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:

See main IMP papers list.
W. Rieping, M. Habeck, M. Nilges. "Inferential structure determination", Science 8;309(5732):303-6, 2005.

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 `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

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::WeakPointer< ISDRestraint > > IMP::isd::ISDRestraintsTemp

Pass a set of objects.

See Also: ISDRestraint

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.

See Also: RepulsiveDistancePairScore

Definition at line 45 of file RepulsiveDistancePairScore.h.

typedef IMP::Vector< Weight > IMP::isd::Weights

Pass or store a set of Weight .

Definition at line 62 of file Weight.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.

Detailed Description

Info

Namespaces

Classes

Typedefs

Standard module functions

Typedef Documentation

Function Documentation