IMP  2.3.0
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.
 
 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  BivariateFunction
 Base class for functions of two variables. More...
 
class  Covariance1DFunction
 Covariance function. More...
 
class  CrossLinkData
 CrossLinkData. More...
 
class  CrossLinkMSRestraint
 
class  CysteineCrossLinkData
 CysteineCrossLinkData. More...
 
class  CysteineCrossLinkRestraint
 
class  FNormal
 FNormal. More...
 
class  FretData
 Auxiliary class for FRET_R restraint. More...
 
class  FretRestraint
 
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  JeffreysRestraint
 
class  Linear1DFunction
 Linear one-dimensional function. More...
 
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
 
class  vonMisesSufficient
 vonMisesSufficient More...
 
class  Weight
 Add weights for a set of states to a particle. More...
 
class  WeightMover
 Modify the transformation of a rigid body. More...
 
class  WeightRestraint
 

Typedefs

typedef IMP::base::Vector
< Nuisance
Nuisances
 
typedef IMP::base::Vector
< IMP::base::Pointer
< RepulsiveDistancePairScore > > 
RepulsiveDistancePairScores
 
typedef IMP::base::Vector
< IMP::base::WeakPointer
< RepulsiveDistancePairScore > > 
RepulsiveDistancePairScoresTemp
 
typedef IMP::base::Vector< ScaleScales
 
typedef IMP::base::Vector
< Switching
Switchings
 
typedef IMP::base::Vector< WeightWeights
 

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 installed data. More...
 
std::string get_example_path (std::string file_name)
 Return the path to installed example data for this module. More...
 

Typedef Documentation

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 installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

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

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

std::string IMP::isd::get_example_path ( std::string  file_name)

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

model));

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