IMP  2.0.0
The Integrative Modeling Platform
IMP::isd Namespace Reference

See IMP.isd Overview for more information.

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  FNormal
 FNormal. 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
 Apply an NOE distance restraint between two particles. More...
 
class  JeffreysRestraint
 
class  Linear1DFunction
 Linear one-dimensional function. More...
 
class  LogicalORRestraint
 Apply an NOE distance restraint between two particles. More...
 
class  LognormalRestraint
 Normal probability distribution as a restraint. More...
 
class  MaintainScaleOrderConstraint
 Constrain scales to be ordered and positive. 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  SlidingPriorRestraint
 Score a Scale particle with unnormalized probability. More...
 
class  Switching
 Add switching parameter to particle. More...
 
class  TALOSRestraint
 phi/psi dihedral restraint between four particles, using data from TALOS. 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...
 

Typedefs

typedef IMP::base::Vector
< IMP::base::Pointer
< RepulsiveDistancePairScore > > 
RepulsiveDistancePairScores
 

Functions

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...
 

Standard module methods

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

std::string get_module_version ()
 
std::string get_module_name ()
 

Typedef Documentation

Function Documentation

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

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 tools/imppy.sh script.

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

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

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

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