IMP::isd Namespace Reference

See IMP.isd for more information.

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	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	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	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< Scale >	Scales
typedef IMP::base::Vector < Switching >	Switchings
typedef IMP::base::Vector< Weight >	Weights

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

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

Store a set of objects.

Definition at line 45 of file RepulsiveDistancePairScore.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< RepulsiveDistancePairScore > > IMP::isd::RepulsiveDistancePairScoresTemp

Pass a set of objects. See RepulsiveDistancePairScore

Definition at line 45 of file RepulsiveDistancePairScore.h.

typedef IMP::base::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

)

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

)

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 setup_environment.sh script.