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IMP Reference Guide  develop.cd20b1e321,2019/12/14
The Integrative Modeling Platform
IMP::isd Namespace Reference

Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD). More...

Detailed Description

Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD).

Info

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  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
 

Typedefs

typedef IMP::Vector
< IMP::Pointer< Distribution > > 
Distributions
 
typedef IMP::Vector
< IMP::WeakPointer
< Distribution > > 
DistributionsTemp
 
typedef IMP::Vector
< IMP::Pointer< FStudentT > > 
FStudentTs
 
typedef IMP::Vector
< IMP::WeakPointer< FStudentT > > 
FStudentTsTemp
 
typedef IMP::Vector
< IMP::Pointer< ISDRestraint > > 
ISDRestraints
 
typedef IMP::Vector
< IMP::WeakPointer
< ISDRestraint > > 
ISDRestraintsTemp
 
typedef IMP::Vector< NuisanceNuisances
 
typedef IMP::Vector
< IMP::Pointer
< OneDimensionalDistribution > > 
OneDimensionalDistributions
 
typedef IMP::Vector
< IMP::WeakPointer
< OneDimensionalDistribution > > 
OneDimensionalDistributionsTemp
 
typedef IMP::Vector
< IMP::Pointer
< OneDimensionalSufficientDistribution > > 
OneDimensionalSufficientDistributions
 
typedef IMP::Vector
< IMP::WeakPointer
< OneDimensionalSufficientDistribution > > 
OneDimensionalSufficientDistributionsTemp
 
typedef IMP::Vector
< IMP::Pointer
< PenalizedComplexityPrior > > 
PenalizedComplexityPriors
 
typedef IMP::Vector
< IMP::WeakPointer
< PenalizedComplexityPrior > > 
PenalizedComplexityPriorsTemp
 
typedef IMP::Vector
< IMP::Pointer
< RepulsiveDistancePairScore > > 
RepulsiveDistancePairScores
 
typedef IMP::Vector
< IMP::WeakPointer
< RepulsiveDistancePairScore > > 
RepulsiveDistancePairScoresTemp
 
typedef IMP::Vector< ScaleScales
 
typedef IMP::Vector< SwitchingSwitchings
 
typedef IMP::Vector< WeightWeights
 

Variables

static const int IMPISD_MAX_WEIGHTS = 1000
 

Standard module functions

All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.

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 Documentation

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.

See Also
Distribution

Definition at line 30 of file isd/distribution.h.

A vector of reference-counting object pointers.

Definition at line 156 of file FStudentT.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
FStudentT

Definition at line 156 of file FStudentT.h.

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.

See Also
ISDRestraint

Definition at line 37 of file isd/ISDRestraint.h.

A vector of reference-counting object pointers.

Definition at line 62 of file isd/distribution.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
OneDimensionalDistribution

Definition at line 62 of file isd/distribution.h.

A vector of reference-counting object pointers.

Definition at line 109 of file isd/distribution.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
OneDimensionalSufficientDistribution

Definition at line 109 of file isd/distribution.h.

A vector of reference-counting object pointers.

Definition at line 111 of file PenalizedComplexityPrior.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
PenalizedComplexityPrior

Definition at line 111 of file PenalizedComplexityPrior.h.

A vector of reference-counting object pointers.

Definition at line 45 of file RepulsiveDistancePairScore.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
RepulsiveDistancePairScore

Definition at line 45 of file RepulsiveDistancePairScore.h.

Function Documentation

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

std::ifstream in(IMP::isd::get_data_path("data_library"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note
Each module has its own data directory, so be sure to use this function from the correct module.
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

std::ifstream in(IMP::isd::get_example_path("example_protein.pdb"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note
Each module has its own example directory, so be sure to use this function from the correct module.