |
CombineProvenance | Track creation of a system fragment by combination |
ConjugateGradients | Simple conjugate gradients optimizer |
ConnectivityRestraint | Ensure that a set of particles remains connected with one another |
ConstantPairPredicate | Always return a constant value |
ConstantQuadPredicate | Always return a constant value |
ConstantRestraint | Return a constant value |
ConstantSingletonPredicate | Always return a constant value |
ConstantTripletPredicate | Always return a constant value |
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 | Helper class for creating an IMP object storing some data |
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 |
Direction | A decorator for a particle that represents a direction in 3D |
DirectionAngle | A decorator for an angle between two directions |
DirectionMover | Modify a direction |
DistancePairScore | Score a pair of particles based on the distance between their centers |
DistanceRestraint | Distance restraint between two particles |
EdgePairGeometry | Display a segment connecting a pair of particles |
EdgePairsGeometry | Display a segment for each pair in a IMP::PairContainer |
ExcludedVolumeRestraint | Prevent a set of particles and rigid bodies from inter-penetrating |
FilterProvenance | Track creation of a system fragment by filtering |
FixedRefiner | The refiner can refine any particle by returning a fixed set |
Gaussian | |
GenericAttributeSingletonScore | Apply a function to an attribute |
GenericBoundingBox3DSingletonScore | |
GenericBoundingSphere3DSingletonScore | Score XYZ or XYZR particles based on how far outside a sphere 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 | Score distance between two particle centers using a harmonic function |
HarmonicLowerBound | Lower bound harmonic function (non-zero when feature < mean) |
HarmonicSphereDistancePairScore | A harmonic score on the distance between two spheres |
HarmonicSurfaceDepthPairScore | A harmonic score on the depth of a sphere's surface below a surface |
HarmonicSurfaceDistancePairScore | A harmonic score on the distance between a surface and a sphere surface |
HarmonicSurfaceHeightPairScore | A harmonic score on the height of a sphere's surface above a surface |
HarmonicUpperBound | Upper bound harmonic function (non-zero when feature > mean) |
HarmonicUpperBoundSphereDiameterPairScore | A harmonic upper bound on the diameter of the span of two spheres |
HarmonicUpperBoundSphereDistancePairScore | A harmonic upper bound on the distance between two spheres |
HarmonicWell | A well with harmonic barriers |
Hierarchy | A decorator for helping deal with a generalized hierarchy |
HierarchyCounter | A simple functor to count the number of particles in a hierarchy |
HierarchyTraits | Define the type for a type of hierarchy |
HierarchyVisitor | A visitor for traversal of a hierarchy |
InBoundingBox3DSingletonPredicate | Return 1 if the XYZ is in the bounding box, 0 otherwise |
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 |
LogNormalMover | Modify a set of continuous variables using a log-normal distribution |
MCCGSampler | A simple sampler |
MinimumRestraint | Score based on the minimum scoring members of a set of restraints |
ModifierVisitor | A visitor which applies a modifier to each Particle in a hierarchy |
MonteCarlo | A Monte Carlo optimizer |
MonteCarloMover | A base class for classes which perturb particles |
MonteCarloMoverResult | Return value of the MonteCarloMover::propose() function |
MonteCarloWithBasinHopping | This variant of Monte Carlo uses basis hopping |
MonteCarloWithLocalOptimization | This variant of Monte Carlo that relaxes after each move |
MoveStatisticsScoreState | Keep track of statistics about how particles move |
MSConnectivityRestraint | Ensure that a set of particles remains connected with one another |
MultipleBinormalRestraint | Modeller-style multiple binormal (phi/psi) restraint |
NearestNeighborsClosePairsFinder | Find all nearby pairs using the algebra::NearestNeighbor code |
NeighborsTable | |
NonRigidMember | A decorator for a particle that is part of a rigid body but not rigid |
NormalizedSphereDistancePairScore | A score on the normalized distance between the surfaces of two spheres |
NormalMover | Modify a set of continuous variables using a normal distribution |
OpenCubicSpline | An OpenCubicSpline |
OrderedTypePairPredicate | Return a unique predicate value for each ordered set of ParticleTypes |
OrderedTypeQuadPredicate | Return a unique predicate value for each ordered set of ParticleTypes |
OrderedTypeSingletonPredicate | Return a unique predicate value for each ordered set of ParticleTypes |
OrderedTypeTripletPredicate | Return a unique predicate value for each ordered set of ParticleTypes |
PairConstraint | Apply a PairFunction to a Pair |
PairRestraint | Applies a PairScore to a Pair |
PredicateSingletonScore | |
Provenance | Track how parts of the system were created |
Provenanced | Tag part of the system to track how it was created |
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 | Create a scoring function on a list of restraints |
RigidBody | A decorator for a rigid body |
RigidBodyAnglePairScore | Score on the crossing angle between two rigid bodies |
RigidBodyDerivativeGeometry | |
RigidBodyDerivativesGeometry | |
RigidBodyDistancePairScore | Accelerated computation of the distance between two rigid bodies |
RigidBodyFrameGeometry | |
RigidBodyFramesGeometry | |
RigidBodyHierarchyGeometry | |
RigidBodyMember | A member of a rigid body, it has internal (local) coordinates |
RigidBodyMover | Modify the transformation of a rigid body |
RigidBodyTorque | |
RigidBodyTunneler | Modify the transformation of a rigid body |
RigidBodyUmbrella | Umbrella-like restraint for rigid bodies |
RigidClosePairsFinder | Perform more efficient close pair finding when rigid bodies are involved |
RigidMember | |
SampleProvenance | Track creation of a system fragment from sampling |
ScriptProvenance | Track creation of a system fragment from running a script |
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's surface below a surface |
SoftSuperSurfacePairScore | A harmonic score that keeps a sphere's surface above a surface |
SoftwareProvenance | Track creation of a system fragment from running some software |
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 |
StructureProvenance | Track creation of a system fragment from a PDB file |
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's surface below a surface |
SurfaceDistancePairScore | A score on the distance between a surface and a sphere surface |
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's surface above a surface |
SurfaceMover | Modify a surface orientation |
SurfaceSymmetryConstraint | Constrain orientation of surfaces with respect to rigid bodies |
SurfaceTetheredChain | Score on surface-to-end distance of chain tethered to impenetrable surface |
TableRefiner | A lookup based particle refiner |
Transform | Apply a transformation to a passed particle |
TransformationAndReflectionSymmetry | Set the coordinates of a particle to be a transformed version of a reference |
TransformationSymmetry | Set the coordinates of a particle to be a transformed version of a reference |
TransformationSymmetryMover | Modify the given TransformationSymmetry |
TransformedDistancePairScore | Apply a function to the distance between two particles after transforming the second |
TripletConstraint | Apply a TripletFunction to a Triplet |
