IMP::container Namespace Reference

Detailed Description

This module provides containers in IMP.

Author:: Daniel Russel

Version:: 1.0

Overview:: Containers provide a layer of indirection between code that defines sets of particles and restraints and constraints. This indirection allows the set of particles acted upon to be changed on the fly. For example, the IMP::container::ClosePairContainer defines a set of all particle pairs that are close to one another.

Examples: Examples can be found on the IMP.container examples page.

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:

Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velazquez-Muriel, Andrej Sali, “Integrative assembly modeling using IMP”, submitted, 2010. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.


Data Structures
class	AllBipartitePairContainer
	Return all bipartite pairs between two containers. More...
class	AllPairContainer
	Return all unordered pairs of particles taken from the SingletonContainer. More...
class	CloseBipartitePairContainer
	Return all close unordered pairs of particles taken from the SingletonContainer. More...
class	ClosePairContainer
	Return all close unordered pairs of particles taken from the SingletonContainer. More...
class	ListPairContainer
	Store a list of ParticlePairs. More...
class	ListQuadContainer
	Store a list of ParticleQuads. More...
class	ListSingletonContainer
	Store a list of Particles. More...
class	ListTripletContainer
	Store a list of ParticleTriplets. More...
class	MaximumPairRestraint
	Score based on the maximum pair over a set of Pairs. More...
class	MaximumPairScore
	Evaluate the maximum n pair scores of the passed set of PairScores. More...
class	MaximumQuadRestraint
	Score based on the maximum quad over a set of Quads. More...
class	MaximumQuadScore
	Evaluate the maximum n quad scores of the passed set of QuadScores. More...
class	MaximumSingletonRestraint
	Score based on the maximum singleton over a set of Singletons. More...
class	MaximumSingletonScore
	Evaluate the maximum n singleton scores of the passed set of SingletonScores. More...
class	MaximumTripletRestraint
	Score based on the maximum triplet over a set of Triplets. More...
class	MaximumTripletScore
	Evaluate the maximum n triplet scores of the passed set of TripletScores. More...
class	MinimumPairRestraint
	Score based on the minimum pair over a set of Pairs. More...
class	MinimumPairScore
	Evaluate the minimum n pair scores of the passed set of PairScores. More...
class	MinimumQuadRestraint
	Score based on the minimum quad over a set of Quads. More...
class	MinimumQuadScore
	Evaluate the minimum n quad scores of the passed set of QuadScores. More...
class	MinimumSingletonRestraint
	Score based on the minimum singleton over a set of Singletons. More...
class	MinimumSingletonScore
	Evaluate the minimum n singleton scores of the passed set of SingletonScores. More...
class	MinimumTripletRestraint
	Score based on the minimum triplet over a set of Triplets. More...
class	MinimumTripletScore
	Evaluate the minimum n triplet scores of the passed set of TripletScores. More...
class	PairContainerSet
	Stores a set of PairContainers. More...
class	PairsConstraint
	Apply a PairFunction to a PairContainer to maintain an invariant. More...
class	PairsOptimizerState
	Apply a PairFunction to a PairContainer to maintain an invariant. More...
class	PairsRestraint
	Applies a PairScore to each ParticlePair in a list. More...
class	QuadContainerSet
	Stores a set of QuadContainers. More...
class	QuadsConstraint
	Apply a QuadFunction to a QuadContainer to maintain an invariant. More...
class	QuadsOptimizerState
	Apply a QuadFunction to a QuadContainer to maintain an invariant. More...
class	QuadsRestraint
	Applies a QuadScore to each ParticleQuad in a list. More...
class	SingletonContainerSet
	Stores a set of SingletonContainers. More...
class	SingletonsConstraint
	Apply a SingletonFunction to a SingletonContainer to maintain an invariant. More...
class	SingletonsOptimizerState
	Apply a SingletonFunction to a SingletonContainer to maintain an invariant. More...
class	SingletonsRestraint
	Applies a SingletonScore to each Particle in a list. More...
class	TripletContainerSet
	Stores a set of TripletContainers. More...
class	TripletsConstraint
	Apply a TripletFunction to a TripletContainer to maintain an invariant. More...
class	TripletsOptimizerState
	Apply a TripletFunction to a TripletContainer to maintain an invariant. More...
class	TripletsRestraint
	Applies a TripletScore to each ParticleTriplet in a list. More...
Functions
std::string	get_data_path (std::string file_name)
	Return the path to installed data for this module.
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module.
std::string	get_module_name ()
const VersionInfo &	get_module_version_info ()

Function Documentation

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

Return the path to installed data for this module.

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::container::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

    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.

IMP::container Namespace Reference

Detailed Description

Data Structures

Functions

Function Documentation