Detailed Description

This module provides containers in IMP.

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:

Author(s): Daniel Russel

Version: SVN.r12662

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 Velázquez-Muriel, Andrej Sali, “Putting the pieces together: integrative structure determination of macromolecular assemblies”, PLoS Biology, 2012. 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.

Classes
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 ordered pairs of particles taken from the two SingletonContainers. More...
class	ClosePairContainer
	Return all close unordered pairs of particles taken from the SingletonContainer. More...
class	ConnectingPairContainer
	A container which keeps a set of pairs that connect a set of spheres. More...
class	ConsecutivePairContainer
	A container which contains all consecutive pairs from a list. More...
class	EventPairsOptimizerState
class	EventQuadsOptimizerState
class	EventSingletonsOptimizerState
class	EventTripletsOptimizerState
class	ExclusiveConsecutivePairContainer
class	ExclusiveConsecutivePairFilter
class	InContainerPairFilter
	A filter which returns true if a container containers the Pair. More...
class	InContainerQuadFilter
	A filter which returns true if a container containers the Quad. More...
class	InContainerSingletonFilter
	A filter which returns true if a container containers the Singleton. More...
class	InContainerTripletFilter
	A filter which returns true if a container containers the Triplet. More...
class	ListPairContainer
	Store a list of ParticlePairsTemp. More...
class	ListQuadContainer
	Store a list of ParticleQuadsTemp. More...
class	ListSingletonContainer
	Store a list of ParticlesTemp. More...
class	ListTripletContainer
	Store a list of ParticleTripletsTemp. More...
class	MinimumPairRestraint
	Score based on the min or max PairScore over a set. More...
class	MinimumPairScore
	Evaluate the min or max n particle_pair scores of the passed set. More...
class	MinimumQuadRestraint
	Score based on the min or max QuadScore over a set. More...
class	MinimumQuadScore
	Evaluate the min or max n particle_quad scores of the passed set. More...
class	MinimumSingletonRestraint
	Score based on the min or max SingletonScore over a set. More...
class	MinimumSingletonScore
	Evaluate the min or max n particle scores of the passed set. More...
class	MinimumTripletRestraint
	Score based on the min or max TripletScore over a set. More...
class	MinimumTripletScore
	Evaluate the min or max n particle_triplet scores of the passed set. More...
class	PairContainerSet
	Stores a set of PairContainers. More...
class	PairContainerStatistics
	Track statistics on a PairContainer. More...
class	PairsConstraint
	Apply a PairFunction to a PairContainer to maintain an invariant. More...
class	PairsEventOptimizerState
class	PairsOptimizerState
	Apply a PairFunction to a PairContainer to maintain an invariant. More...
class	PairsRestraint
	Applies a PairScore to each Pair in a list. More...
class	PredicatePairsRestraint
	Applies a PairScore to each Pair in a list based on a predicate. More...
class	PredicateQuadsRestraint
	Applies a QuadScore to each Quad in a list based on a predicate. More...
class	PredicateSingletonsRestraint
	Applies a SingletonScore to each Singleton in a list based on a predicate. More...
class	PredicateTripletsRestraint
	Applies a TripletScore to each Triplet in a list based on a predicate. More...
class	QuadContainerSet
	Stores a set of QuadContainers. More...
class	QuadContainerStatistics
	Track statistics on a QuadContainer. More...
class	QuadsConstraint
	Apply a QuadFunction to a QuadContainer to maintain an invariant. More...
class	QuadsEventOptimizerState
class	QuadsOptimizerState
	Apply a QuadFunction to a QuadContainer to maintain an invariant. More...
class	QuadsRestraint
	Applies a QuadScore to each Quad in a list. More...
class	SingletonContainerSet
	Stores a set of SingletonContainers. More...
class	SingletonContainerStatistics
	Track statistics on a SingletonContainer. More...
class	SingletonsConstraint
	Apply a SingletonFunction to a SingletonContainer to maintain an invariant. More...
class	SingletonsEventOptimizerState
class	SingletonsOptimizerState
	Apply a SingletonFunction to a SingletonContainer to maintain an invariant. More...
class	SingletonsRestraint
	Applies a SingletonScore to each Singleton in a list. More...
class	TripletContainerSet
	Stores a set of TripletContainers. More...
class	TripletContainerStatistics
	Track statistics on a TripletContainer. More...
class	TripletsConstraint
	Apply a TripletFunction to a TripletContainer to maintain an invariant. More...
class	TripletsEventOptimizerState
class	TripletsOptimizerState
	Apply a TripletFunction to a TripletContainer to maintain an invariant. More...
class	TripletsRestraint
	Applies a TripletScore to each Triplet in a list. More...
Functions
template<class Container , class Before , class After >
Constraint *	create_constraint (Before b, After a, Container *c, std::string name=std::string())
template<class Container >
PairFilter *	create_in_container_filter (Container *c, std::string name=std::string())
template<class Score , class Container >
Restraint *	create_restraint (Score s, Container c, std::string name=std::string())
double	get_slack_estimate (const ParticlesTemp &ps, double upper_bound, double step, const RestraintsTemp &restraints, bool derivatives, Optimizer opt, ClosePairContainer cpc)

Function Documentation

template<class Container , class Before , class After >

Constraint * IMP::container::create_constraint	(	Before *	b,
		After *	a,
		Container *	c,
		std::string	name = `std::string()`
	)

Helper to create a ContainerConstraint.

template<class Container >

PairFilter* IMP::container::create_in_container_filter	(	Container *	c,
		std::string	name = `std::string()`
	)

Create a filter that returns whether the pair, or its flip is contained in the passed container.

template<class Score , class Container >

Restraint * IMP::container::create_restraint	(	Score *	s,
		Container *	c,
		std::string	name = `std::string()`
	)

Create a restraint from a score and a container. The resulting restraint is, in general, more efficient than creating an, eg, PairsRestraint.

double IMP::container::get_slack_estimate	(	const ParticlesTemp &	ps,
		double	upper_bound,
		double	step,
		const RestraintsTemp &	restraints,
		bool	derivatives,
		Optimizer *	opt,
		ClosePairContainer *	cpc
	)

Estimate the proper slack based on

the time taken to evaluate the passed restraints for a given number of particles in the non-bonded list
the number of pairs in the list as a function of slack size
the amount the particles are moved by the optimizer
the time taken to compute the close pairs as a function of slack size

For best results, make the particles start in a that is "typical" for the optimization.

Detailed Description

Classes

Functions

Function Documentation