TripletRestraint | Applies a TripletScore to a Triplet |
TruncatedHarmonic | A function that is harmonic over an bounded interval |
Typed | A decorator for classifying particles in your system |
TypedPairScore | Delegate to another PairScore depending on particle types |
UnorderedTypePairPredicate | Return a unique predicate value for each unordered set of ParticleTypes |
UnorderedTypeQuadPredicate | Return a unique predicate value for each unordered set of ParticleTypes |
UnorderedTypeSingletonPredicate | Return a unique predicate value for each unordered set of ParticleTypes |
UnorderedTypeTripletPredicate | Return a unique predicate value for each unordered set of ParticleTypes |
VolumeRestraint | A restraint that prevents spheres from inter-penetrating |
WeightedDerivativesToRefined | Copy the derivatives from a coarse particle to its refined particles |
WeightedSphereDistancePairScore | A score on a weighted distance between the surfaces of two spheres |
WeightedSum | Weighted sum of unary functions |
WeightedSumOfExponential | Negative logarithm of weighted sum of negative exponential of unary functions |
WriteRestraintScoresOptimizerState | Write the scores of the passed restraints to a file during optimization |
XYZ | A decorator for a particle with x,y,z coordinates |
XYZDerivativeGeometry | |
XYZDerivativesGeometry | |
XYZR | A decorator for a particle with x,y,z coordinates and a radius |
XYZRGeometry | Display an IMP::core::XYZR particle as a ball |
XYZRsGeometry | Display an IMP::SingletonContainer of IMP::core::XYZR particles as balls |
display | Output IMP model data in various file formats |
BoundingBoxGeometry | Display a bounding box |
Color | Represent an RGB color |
Colored | A particle with a color |
CylinderGeometry | Display a cylinder |
EllipsoidGeometry | Display a ellipsoid |
FilterGeometry | Remove geometry which is not above a plane |
Geometry | The base class for geometry |
GeometryProcessor | Provide a standard geometry processing framework |
GeometrySet | Group of set of geometric elements |
IsosurfaceGeometry | Display an isosurface of a density map |
LabelGeometry | A text label for a ball in space |
PairGeometry | A base class for geometry contained in particles |
PairsGeometry | A base class for geometry from a set of particles |
PivyWriter | |
PlaneGeometry | Display a plane as truncated to a bounding box |
PointGeometry | Display a point |
PolygonGeometry | |
PymolWriter | Write a CGO file with the geometry |
ReferenceFrameGeometry | Display a reference frame |
RestraintGeometry | Try to draw some stuff for a generic restraint |
RestraintSetGeometry | Geometry for a whole set of restraints |
SegmentGeometry | Display a segment |
SingletonGeometry | A base class for geometry contained in particles |
SingletonsGeometry | A base class for geometry from a set of particles |
SkinSurfaceGeometry | Display an isosurface of a density map |
SphereGeometry | Display a sphere |
SurfaceMeshGeometry | Display a surface mesh |
TextWriter | |
TriangleGeometry | Display a triangle |
WriteOptimizerState | |
Writer | Base class for writing geometry to a file |
WriterAdaptor | |
domino | Divide-and-conquer inferential optimization in discrete space |
Assignment | Store a configuration of a subset |
AssignmentContainer | The base class for containers of assignments |
AssignmentsTable | |
BranchAndBoundAssignmentsTable | |
BranchAndBoundSampler | Sample best solutions using BranchAndBound |
CappedAssignmentContainer | Store no more than a max number of states |
CompoundStates | |
DependencyScoreState | Add a dependency to the dependency graph |
DiscreteSampler | A base class for discrete samplers in Domino2 |
DisjointSetsSubsetFilterTable | A base class |
DominoSampler | Sample best solutions using Domino |
EqualitySubsetFilterTable | Do not allow two particles to be in the same state |
EquivalenceAndExclusionSubsetFilterTable | Define sets of equivalent and exclusive particles |
EquivalenceSubsetFilterTable | Define sets of equivalent particles |
ExclusionSubsetFilterTable | Do not allow two particles to be in the same state |
HeapAssignmentContainer | Store a set of k top scoring assignments |
IndexStates | |
ListAssignmentContainer | Simple storage of a set of Assignments |
ListAssignmentsTable | |
ListSubsetFilterTable | Maintain an explicit list of what states each particle is allowed to have |
MinimumRestraintScoreSubsetFilterTable | Filter a configuration of the subset using the Model thresholds |
NestedRigidBodyStates | |
Order | Store a persistent ordering for a subset based on the list |
PackedAssignmentContainer | Store assignments in a compact form in memory |
PairListSubsetFilterTable | |
ParticlesAdaptor | |
ParticleStates | |
ParticleStatesTable | |
PermutationStates | |
ProbabilisticSubsetFilterTable | |
RangeViewAssignmentContainer | Expose a range [begin, end) of an inner assignment container to consumers |
ReadAssignmentContainer | Read the assignments from binary data on disk |
ReadHDF5AssignmentContainer | Store the assignments in an HDF5DataSet |
RecursiveAssignmentsTable | |
RecursiveStates | |
RestraintCache | |
RestraintScoreSubsetFilterTable | Filter a configuration of the subset using the Model thresholds |
RigidBodyStates | |
SampleAssignmentContainer | Store a list of k assignments chosen from all those added to this table |
SimpleAssignmentsTable | |
Slice | Store a subset of a subset or assignment |
Subset | Represent a subset of the particles being optimized |
SubsetFilter | |
SubsetFilterTable | |
WriteAssignmentContainer | Store the assignments on disk as binary data |
WriteHDF5AssignmentContainer | Store the assignments in an HDF5DataSet |
XYZStates | |
em | Basic utilities for handling cryo-electron microscopy 3D density maps |
CoarseCCatIntervals | Cross correlation coefficient calculator |
CoarseConvolution | Convolutes two grids |
DensityFillingRestraint | Calculate score based on fit to EM map |
DensityHeader | |
DensityMap | Class for handling density maps |
DistanceMask | Calculates and stores a distance mask |
EMReaderWriter | |
EnvelopeFitRestraint | A restraint for envelope-based scoring of particles in the density map |
EnvelopePenetrationRestraint | Calculate score based on fit to EM map |
EnvelopeScore | Class for envelope based scoring using MapDistanceTransform |
FitRestraint | Calculate score based on fit to EM map |
FitRestraintBayesEM3D | Calculate score based on fit to EM map |
FittingSolutions | A simple list of fitting solutions |
HighDensityEmbedding | |
ImageHeader | Class to deal with the header of Electron Microscopy images in IMP |
KernelParameters | Calculates and stores Gaussian kernel parameters |
MapDistanceTransform | Class for getting the distance from the map envelope |
MapReaderWriter | The base class to handle reading and writing of density maps |
MRCReaderWriter | |
PCAAligner | Fast alignment of points to a density map using principal components |
PCAFitRestraint | Calculate score based on fit to EM map |
RadiusDependentDistanceMask | |
SampledDensityMap | Class for sampling a density map from particles |
SpiderHeader | Header for Spider images. IMP-EM is designed to be compatible with it |
SpiderMapReaderWriter | Class to read EM maps (3D) in Spider and Xmipp formats |
SurfaceShellDensityMap | The class represents a molecule as shells of distance from the surface |
Voxel | |
XplorReaderWriter | |
em2d | Restraints using electron microscopy 2D images (class averages) |
AverageDistanceLinkage | Functor for hierarchical clustering based on average-linkage |
