IMP Reference Guide
2.20.0
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 | Distribution |
Base class for all distributions, provided for common inheritance. More... | |
class | FNormal |
FNormal. More... | |
class | FretData |
Auxiliary class for FRET_R restraint. More... | |
class | FretRestraint |
class | FStudentT |
Joint Student's t-distribution of Function. More... | |
class | GammaPrior |
Uniform distribution with harmonic boundaries. More... | |
class | GaussianAnchorEMRestraint |
Restraint between two sets of anchor points "model" and "EM density". More... | |
class | GaussianEMRestraint |
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 | NormalSigmaPCRestraint |
A Penalized Complexity prior on sigma of a normal distribution. More... | |
class | Nuisance |
Add nuisance parameter to particle. More... | |
class | OneDimensionalDistribution |
Base class for distributions that are passed a single random variable. More... | |
class | OneDimensionalSufficientDistribution |
Base class for single-variate distributions that cache sufficient statistics. More... | |
class | PenalizedComplexityPrior |
Penalized complexity prior. More... | |
class | RepulsiveDistancePairScore |
A repulsive potential on the distance between two atoms. More... | |
class | ResidueProteinProximityRestraint |
class | Scale |
Add scale parameter to particle. More... | |
class | StudentTRestraint |
A Student-t distribution restraint. 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 to a particle. More... | |
class | WeightMover |
A mover that perturbs a Weight particle. More... | |
class | WeightRestraint |
Variables | |
static const int | IMPISD_MAX_WEIGHTS = 1000 |
Standard module functions | |
All | |
std::string | get_module_version () |
Return the version of this module, as a string. More... | |
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< Distribution > > IMP::isd::Distributions |
A vector of reference-counting object pointers.
Definition at line 30 of file isd/distribution.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 30 of file isd/distribution.h.
typedef IMP::Vector<IMP::Pointer< FStudentT > > IMP::isd::FStudentTs |
A vector of reference-counting object pointers.
Definition at line 156 of file FStudentT.h.
typedef IMP::Vector<IMP::WeakPointer< FStudentT > > IMP::isd::FStudentTsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 156 of file FStudentT.h.
typedef IMP::Vector<IMP::Pointer< ISDRestraint > > IMP::isd::ISDRestraints |
A vector of reference-counting object pointers.
Definition at line 37 of file isd/ISDRestraint.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 37 of file isd/ISDRestraint.h.
typedef IMP::Vector<IMP::Pointer< OneDimensionalDistribution > > IMP::isd::OneDimensionalDistributions |
A vector of reference-counting object pointers.
Definition at line 62 of file isd/distribution.h.
typedef IMP::Vector<IMP::WeakPointer< OneDimensionalDistribution > > IMP::isd::OneDimensionalDistributionsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 62 of file isd/distribution.h.
typedef IMP::Vector<IMP::Pointer< OneDimensionalSufficientDistribution > > IMP::isd::OneDimensionalSufficientDistributions |
A vector of reference-counting object pointers.
Definition at line 109 of file isd/distribution.h.
typedef IMP::Vector<IMP::WeakPointer< OneDimensionalSufficientDistribution > > IMP::isd::OneDimensionalSufficientDistributionsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 109 of file isd/distribution.h.
A vector of reference-counting object pointers.
Definition at line 111 of file PenalizedComplexityPrior.h.
typedef IMP::Vector<IMP::WeakPointer< PenalizedComplexityPrior > > IMP::isd::PenalizedComplexityPriorsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 111 of file PenalizedComplexityPrior.h.
typedef IMP::Vector<IMP::Pointer< RepulsiveDistancePairScore > > IMP::isd::RepulsiveDistancePairScores |
A vector of reference-counting object pointers.
Definition at line 45 of file RepulsiveDistancePairScore.h.
typedef IMP::Vector<IMP::WeakPointer< RepulsiveDistancePairScore > > IMP::isd::RepulsiveDistancePairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 45 of file RepulsiveDistancePairScore.h.
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.
std::string IMP::isd::get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 5 of file EMageFit/__init__.py.