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Inferential scoring.
This module implements inferential scoring in IMP, building on methods developed as part of the Inferential Structure Determination software (ISD).
Examples:
Author(s): Yannick Spill, Riccardo Pellarin, Charles Greenberg, Ben Webb, Daniel Russel
Version: SVN.r14091
License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
IMP and how to apply them to biological problems.Classes | |
| class | AmbiguousNOERestraint |
| Ambiguous NOE distance restraint between a number of pairs of particles. More... | |
| class | AmbiguousRestraint |
| Apply an ambiguous restraint by computing the d-norm. More... | |
| class | BivariateFunction |
| Base class for functions of two variables. More... | |
| class | Covariance1DFunction |
| Covariance function. More... | |
| class | Entry |
| class | FileBasedGrid |
| class | FNormal |
| FNormal. More... | |
| class | GaussianProcessInterpolation |
| GaussianProcessInterpolation. More... | |
| class | GaussianProcessInterpolationRestraint |
| gaussian process restraint More... | |
| class | GaussianRestraint |
| Normal probability distribution as a restraint. More... | |
| class | GeneralizedGuinierPorodFunction |
| 1D mean function for SAS data More... | |
| class | HybridMonteCarlo |
| Hybrid Monte Carlo optimizer. More... | |
| class | ISDRestraint |
| Apply an NOE distance restraint between two particles. More... | |
| class | JeffreysRestraint |
| class | Linear1DFunction |
| Linear one-dimensional function. More... | |
| class | LogicalORRestraint |
| Apply an NOE distance restraint between two particles. More... | |
| class | LognormalRestraint |
| Normal probability distribution as a restraint. More... | |
| class | MaintainScaleOrderConstraint |
| Constrain scales to be ordered and positive. More... | |
| class | MarginalHBondRestraint |
| Apply a lognormal distance restraint between two particles. More... | |
| class | MarginalNOERestraint |
| Apply an NOE distance restraint between two particles. More... | |
| class | MolecularDynamics |
| Molecular dynamics optimizer on 1-D and 3-D particles. More... | |
| class | MolecularDynamicsMover |
| Modify a set of continuous variables using a MD simulation. More... | |
| class | MultivariateFNormalSufficient |
| MultivariateFNormalSufficient. More... | |
| class | NOERestraint |
| Apply an NOE distance restraint between two particles. More... | |
| class | Nuisance |
| Add nuisance parameter to particle. More... | |
| class | PyroGrid |
| class | Replica |
| class | RepulsiveDistancePairScore |
| A repulsive potential on the distance between two atoms. More... | |
| class | Scale |
| Add scale parameter to particle. More... | |
| class | SlidingPriorRestraint |
| Score a Scale particle with unnormalized probability. More... | |
| class | Statistics |
| class | Switching |
| Add switching parameter to particle. More... | |
| class | TALOSRestraint |
| phi/psi dihedral restraint between four particles, using data from TALOS. More... | |
| class | UnivariateFunction |
| Base class for functions of one variable. More... | |
| class | vonMises |
| vonMises More... | |
| class | vonMisesKappaConjugateRestraint |
| Conjugate prior for the concentration parameter of a von Mises distribution. More... | |
| class | vonMisesKappaJeffreysRestraint |
| class | vonMisesSufficient |
| vonMisesSufficient More... | |