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 | |
GridStates | |
HasHigherCCC | Comparison by value of the ccc |
HasLowerScore | Compare two classes that return a score |
Image | 2D Electron Microscopy images in IMP |
ImageReaderWriter | Virtual class for reader/writers of images |
IntsOrder | |
JPGImageReaderWriter | Class to read and write EM images in JPG format |
LessPairBySecond | Comparison of pairs by checking the second element |
MasksManager | Management of projection masks |
MatchTemplateResult | |
MeanAbsoluteDifference | Score based on the mean of the absolute difference |
ParticlesDummyRestraint | Dummy restraint for a set of particles. Same use as DummyRestraint |
PCAFitRestraint | Fast scoring of Particles against electron microscopy class averages |
PolarResamplingParameters | |
ProjectingOptions | Parameters given as options to the get_projections() functions |
ProjectingParameters | Parameters needed for the core projection routine |
ProjectionFinder | Class to perform registration of model projections to images |
ProjectionMask | |
ProjectionParameters | |
ProjectionParametersScoreState | |
ProjectionStates | |
RegistrationResult | Class to manage registration results |
RelativePositionMover | |
RigidBodiesImageFitRestraint | Fit rigid bodies to an image |
ScoreFunction | Base class for all scoring functions related to em2d |
SegmentationParameters | Class to provide all the parameters to the segmentation function |
SingleLinkage | Functor for hierarchical clustering based on single linkage |
SpiderImageReaderWriter | |
TIFFImageReaderWriter | Management of reading/writing TIFF images |
EMageFit | Build assembly models consistent with EM images (class averages) |
argminmax | Utility functions to extract min/max from the inputs |
buildxlinks | Utility functions to handle cross links |
DockOrder | Compute the order of the docking experiments |
InitialDockingFromXlinks | Puts two subunits together using the Xlinkins restraints |
Xlink | Class defining a cross-link |
XlinksDict | Description of crosslinking restraints as a python dictionary |
csv_related | Utility functions to handle CSV files |
database | Utility functions to manage SQL databases with sqlite3 |
Database2 | Class to manage a SQL database built with sqlite3 |
domino_model | Classes to manage a model using DOMINO |
DominoModel | Management of a model using DOMINO |
imp_general | Utility functions that are supposedly not EMageFit-specific |
alignments | Utility functions to handle alignments |
comparisons | Utility functions for comparisons |
io | Utility functions to handle IO |
ReferenceFrameToText | Transform a IMP reference frame into parseable output |
Transformation3DToText | Parseable output for a IMP Transformation3D |
movement | Utility functions to handle movement |
representation | Utility functions to handle representation |
monte_carlo | Classes for Monte Carlo sampling using rigid body relative moves |
MonteCarloRelativeMoves | Class to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies |
restraints | Utility functions to handle restraints |
sampling | Utility functions to handle sampling |
solutions_io | Utility functions to store and retrieve solution information |
HeapRecord | The heapq algorithm is a min-heap |
ResultsDB | Class for managing the results of the experiments |
utility | Utility functions |
example | Example module |
ExampleComplexRestraint | Restrain the diameter of a set of points |
ExampleConstraint | A trivial constraint that just increments a counter |
ExampleDecorator | A simple decorator which adds a name to a particle |
ExampleObject | An example simple object which is reference counted |
ExamplePairScore | Apply a harmonic to the distance between two particles |
ExampleRestraint | Restrain a particle to be in the x,y plane |
ExampleSingletonModifier | An example singleton modifier |
ExampleSubsetFilterTable | |
ExampleTemplateClassD | A line segment templated on the dimension |
ExampleUnaryFunction | A simple unary function |
PythonExampleConstraint | An example Constraint written in Python |
PythonExamplePairScore | An example PairScore written in Python |
PythonExampleRestraint | An example restraint written in Python |
PythonExampleSingletonModifier | An example SingletonModifier written in Python |
PythonExampleUnaryFunction | An example UnaryFunction written in Python |
foxs | Determine small angle X-ray (SAXS) profiles |
gsl | Several general purpose optimizers from the GNU Scientific Library (GSL) |
ConjugateGradients | A conjugate gradients optimizer taken from GSL |
GSLOptimizer | A base class for GSL-based optimizers |
QuasiNewton | A quasi-Newton optimizer taken from GSL |
Simplex | A simplex optimizer taken from GSL |
integrative_docking | Pairwise docking incorporating additional data |
isd | Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD) |
Analysis | |
Analysis | Class that produces analysis-related output, and is able to parse the output of a file produced by the Statistics class |
demux_trajs | |
Demuxer | Uses column to demux a replica trajectory |
LogHolder | Manages information on a given simulation |
Entry | Classes to handle ISD statistics files |
Entry | The entry class represents a column in the statistics file |
gmm_tools | Tools for handling Gaussian Mixture Models |
History | Classes to store output from replicas |
History | Class that contains the output of one replica, used by the Analysis class |
shared_functions | |
sfo_common | Nonspecific methods used across all shared function objects |
Statistics | |
Statistics | Statistics gathering and printing class for ISD gibbs sampling |
TALOSReader | Classes to handle TALOS files or folders |
TALOSReader | Reads a TALOS file, or a TALOS folder, and stores the data |
TBLReader | Classes to handle TBL files |
TuneRex | |
CvEstimator | When created, estimates the heat capacity from the energies or from the indicator functions using the specified method |
utils | Miscellaneous utilities |
Pipe | Implements a FIFO pipe that merges lists (see self.put) |
AmbiguousNOERestraint | Ambiguous NOE distance restraint between a number of pairs of particles |
AmbiguousRestraint | Apply an ambiguous restraint by computing the d-norm |
AtomicCrossLinkMSRestraint | Restrain atom pairs based on a set of crosslinks |
BivariateFunction | Base class for functions of two variables |
Covariance1DFunction | Covariance function |
CrossLinkData | CrossLinkData |
CrossLinkMSRestraint | A restraint for ambiguous cross-linking MS data and multiple state approach |
CysteineCrossLinkData | CysteineCrossLinkData |
CysteineCrossLinkRestraint | A restraint for cysteine cross-linking data |
Distribution | Base class for all distributions, provided for common inheritance |
FNormal | FNormal |
FretData | Auxiliary class for FRET_R restraint |
FretRestraint | |
FStudentT | Joint Student's t-distribution of Function |
GammaPrior | Uniform distribution with harmonic boundaries |
GaussianAnchorEMRestraint | Restraint between two sets of anchor points "model" and "EM density" |
GaussianEMRestraint | Restraint between two Gaussian Mixture Models, "model" and "density" |
GaussianProcessInterpolation | GaussianProcessInterpolation |
GaussianProcessInterpolationRestraint | Gaussian process restraint |
GaussianRestraint | Normal probability distribution as a restraint |
GeneralizedGuinierPorodFunction | 1D mean function for SAS data |
HybridMonteCarlo | Hybrid Monte Carlo optimizer |
