IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD). More...
Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD).
Author(s): Yannick Spill, Riccardo Pellarin, Charles Greenberg, Ben Webb, Daniel Russel
Maintainer: yannickspill
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:
Namespaces | |
Entry | |
Classes to handle ISD statistics files. | |
gmm_tools | |
Tools for handling Gaussian Mixture Models. | |
History | |
Classes to store output from replicas. | |
TALOSReader | |
Classes to handle TALOS files or folders. | |
TBLReader | |
Classes to handle TBL files. | |
utils | |
Miscellaneous utilities. | |
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 | AtomicCrossLinkMSRestraint |
Restrain atom pairs based on a set of crosslinks. More... | |
class | BivariateFunction |
Base class for functions of two variables. More... | |
class | Covariance1DFunction |
Covariance function. More... | |
class | CrossLinkData |
CrossLinkData. More... | |
class | CrossLinkMSRestraint |
A restraint for ambiguous cross-linking MS data and multiple state approach. More... | |
class | CysteineCrossLinkData |
CysteineCrossLinkData. More... | |
class | CysteineCrossLinkRestraint |
A restraint for cysteine cross-linking data. More... | |
class | FNormal |
FNormal. More... | |
class | FretData |
Auxiliary class for FRET_R restraint. More... | |
class | FretRestraint |
class | GaussianEMRestraint |
Creates a restraint between two Gaussian Mixture Models, "model" and "density". 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 |
A base class for ISD Restraints. More... | |
class | JeffreysRestraint |
class | Linear1DFunction |
Linear one-dimensional function. More... | |
class | LognormalAmbiguousRestraint |
class | LognormalRestraint |
Normal probability distribution as a restraint. More... | |
class | LogWrapper |
Calculate the -Log of a list of restraints. 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 | RepulsiveDistancePairScore |
A repulsive potential on the distance between two atoms. More... | |
class | Scale |
Add scale parameter to particle. More... | |
class | Switching |
Add switching parameter to particle. More... | |
class | TALOSRestraint |
phi/psi dihedral restraint between four particles, using data from TALOS. More... | |
class | UniformPrior |
Uniform distribution with harmonic boundaries. 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 |
Jeffreys prior for the \(\kappa\) concentration parameter of a von Mises distribution. More... | |
class | vonMisesSufficient |
vonMisesSufficient More... | |
class | Weight |
Add weights for a set of states to a particle. More... | |
class | WeightMover |
A mover that perturbs a Weight particle. More... | |
class | WeightRestraint |
Typedefs | |
typedef IMP::Vector < IMP::Pointer< ISDRestraint > > | ISDRestraints |
typedef IMP::Vector < IMP::WeakPointer < ISDRestraint > > | ISDRestraintsTemp |
typedef IMP::Vector< Nuisance > | Nuisances |
typedef IMP::Vector < IMP::Pointer < RepulsiveDistancePairScore > > | RepulsiveDistancePairScores |
typedef IMP::Vector < IMP::WeakPointer < RepulsiveDistancePairScore > > | RepulsiveDistancePairScoresTemp |
typedef IMP::Vector< Scale > | Scales |
typedef IMP::Vector< Switching > | Switchings |
typedef IMP::Vector< Weight > | Weights |
Standard module functions | |
All | |
std::string | get_module_version () |
std::string | get_module_name () |
std::string | get_data_path (std::string file_name) |
Return the full path to one of this module's data files. More... | |
std::string | get_example_path (std::string file_name) |
Return the full path to one of this module's example files. More... | |
typedef IMP::Vector<IMP::Pointer< ISDRestraint > > IMP::isd::ISDRestraints |
Store a set of objects.
Definition at line 37 of file ISDRestraint.h.
typedef IMP::Vector<IMP::Pointer< RepulsiveDistancePairScore > > IMP::isd::RepulsiveDistancePairScores |
Store a set of objects.
Definition at line 45 of file RepulsiveDistancePairScore.h.
typedef IMP::Vector<IMP::WeakPointer< RepulsiveDistancePairScore > > IMP::isd::RepulsiveDistancePairScoresTemp |
Pass a set of objects.
Definition at line 45 of file RepulsiveDistancePairScore.h.
typedef IMP::Vector< Weight > IMP::isd::Weights |
std::string IMP::isd::get_data_path | ( | std::string | file_name | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::isd::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.