IMP Reference Guide
develop.36b5e40f34,2024/10/13
The Integrative Modeling Platform
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Files | |
file | AngleRestraint.h [code] |
Angle restraint between three particles. | |
file | AngleTripletScore.h [code] |
A Score on the angle between three particles. | |
file | core/BallMover.h [code] |
A modifier which variables within a ball. | |
file | blame.h [code] |
Various important functionality for implementing decorators. | |
file | BoundingBox3DSingletonScore.h [code] |
Score particles based on a bounding box. | |
file | BoundingSphere3DSingletonScore.h [code] |
Score particles based on a bounding sphere - score would typically increase as particles are exiting the sphere boundaries, and must be zero within the sphere and positive outside of it. | |
file | BoxSweepClosePairsFinder.h [code] |
Test all pairs of particles to find close pairs. | |
file | CentroidOfRefined.h [code] |
Set the coordinates of the particle to be the centroid of the refined particles. | |
file | ChecksScoreState.h [code] |
Turn checks on and off. | |
file | ChildrenRefiner.h [code] |
Return the hierarchy children of a particle. | |
file | ClosedCubicSpline.h [code] |
Closed cubic spline function. | |
file | ClosePairsFinder.h [code] |
A base class for algorithms to detect proximities. | |
file | ClosePairsPairScore.h [code] |
Apply a PairScore to close pairs. | |
file | core/ConjugateGradients.h [code] |
Simple conjugate gradients optimizer. | |
file | ConnectivityRestraint.h [code] |
Connectivity restraint. | |
file | ConstantRestraint.h [code] |
Constant restraint. | |
file | core_config.h [code] |
file | Cosine.h [code] |
Cosine function. | |
file | CoverRefined.h [code] |
Set the position and radius of a particle to enclose the refined. | |
file | DataObject.h [code] |
Helper class for creating an IMP object storing some data. | |
file | DerivativesFromRefined.h [code] |
Accumulate the derivatives of the refined particles. | |
file | DerivativesToRefined.h [code] |
Accumulate the derivatives of the refined particles. | |
file | DiameterRestraint.h [code] |
A restraint to maintain the diameter of a set of points. | |
file | DihedralRestraint.h [code] |
Dihedral restraint between four particles. | |
file | direction.h [code] |
Decorators for directions and the angle between them. | |
file | DirectionMover.h [code] |
A mover that transforms a Direction. | |
file | core/DistancePairScore.h [code] |
A Score on the distance between a pair of particles. | |
file | DistanceRestraint.h [code] |
Distance restraint between two particles. | |
file | DistanceToSingletonScore.h [code] |
A Score on the distance to a fixed point. | |
file | ExcludedVolumeRestraint.h [code] |
Prevent spheres from inter-penetrating. | |
file | FixedRefiner.h [code] |
A particle refiner which returns a fixed set of particles. | |
file | core/Gaussian.h [code] |
Decorator to hold Gaussian3D. | |
file | core/generic.h [code] |
Various important functionality for implementing decorators. | |
file | GenericAttributeSingletonScore.h [code] |
A score based on the unmodified value of an attribute. | |
file | GridClosePairsFinder.h [code] |
Use a hierarchy of grids to find close pairs. | |
file | core/Harmonic.h [code] |
Harmonic function. | |
file | core/HarmonicLowerBound.h [code] |
Harmonic lower bound function. | |
file | core/HarmonicUpperBound.h [code] |
Harmonic upper bound function. | |
file | HarmonicWell.h [code] |
Harmonic function. | |
file | core/Hierarchy.h [code] |
Decorator for helping deal with a hierarchy. | |
file | LeavesRefiner.h [code] |
Return the hierarchy leaves under a particle. | |
file | Linear.h [code] |
A linear function. | |
file | LogNormalMover.h [code] |
A modifier that perturbs a point with a log-normal distribution. | |
file | MCCGSampler.h [code] |
A Monte Carlo/Conjugate Gradients based sampler. | |
file | MinimumRestraint.h [code] |
Score based on the k minimum restraints. | |
file | model_statistics.h [code] |
Write the scores of the passed restraints to a file. | |
file | MonteCarlo.h [code] |
Simple Monte Carlo optimizer. | |
file | MonteCarloMover.h [code] |
The base class for movers for Monte Carlo optimization. | |
file | MoveStatisticsScoreState.h [code] |
Write geometry to a file during optimization. | |
file | MSConnectivityRestraint.h [code] |
Mass Spec Connectivity restraint. | |
file | MultipleBinormalRestraint.h [code] |
Modeller-style multiple binormal (phi/psi) restraint. | |
file | NearestNeighborsClosePairsFinder.h [code] |
Test all pairs of particles to find close pairs. | |