ISDRestraint | A base class for ISD Restraints |
JeffreysRestraint | |
Linear1DFunction | Linear one-dimensional function |
LognormalAmbiguousRestraint | |
LognormalRestraint | Normal probability distribution as a restraint |
LogWrapper | Calculate the -Log of a list of restraints |
MarginalHBondRestraint | Apply a lognormal distance restraint between two particles |
MarginalNOERestraint | Apply an NOE distance restraint between two particles |
MolecularDynamics | Molecular dynamics optimizer on 1-D and 3-D particles |
MolecularDynamicsMover | Modify a set of continuous variables using a MD simulation |
MultivariateFNormalSufficient | MultivariateFNormalSufficient |
NOERestraint | Apply an NOE distance restraint between two particles |
NormalSigmaPCRestraint | A Penalized Complexity prior on sigma of a normal distribution |
Nuisance | Add nuisance parameter to particle |
OneDimensionalDistribution | Base class for distributions that are passed a single random variable |
OneDimensionalSufficientDistribution | Base class for single-variate distributions that cache sufficient statistics |
PenalizedComplexityPrior | Penalized complexity prior |
RepulsiveDistancePairScore | A repulsive potential on the distance between two atoms |
ResidueProteinProximityRestraint | |
Scale | Add scale parameter to particle |
StudentTRestraint | A Student-t distribution restraint |
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 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 |
DihedralMover | Modify a set of joints using a normal distribution |
DirectionalDOF | |
DOF | Representation 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 |
FibrilSampler | Simultaneous sampling of diheral angles and fibril symmetry operations |
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 | |
RevoluteJoint | Abstract class for all revolute joints |
RevoluteJointMover | Modify a set of joints using a normal distribution |
RRT | Simple implementation of the Rapidly-exploring Random Trees algorithm |
RRTNode | Simple RRT node implementation |
TransformationJoint | |
UniformBackboneSampler | Sample uniformly over a set of backbone dihedral joints |
kmeans | Interface to the GPL k-means clustering library |
KMeans | |
misc | Miscellaneous functionality that is not expected to be used by many IMP users |
CommonEndpointPairFilter | Return true for any pair of bonds sharing an endpoint |
CustomXYZR | A decorator for a particle with x,y,z coordinates and a radius |
DecayPairContainerOptimizerState | Maintain a pair container with a decaying list of pairs |
FreelyJointedChain | Score on end-to-end distance of freely jointed chain |
LogPairScore | Track the pairs of particles passed |
LowestRefinedPairScore | Refine both particles with the refiner and score on the lowest pair |
MetricClosePairsFinder | |
SoftCylinderPairScore | Apply a function to the distance between the cylinders defined by two bonds |
StateAdaptor | Allow OptimizerStates to be used as ScoreStates |
WormLikeChain | Worm-like-chain energy for polymer chains |
mmcif | Support for output of models in mmCIF format |
data | Classes to represent data structures used in mmCIF |
metadata | Classes to extract metadata for various input files |
restraint | Map IMP restraints to mmCIF categories |
util | Utility functions for IMP.mmcif |
Writer | Convert one or more IMP Models and/or RMF frames to mmCIF or BinaryCIF |
modeller | Interface to the Modeller comparative modeling package |
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 |
mpi | Code that uses the MPI parallel library |
ReplicaExchange | A class to implement Hamiltonian Replica Exchange |
multi_state | Functionality for handling multi-state models |
CompareMultiStateModels | Utility class to help sort MultiStateModel objects |
EnsembleGenerator | Enumeration of an ensemble of good scoring MultiStateModels |
MultiStateModel | Keep track of multiple states |
MultiStateModelScore | Base class for MultiStateModel scoring classes |
SAXSMultiCombinationScore | |
SAXSMultiStateModelScore | |
multifit | Fitting atomic structures into a cryo-electron microscopy density map |
cluster | |
AlignmentClustering | Clusters assembly models |
transforms | |
ChimeraFormatter | Each line in 'chimera' format lists the transformation index, the cross correlation score, and then the transformation for each component, as a rotation matrix (row-major order) and a translation in angstroms |
DockRefFormatter | Each line in 'dockref' format lists the transformation for each component, as a set of three Euler angles (in radians about the fixed x, y and z axes) and a translation in angstroms |
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 |
nestor | Nested sampling-based optimization of representation |
npc | Restraints designed for modeling the Nuclear Pore Complex (NPC) |
AssemblySymmetryByDihedralRestraint | Restrain two interparticle dihedrals to be the same |
AssemblySymmetryByDistanceRestraint | Restrain two interparticle distances to be the same |
CompositeRestraint | Score a set of particles that form a composite |
MembraneExclusionRestraint | Try to keep particles away from a membrane |
MembraneSurfaceLocationConditionalRestraint | Try to keep one set of particles localized on a membrane surface |
MembraneSurfaceLocationRestraint | Try to keep particles localized on a membrane surface |
MinimumSphereDistancePairScore | Apply a UnaryFunction to the minimum transformed sphere-sphere distance |
OverallPositionRestraint | Restrain particle to a specific position |
PerinuclearVolumeLocationRestraint | Try to keep particles on the perinuclear side of a membrane |
PoreSideVolumeLocationRestraint | Try to keep particles on the pore side of a membrane |
ProteinChainRestraint | Try to keep particle surfaces in contact in a chain |
ProteinContactRestraint | Try to keep all particle surfaces in contact |
ProteinProximityRestraint | Restrain a set of particles to be proximate to each other |
SlabWithPore | |
SlabWithSphericalIndent | A decorator for a particle that represents a slab containing a spherical cap indent |
SlabWithSphericalIndentGeometry | |
SlabWithSphericalIndentMBMScore | |
SlabWithToroidalPore | |
SlabWithToroidalPoreGoPairScore | Apply a harmonic to the distance between a particle and the normal to toroidal membrane |
SlabWithToroidalPoreMBMScore | Apply harmonic walls to the distance between a particle and the normal to toroidal membrane |
SlabWithToroidalPoreWireGeometry | A decorator for a particle that represents a toroidal pore |
SphericalIndentSurfaceDepthPairScore | |
ToroidalPoreSurfaceDepthPairScore | Apply repulsive force to the distance between a particle and the normal to toroidal membrane |
XAxialPositionLowerRestraint | Restrain particles by their x coordinate |
XAxialPositionRestraint | Restrain particles by their x coordinate |
XAxialPositionUpperRestraint | Restrain particles by their x coordinate |
XYRadialPositionLowerRestraint | Restrain particles by their distance from the z axis in the xy plane |
XYRadialPositionRestraint | Restrain particles by their distance from the z axis in the xy plane |
XYRadialPositionUpperRestraint | Restrain particles by their distance from the z axis in the xy plane |
YAxialPositionLowerRestraint | Restrain particles by their y coordinate |
YAxialPositionRestraint | Restrain particles by their y coordinate |
YAxialPositionUpperRestraint | Restrain particles by their y coordinate |
ZAxialPositionLowerRestraint | Restrain particles by their z coordinate |
ZAxialPositionRestraint | Restrain particles by their z coordinate |
ZAxialPositionUpperRestraint | Restrain particles by their z coordinate |
npctransport | Simulation of transport through the Nuclear Pore Complex |
AnchorToCylidnricalPorePairScore | |
BipartitePairsStatisticsOptimizerState | |
BodyStatisticsOptimizerState | |
BrownianDynamicsTAMDWithSlabSupport | Simple Brownian dynamics simulator |
ChainStatisticsOptimizerState | |
ExcludeZRangeSingletonScore | Exclude particles from the given range of z coordinates |
FGChain | |
FunctorLinearInteractionPairScore | Score a pair of particles |
FunctorLinearSoftSpherePairScore | Score a pair of particles |
GlobalStatisticsOptimizerState | |
HarmonicSpringSingletonScore | |
HarmonicWellPairScore | |
HierarchyWithSitesLoadLink | Load sites data from an RMF file |
HierarchyWithSitesSaveLink | Save sites data to an RMF file |
LinearInteraction | |
LinearInteractionPairScore | |
EvaluationCache | |
LinearSoftSpherePairScore | |
LinearWellPairScore | |
ParticleFactory | Factory that produces diffusing particles with specified attributes |
ParticleTransportStatisticsOptimizerState | |
PoreRadiusSingletonScore | |
RelaxingSpring | A decorator for a spring particle connecting two diffusing particles |
Scoring | Scoring associated with a SimulationData object |
SimulationData | Store all parameters for a simulation |
SitesGeometry | |
SitesPairScore | Apply a function to the distance between two particles with a set of specific binding sites |
SitesPairScoreParameters | |
SlabWithCylindricalPore | |
SlabWithCylindricalPorePairScore | XXXX |
SlabWithCylindricalPoreWireGeometry | XXXX |
SlabWithPore | |
SlabWithToroidalPore | |
SlabWithToroidalPorePairScore | Score for a slab with a toroidal pore |
SlabWithToroidalPoreWireGeometry | XXXX |
Statistics | Statistics and order parameters about the simulations |
Transporting | A decorator for a particle transporting through a barrier |
TypedSitesGeometry | |
ZBiasSingletonScore | Score that biases particles to go down the Z axis |
parallel | Distribute IMP tasks to multiple processors or machines |
manager_communicator | Classes for communicating from the manager to workers |
ManagerCommunicator | For communicating from the manager to workers |
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 |
LocalWorker | A worker running on the same machine as the manager |
Manager | Manages workers and contexts |
NetworkError | Error raised if a problem occurs with the network |
NoMoreWorkersError | Error raised if all workers failed, so tasks cannot be run |
RemoteError | Error raised if a worker has an unhandled exception |
SGEPEWorkerArray | An array of workers in a Sun Grid Engine system parallel environment |
SGEQsubWorkerArray | An array of workers on a Sun Grid Engine system, started with 'qsub' |
Worker | Representation of a single worker |
WorkerArray | Representation of an array of workers |
pepdock | Initial peptide docking |
pmi | Python classes to represent, score, sample and analyze models |
alphabets | Mapping between FASTA one-letter codes and residue types |
ResidueAlphabet | Map between FASTA codes and residue types |
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 cross-links |
GetModelDensity | Compute mean density maps from structures |
Precision | A class to evaluate the precision of an ensemble |
RMSD | Compute the RMSD (without alignment) taking into account the copy ambiguity |
dof | Create movers and set up constraints for PMI objects |
DegreesOfFreedom | Simplify creation of constraints and movers for an IMP Hierarchy |
io | Utility classes and functions for reading and storing PMI files |
crosslink | Handles cross-link data sets |
CrossLinkDataBase | This class handles a cross-link dataset and do filtering operations, adding cross-links, merge datasets.. |
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 |
JaccardDistanceMatrix | This class allows to compute and plot the distance between datasets |
MapCrossLinkDataBaseOnStructure | This class maps a CrossLinkDataBase on a given structure and save an rmf file with color-coded cross-links |
ResiduePairListParser | A class to handle different styles of site pairs parsers |
TotalScoreOutput | A helper output for model evaluation |
macros | Protocols for sampling structures and analyzing them |
AnalysisReplicaExchange | This class contains analysis utilities to investigate ReplicaExchange results |
AnalysisReplicaExchange0 | A macro for running all the basic operations of analysis |
BuildSystem | A macro to build a IMP::pmi::topology::System based on a TopologyReader object |
ReplicaExchange | A macro to help setup and run replica exchange |
mmcif | Support for the mmCIF file format |
AsymUnit | A single asymmetric unit in the system |
Entity | A single entity in the system |
GMMParser | Extract metadata from an EM density GMM file |
ProtocolOutput | Class to encode a modeling protocol as mmCIF |
output | Classes for writing output files and processing them |
Cluster | A container for models organized into clusters |
DataEntry | A class to store data associated to a model |
Output | Class for easy writing of PDBs, RMFs, and stat files |
OutputStatistics | Collect statistics from ProcessOutput.get_fields() |
ProcessOutput | A class for reading stat files (either rmf or ascii v1 and v2) |
ProtocolOutput | Base class for capturing a modeling protocol |
RMFHierarchyHandler | Class to allow more advanced handling of RMF files |
StatHierarchyHandler | Class to link stat files to several rmf files |
plotting | |
topology | |
TopologyPlot | A class to read RMF files and make a network contact map |
restraints | Classes to handle different kinds of restraints |
basic | Some miscellaneous simple restraints |
BiStableDistanceRestraint | Distance restraint with bistable potential Authors: G |
CylinderRestraint | Restrain particles within (or outside) a cylinder |
DistanceRestraint | A simple distance restraint |
DistanceToPointRestraint | Anchor a particle to a specific coordinate |
ExternalBarrier | Keeps all structures inside a sphere |
MembraneRestraint | Restrain particles to be above, below, or inside a planar membrane |
ResidueProteinProximityRestraint | Restrain residue/residues to bind to unknown location in a target |
crosslinking | Restraints for handling cross-linking data |
AtomicCrossLinkMSRestraint | Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian |
CrossLinkingMassSpectrometryRestraint | Setup cross-link distance restraints from mass spectrometry data |
em | Restraints for handling electron microscopy maps |
GaussianEMRestraint | Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) |
em2d | Restraints for handling electron microscopy images |
ElectronMicroscopy2D | Fit particles against a set of class averages by principal components |
ElectronMicroscopy2D_FFT | FFT based image alignment, developed by Javier Velazquez-Muriel |
npc | Specialized restraints for modeling the Nuclear Pore Complex |
MembraneExclusionRestraint | Keep protein away from a half torus in the xy plane |
MembraneSurfaceLocationConditionalRestraint | Localize one protein on the surface of a half torus in the xy plane |
MembraneSurfaceLocationRestraint | Localize protein on the surface of a half torus in the xy plane |
XYRadialPositionLowerRestraint | Restrain a protein's distance from the z axis to above a lower bound |
XYRadialPositionRestraint | Restrain a protein's distance from the z axis to within a given range |