file | NeighborsTable.h [code] |
Copyright 2007-2022 IMP Inventors. All rights reserved. | |
file | NormalMover.h [code] |
A modifier which perturbs a point with a normal distribution. | |
file | core/OpenCubicSpline.h [code] |
Open cubic spline function. | |
file | pair_predicates.h [code] |
Define some predicates. | |
file | PairConstraint.h [code] |
Use a PairModifier applied to a ParticlePairsTemp to maintain an invariant. | |
file | PairRestraint.h [code] |
Apply a PairScore to a Pair. | |
file | PeriodicOptimizerState.h [code] |
Angle restraint between three particles. | |
file | predicates.h [code] |
Score particles based on a bounding box. | |
file | provenance.h [code] |
Classes to track how the model was created. | |
file | core/python_only.h [code] |
Functionality only available in Python. | |
file | quad_predicates.h [code] |
Define some predicates. | |
file | QuadConstraint.h [code] |
Use a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant. | |
file | QuadraticClosePairsFinder.h [code] |
Test all pairs of particles to find close pairs. | |
file | QuadRestraint.h [code] |
Apply a QuadScore to a Quad. | |
file | RefinedPairsPairScore.h [code] |
Generate pairs by applying a Refiner to the particles. | |
file | RestraintsScoringFunction.h [code] |
A scoring function on a list of restraints. | |
file | rigid_bodies.h [code] |
functionality for defining rigid bodies | |
file | rigid_body_geometries.h [code] |
functionality for defining rigid bodies | |
file | RigidBodyAnglePairScore.h [code] |
A Score on the crossing angle between two rigid bodies. | |
file | RigidBodyDistancePairScore.h [code] |
Act on the distance between two rigid bodies. | |
file | core/RigidBodyMover.h [code] |
A mover that transforms a rigid body. | |
file | RigidBodyTunneler.h [code] |
A mover that transform a rigid body. | |
file | RigidBodyUmbrella.h [code] |
Distance restraint between two particles. | |
file | RigidClosePairsFinder.h [code] |
Handle rigid bodies by looking at their members. | |
file | SerialMover.h [code] |
A mover that applies other movers one at a time. | |
file | singleton_predicates.h [code] |
Define some predicates. | |
file | SingletonConstraint.h [code] |
Use a SingletonModifier applied to a ParticlesTemp to maintain an invariant. | |
file | SingletonRestraint.h [code] |
Apply a SingletonScore to a Singleton. | |
file | SphereDistancePairScore.h [code] |
A score on the distance between the surfaces of two spheres. | |
file | StatisticalPairScore.h [code] |
Functions to read mol2s. | |
file | SteepestDescent.h [code] |
Simple steepest descent optimizer. | |
file | SubsetMover.h [code] |
A mover that applies a random subset of movers. | |
file | Surface.h [code] |
Simple surface decorator. | |
file | core/SurfaceDistancePairScore.h [code] |
A score on the distance between a surface and a sphere. | |
file | SurfaceMover.h [code] |
A mover that transforms a Surface. | |
file | SurfaceSymmetryConstraint.h [code] |
Constrain orientation of surfaces with respect to rigid bodies. | |
file | SurfaceTetheredChain.h [code] |
Score on surface-to-end distance of chain tethered to impenetrable surface. | |
file | core/symmetry.h [code] |
Implement various types of symmetry. | |
file | TableRefiner.h [code] |
A lookup based particle refiner. | |
file | Transform.h [code] |
Transform a particle. | |
file | TransformedDistancePairScore.h [code] |
A score on the distance between a pair of particles after transforming one. | |
file | triplet_predicates.h [code] |
Define some predicates. | |
file | TripletConstraint.h [code] |
Use a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant. | |
file | TripletRestraint.h [code] |
Apply a TripletScore to a Triplet. | |
file | TruncatedHarmonic.h [code] |
Truncated harmonic. | |
file | Typed.h [code] |
A particle with a user-defined type. | |
file | TypedPairScore.h [code] |
Delegate to another PairScore depending on particle types. | |
file | core/utility.h [code] |
Various important functionality for implementing decorators. | |
file | VolumeRestraint.h [code] |
A restraint that prevents spheres from inter-penetrating. | |
file | WeightedDerivativesToRefined.h [code] |
Copies derivatives from coarse grained particle to its refined set of particles using weights indicated by a weight key. | |
file | WeightedSum.h [code] |
Weighted sum of unary functions. | |
file | WeightedSumOfExponential.h [code] |
Negative logarithm of weighted sum of negative exponential of unary functions. | |
file | XYZ.h [code] |
Simple XYZ decorator. | |
file | XYZR.h [code] |
Decorator for a sphere-like particle. | |