XYRadialPositionUpperRestraint | Restrain a protein's distance from the z axis to below an upper bound |
YAxialPositionLowerRestraint | Restrain a protein's y coordinate to above a lower bound |
YAxialPositionRestraint | Restrain a protein's y coordinate to within a given range |
YAxialPositionUpperRestraint | Restrain a protein's y coordinate to below an upper bound |
ZAxialPositionLowerRestraint | Restrain a protein's z coordinate to above a lower bound |
ZAxialPositionRestraint | Restrain a protein's z coordinate to within a given range |
ZAxialPositionUpperRestraint | Restrain a protein's z coordinate to below an upper bound |
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 cross-linking between multiple copies excluding between symmetric copies It allows name ambiguity |
CompositeRestraint | Handleparticles a list of particles compositeparticles is a list of list of particles |
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: sel1 = IMP.atom.Selection(root_hier, molecule="Rpb3", residue_indexes=range(1,100)) sel2 = IMP.atom.Selection(root_hier, molecule="Rpb4", residue_indexes=range(1,100)) cr=restraints.ConnectivityRestraint((sel1, sel2), label='CR1') cr.add_to_model() Multistate support =No 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") |
saxs | Restraints for handling small angle x-ray (SAXS) data |
SAXSISDRestraint | Basic SAXS restraint using ISD |
SAXSRestraint | Basic SAXS restraint |
stereochemistry | Restraints for keeping correct stereochemistry |
CharmmForceFieldRestraint | Enable CHARMM force field |
ConnectivityRestraint | Create 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 | 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 |
SymmetryRestraint | Create harmonic restraints between the reference and (transformed) clones |
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 |
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 |
Stopwatch | Collect timing information |
topology | Set of Python classes to create a multi-state, multi-resolution IMP hierarchy |
Molecule | Stores a named protein chain |
PDBSequences | Data structure for reading and storing sequence data from PDBs |
PMIMoleculeHierarchy | Extends the functionality of IMP.atom.Molecule |
Sequences | A dictionary-like wrapper for reading and storing sequence data |
State | Stores a list of Molecules all with the same State index |
System | Represent the root node of the global IMP.atom.Hierarchy |
TempResidue | Temporarily stores residue information, even without structure available |
TopologyReader | Automatically setup System and Degrees of Freedom with a formatted text file |
CompositeRestraint | A restraint for ambiguous cross-linking MS data and multiple state approach |
CrossLinkRestraintSet | A RestraintSet subclass to track cross-link metadata |
MembraneRestraint | Membrane Restraint |
MissingFileWarning | Warning for an expected, but missing, file |
ParameterWarning | Warning for probably incorrect input parameters |
Resolution | Add resolution to a particle |
StructureWarning | Warning related to handling of structures |
Symmetric | Add symmetric attribute to a particle |
TransformMover | Modify the transformation of a rigid body |
Uncertainty | Add uncertainty to a particle |
pmi1 | Legacy PMI1 module 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 |
Precision | A class to evaluate the precision of an ensemble |
RMSD | Compute the RMSD (without alignment) taking into account the copy ambiguity |
io | Utility classes and functions for reading and storing PMI files |
crosslink | Handles cross-link data sets |
CrossLinkDataBaseFromStructure | This class generates a CrossLinkDataBase from a given structure |
CrossLinkDataBaseKeywordsConverter | This class is needed to convert the keywords from a generic database to the standard ones |
FilterOperator | This class allows to create filter functions that can be passed to the CrossLinkDataBase in this way: |
FixedFormatParser | A class to handle different XL format with fixed format currently support ProXL |
JaccardDistanceMatrix | This class allows to compute and plot the distance between datasets |
MapCrossLinkDataBaseOnStructure | This class maps a CrossLinkDataBase on a given structure and save an rmf file with color-coded crosslinks |
ResiduePairListParser | A class to handle different styles of site pairs parsers |
utilities | Utility classes and functions for IO |
xltable | Tools to plot a contact map overlaid with cross-links |
XLTable | Class to read, analyze, and plot xlink data on contact maps Canonical way to read the data: 1) load sequences and name them 2) load coordinates for those sequences from PDB file 3) add crosslinks 4) create contact map 5) plot |
RMSDOutput | A helper output based on dist to initial coordinates |
TotalScoreOutput | A helper output for model evaluation |
macros | Protocols for sampling structures and analyzing them |
AnalysisReplicaExchange | This class contains analysis utilities to investigate ReplicaExchange results |
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 |
BuildModel1 | Building macro |
ReplicaExchange0 | A macro to help setup and run replica exchange |
metadata | Classes for attaching metadata to PMI objects |
mmcif | Support for the mmCIF file format |
AsymUnit | A single asymmetric unit in the system |
Entity | A single entity in the system |
ProtocolOutput | Class to encode a modeling protocol as mmCIF |
nonmaintained | Nonmaintained code |
nonmantained | |
CrossLinkMS | This class initializes a CrossLinkMS restraint and contains all useful information, such as the cross-link database, contained in self.pairs If restraint_file=None, it will proceed creating simulated data |
output | Classes for writing output files and processing them |
Cluster | A container for models organized into clusters |
DataEntry | A class to store data associated to a model |
Output | Class for easy writing of PDBs, RMFs, and stat files |
OutputStatistics | Collect statistics from ProcessOutput.get_fields() |
ProcessOutput | A class for reading stat files (either rmf or ascii v1 and v2) |
ProtocolOutput | Base class for capturing a modeling protocol |
RMFHierarchyHandler | Class to allow more advanced handling of RMF files |
StatHierarchyHandler | Class to link stat files to several rmf files |
plotting | |
topology | |
TopologyPlot | A class to read RMF files and make a network contact map |
representation | Representation of the system |
Representation | Set up the representation of all proteins and nucleic acid macromolecules |
restraints | Classes to handle different kinds of restraints |
basic | Some miscellaneous simple restraints |
BiStableDistanceRestraint | Python restraint with bistable potential Authors: G |
CylinderRestraint | PMI2 python restraint |
DistanceRestraint | A simple distance restraint |
DistanceToPointRestraint | Restraint for anchoring a particle to a specific coordinate |
ExternalBarrier | Restraint to keep all structures inside sphere |
crosslinking | Restraints for handling crosslinking data |
AtomicCrossLinkMSRestraint | Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes' theory of probability |
ConnectivityCrossLinkMS | This restraint allows ambiguous crosslinking between multiple copies it is a variant of the SimplifiedCrossLinkMS |
CrossLinkingMassSpectrometryRestraint | Setup cross-link distance restraints from mass spectrometry data |
crosslinking_new | Restraints for handling crosslinking data |
em | Restraints for handling electron microscopy maps |
CrossCorrelationRestraint | Fit particles to an EM map |
GaussianEMRestraint | Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) |
em2d | Restraints for handling electron microscopy images |
ElectronMicroscopy2D | Fit particles against a set of class averages by principal components |
ElectronMicroscopy2D_FFT | FFT based image alignment, developed by Javier Velazquez-Muriel |
npc | Specialized restraints for modeling the Nuclear Pore Complex |
MembraneExclusionRestraint | Create Membrane Exclusion Restraint |
MembraneSurfaceLocationConditionalRestraint | Create Membrane Surface Location CONDITIONAL Restraint for Nup120 ALPS Motifs - Mutually Exclusive from (135,152,'Nup120') and (197,216,'Nup120') |
MembraneSurfaceLocationRestraint | Create Membrane Surface Location Restraint |
XYRadialPositionLowerRestraint | Create XYRadial Position Lower restraints |
XYRadialPositionRestraint | Create XYRadial Position Restraint |
XYRadialPositionUpperRestraint | Create XYRadial Position Upper restraints |
YAxialPositionLowerRestraint | Create Y-Axial Position Lower restraints |
YAxialPositionRestraint | Create Y-Axial Position restraints |
YAxialPositionUpperRestraint | Create Y-Axial Position Upper restraints |
ZAxialPositionLowerRestraint | Create Z-Axial Position Lower restraints |
ZAxialPositionRestraint | Create Z-Axial Position restraints |
ZAxialPositionUpperRestraint | Create Z-Axial Position Upper restraints |
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.pmi1.ConnectivityRestraint between domains example: cr=restraints.ConnectivityNetworkRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")]) cr.add_to_model() cr.set_label("CR1") |
SetupMembraneRestraint | |
saxs | Restraints for handling small angle x-ray (SAXS) data |
SAXSISDRestraint | Basic SAXS restraint using ISD |
SAXSRestraint | Basic SAXS restraint |
stereochemistry | Restraints for keeping correct stereochemistry |
CharmmForceFieldRestraint | Enable CHARMM force field |
ConnectivityRestraint | This class creates a restraint between consecutive TempResidue objects OR an entire PMI MOlecule object |
ElasticNetworkRestraint | Add harmonic restraints between all pairs |
ExcludedVolumeSphere | A class to create an excluded volume restraint for a set of particles at a given resolution |
FusionRestraint | This class creates a restraint between the termini two polypeptides, to simulate the sequence connectivity |
HelixRestraint | Enforce ideal Helix dihedrals and bonds for a selection at resolution 0 |
PlaneDihedralRestraint | Restrain the dihedral between planes defined by three particles |
PseudoAtomicRestraint | Add bonds and improper dihedral restraints for the CBs |
ResidueAngleRestraint | Add angular restraint between triplets of consecutive residues/beads to enforce the stereochemistry |
ResidueBondRestraint | Add bond restraint between pair of consecutive residues/beads to enforce the stereochemistry |
ResidueDihedralRestraint | Add dihedral restraints between quadruplet of consecutive residues/beads to enforce the stereochemistry |
SecondaryStructure | Experimental, requires isd_emxl for now |
SymmetryRestraint | Create harmonic restraints between the reference and (transformed) clones |
RestraintBase | Base class for PMI restraints, which wrap IMP.Restraint (s) |
samplers | Sampling of the system |
ConjugateGradients | Sample using conjugate gradients |
MolecularDynamics | Sample using molecular dynamics |
MonteCarlo | Sample using Monte Carlo |
ReplicaExchange | Sample using replica exchange |
tools | Miscellaneous utilities |
ColorChange | Change color code to hexadecimal to rgb |
HierarchyDatabase | Store the representations for a system |
OrderedDefaultDict | Store objects in order they were added, but with default type |
Segments | This class stores integers in ordered compact lists eg: [[1,2,3],[6,7,8]] the methods help splitting and merging the internal lists Example: s=Segments([1,2,3]) is [[1,2,3]] s.add(4) is [[1,2,3,4]] (add right) s.add(3) is [[1,2,3,4]] (item already existing) s.add(7) is [[1,2,3,4],[7]] (new list) s.add([8,9]) is [[1,2,3,4],[7,8,9]] (add item right) s.add([5,6]) is [[1,2,3,4,5,6,7,8,9]] (merge) s.remove(3) is [[1,2],[4,5,6,7,8,9]] (split) etc |
Stopwatch | Collect timing information |
ThreeToOneConverter | This class converts three to one letter codes, and return X for any unknown codes |
topology | Set of python classes to create a multi-state, multi-resolution IMP hierarchy |
PMIMoleculeHierarchy | Extends the functionality of IMP.atom.Molecule |
Sequences | A dictionary-like wrapper for reading and storing sequence data |
TopologyReader | Automatically setup System and Degrees of Freedom with a formatted text file |
CompositeRestraint | A restraint for ambiguous cross-linking MS data and multiple state approach |
InternalCoordinatesConstraint | An example singleton modifier |
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 |
sampcon | Sampling exhaustiveness protocol |
clustering_rmsd | Utilities to cluster and calculate RMSD and precision |
good_scoring_model_selector | Select good-scoring models based on scores and/or data satisfaction |
GoodScoringModelSelector | Select good-scoring models based on scores and/or data satisfaction |
precision_rmsd | Calculation of precision and RMSD |
GetModelDensity | Compute mean density maps from structures |
rmsd_calculation | Utilities to help with RMSD calculation |
scores_convergence | Utilities to manage distributions of scores |
saxs | Support for small angle X-ray scattering (SAXS) data |
ChiFreeScore | |
ChiScore | |
ChiScoreLog | |
DeltaDistributionFunction | |
DerivativeCalculator | |
Distribution | |
FitParameters | Parameters of a fit, from ProfileFitter |
FormFactorTable | |
Profile | |
ProfileClustering | |
ProfileFitter | Fit two profiles with user-defined scoring function as a template parameter |
RadialDistributionFunction | |
RadiusOfGyrationRestraint | Calculate score based on radius of gyration, taken from saxs profile |
RatioVolatilityScore | |
Restraint | Calculate score based on fit to SAXS profile |
RigidBodiesProfileHandler | Handle the profile for a set of particles, which may include rigid bodies |
SolventAccessibleSurface | |
WeightedFitParameters | Parameters of a weighted fit, from WeightedProfileFitter |
WeightedProfileFitter | Fitting of multiple profiles to the experimental one |
saxs_merge | A method for merging SAXS profiles using Gaussian processes |
score_functor | Composable functors to implement scores via compile-time composition |
AddScores | |
DistancePairScore | Create efficient distance-based pair scores |
DistancePairScoreWithCache | Create efficient distance-based pair scores, with cache |
Dope | Score pair of atoms based on DOPE |
Harmonic | |
HarmonicLowerBound | |
HarmonicUpperBound | |
LinearLowerBound | |
LoopStatistical | Score atoms based on the Fiser/Melo loop modeling statistical potential |
OpenCubicSpline | Open cubic spline function |
OrientedSoap | Orientation-dependent SOAP score |
PointToSphereDistance | |
Score | A functor for computing a distance based score for D particles |
ScoreUnaryFunction | |
ScoreWithCache | A cached functor for computing a distance based score for D particles |
Shift | |
SingletonStatistical | Create a single key/single particle statistical potential from a file |
Soap | Score pairs of atoms based on SOAP |
SphereDistance | |
Statistical | |
SurfaceDepthPairScore | Create efficient surface depth-based pair scores |
SurfaceDistancePairScore | Create efficient surface distance-based pair scores |
SurfaceHeightPairScore | Create efficient surface height-based pair scores |
UnaryFunctionEvaluate | |
WeightScore | |
scratch | A space to add temporary classes while experimenting without forcing you to create your own module |
spatiotemporal | Spatialtemporal scoring in IMP |
analysis | Functions to analyze spatiotemporal models |
composition_scoring | Functions for weighting graphNode objects based on stoichiometry data |
create_DAG | Simplified function for creating a spatiotemporal model |
graphNode | Defines the graphNode class |
graphNode | A class to represent a node in a spatiotemporal process |
score_graph | Functions to traverse and score the spatiotemporal graphs |
write_output | Functions to write spatiotemporal graph information to files |
spb | Classes, functions and executables for modeling of the Spindle Pole Body |
AttributeDistancePairScore | Apply a function to an attribute |
BoxedMover | Move a particle and keep it in a box |
CellMover | Apply a mover that moves particles inside the unit cell |
ChiSquareMetric | |
ContactMapMetric | |
DiameterRgyrRestraint | Diameter and radius of gyration Restraint |
DistanceRMSDMetric | |
DistanceTerminiRestraint | A distance restraint between protein termini |
EM2DRestraint | |
Gaussian | Gaussian function (symmetric about the mean) |
HelixDecorator | Add helix parameters to a particle |
ISDRestraint | Apply an NOE distance restraint between two particles |
KinkPairScore | Score on the crossing angles between two helices |
MolecularDynamicsWithWte | Simple molecular dynamics optimizer |
MonteCarloWithWte | MonteCarlo in the Well-Tempered Ensemble |
NuisanceRangeModifier | Ensure that a Nuisance stays within its set range |
PbcBoxedMover | Move a particle and keep it in a box |
PbcBoxedRigidBodyMover | Modify the transformation of a rigid body |
RigidBodyNewMover | Modify the transformation of a rigid body |
RigidBodyPackingScore | Score on the crossing angles between two helices |
RMSDMetric | |
SameParticlePairFilter | |
SameRigidBodyPairFilter | |
TiltSingletonScore | Apply a function to the distance to a fixed point |
TransformationSymmetry | Set the coordinates of a particle to be a transformed version of a reference |
TwoStateGoModelRestraint | Two-state Go-Model Restraint |
UniformBoundedRestraint | |
statistics | Code to compute statistical measures |
ChiSquareMetric | Compute the distance between two configurations using chi2 |
ConfigurationSetRMSDMetric | |
ConfigurationSetXYZEmbedding | Embed a configuration using the XYZ coordinates of a set of particles |
Embedding | Store data to be clustered for embedding based algorithms |
EuclideanMetric | |
HistogramD | Dynamically build a histogram embedded in D-dimensional space |
Metric | Store data to be clustered for distance metric based algorithms |
ParticleEmbedding | |
PartitionalClustering | A base class for clustering results where each item is in one cluster |
PartitionalClusteringWithCenter | |
RecursivePartitionalClusteringEmbedding | |
RecursivePartitionalClusteringMetric | Represent a metric for clustering data that has already been clustered once |
VectorDEmbedding | Simply return the coordinates of a VectorD |
symmetry | Support for basic symmetry, such as periodic boundary conditions (PBC) |
BallMover | Move a particle and keep it in the primitive cell of a periodic lattice |
RigidBodyMover | Move a rigid body and keep it in the primitive cell of a periodic lattice |
test | Support for running tests of IMP functionality |
ApplicationTestCase | Super class for simple IMP application test cases |
DirectorObjectChecker | Check to make sure the number of director references is as expected |
RefCountChecker | Check to make sure the number of C++ object references is as expected |
TestCase | Super class for IMP test cases |
AddBoolFlag | |
AddFloatFlag | |
AddIntFlag | |
AddStringFlag | |
AdvancedFlag | Use this to add an advanced flag to the program |
ArgumentParser | IMP-specific subclass of argparse.ArgumentParser |
Array | A class to store a fixed array of same-typed values |
AttributeOptimizer | Base class for optimizers that act on individual attributes |
CommandDispatcher | Allow command line tools to easily implement multiple commands |
Configuration | A class to store a configuration of a model |
ConfigurationSet | A class to store a set of configurations of a model |
Constraint | Implement a constraint on the Model |
ConstVector | Store an array of values of the same type |
Container | Abstract class for containers of particles |
CreateLogContext | Create a new log context |
Decorator | Interface to specialized Particle types (e.g. atoms) |
DerivativeAccumulator | Class for adding derivatives from restraints to the model |
EvaluationState | |
EventException | An exception that signifies some event occurred |
Exception | The general base class for IMP exceptions |
Flag | |
FloatIndex | A FloatIndex identifies an optimized attribute in a model |
Index | A typed index |
IndexException | An exception for a request for an invalid member of a container |
IndexVector | Implements a vector tied to a particular index of type Index<Tag> |
InputAdaptor | Convenience class to accept multiple input types |
InternalException | A general exception for an internal error in IMP |
IOException | An input/output exception |
Key | A base class for Keys |
LRUCache | Implement a simple least recently used cache |
Memoizer | Helper class for writing memoizers |
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 | Base class for objects in a Model that depend on other objects |
NonCopyable | Base class for all objects that cannot be copied |
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 |
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 | Take Decorator, Particle or ParticleIndex |
ParticleIndexesAdaptor | Take Decorator, Particle or ParticleIndex |
ParticleIndexPairsAdaptor | Take ParticlePairs or ParticleIndexPairs |
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 |
Pointer | A smart pointer to a reference counted object |
PointerMember | A smart pointer to a ref-counted Object that is a class member |
PythonDirectedGraph | |
QuadContainer | A shared container for Quads |
QuadContainerAdaptor | |
QuadModifier | A base class for modifiers of ParticleQuadsTemp |
QuadPredicate | Abstract predicate function |
QuadScore | Abstract class for scoring object(s) of type ParticleIndexQuad |
RAII | Temporarily change something; undo the change when this object is destroyed |
Refiner | Abstract class to implement hierarchical methods |
Restraint | A restraint is a term in an IMP ScoringFunction |
RestraintInfo | Report key:value information on restraints |
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 | Temporarily set log target |
SetNumberOfThreads | |
Showable | Helper class to aid in output of IMP classes to streams |
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 | |
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 class for a simple primitive-like type |
ValueException | An exception for an invalid value being passed to IMP |
Vector | A more IMP-like version of the std::vector |
VersionInfo | Version and module information for Objects |
WarningContext | Warnings with the same key within the context are only output once |
WeakPointer | Smart pointer to Object-derived classes that does not refcount |
IMP_npctransport | |
write_a_metric | |
MyMetric | |
SurfacesGeometry | Display an IMP::SingletonContainer of Surface particles as cylindrical disks |