Various classes to hold sets of particles. More...

Detailed Description

Various classes to hold sets of particles.

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.

Info

Author(s): Daniel Russel

Maintainer: benmwebb

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:

See main IMP papers list.

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 particle pairs from an input list. More...

class	ConsecutivePairFilter

class	DistributePairsScoreState
	Distribute contents of one container into several based on predicates. More...

class	DistributeQuadsScoreState
	Distribute contents of one container into several based on predicates. More...

class	DistributeSingletonsScoreState
	Distribute contents of one container into several based on predicates. More...

class	DistributeTripletsScoreState
	Distribute contents of one container into several based on predicates. More...

class	DynamicListPairContainer
	Store a kernel::ParticleIndexPairs. More...

class	DynamicListQuadContainer
	Store a kernel::ParticleIndexQuads. More...

class	DynamicListSingletonContainer
	Store a kernel::ParticleIndexes. More...

class	DynamicListTripletContainer
	Store a kernel::ParticleIndexTriplets. 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 kernel::ParticleIndexPairs. More...

class	ListQuadContainer
	Store a kernel::ParticleIndexQuads. More...

class	ListSingletonContainer
	Store a kernel::ParticleIndexes. More...

class	ListTripletContainer
	Store a kernel::ParticleIndexTriplets. 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	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	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	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	TripletsOptimizerState
	Apply a TripletFunction to a TripletContainer to maintain an invariant. More...

class	TripletsRestraint
	Applies a TripletScore to each Triplet in a list. More...

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < AllBipartitePairContainer > >	AllBipartitePairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < AllBipartitePairContainer > >	AllBipartitePairContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < AllPairContainer > >	AllPairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < AllPairContainer > >	AllPairContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < ClosePairContainer > >	ClosePairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < ClosePairContainer > >	ClosePairContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < ConnectingPairContainer > >	ConnectingPairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < ConnectingPairContainer > >	ConnectingPairContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < ConsecutivePairContainer > >	ConsecutivePairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < ConsecutivePairContainer > >	ConsecutivePairContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < DynamicListPairContainer > >	DynamicListPairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < DynamicListPairContainer > >	DynamicListPairContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < DynamicListQuadContainer > >	DynamicListQuadContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < DynamicListQuadContainer > >	DynamicListQuadContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < DynamicListSingletonContainer > >	DynamicListSingletonContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < DynamicListSingletonContainer > >	DynamicListSingletonContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < DynamicListTripletContainer > >	DynamicListTripletContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < DynamicListTripletContainer > >	DynamicListTripletContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < InContainerPairFilter > >	InContainerPairFilters

typedef IMP::base::Vector < IMP::base::WeakPointer < InContainerPairFilter > >	InContainerPairFiltersTemp

typedef IMP::base::Vector < IMP::base::Pointer < InContainerQuadFilter > >	InContainerQuadFilters

typedef IMP::base::Vector < IMP::base::WeakPointer < InContainerQuadFilter > >	InContainerQuadFiltersTemp

typedef IMP::base::Vector < IMP::base::Pointer < InContainerSingletonFilter > >	InContainerSingletonFilters

typedef IMP::base::Vector < IMP::base::WeakPointer < InContainerSingletonFilter > >	InContainerSingletonFiltersTemp

typedef IMP::base::Vector < IMP::base::Pointer < InContainerTripletFilter > >	InContainerTripletFilters

typedef IMP::base::Vector < IMP::base::WeakPointer < InContainerTripletFilter > >	InContainerTripletFiltersTemp

typedef IMP::base::Vector < IMP::base::Pointer < ListPairContainer > >	ListPairContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < ListPairContainer > >	ListPairContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < ListQuadContainer > >	ListQuadContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < ListQuadContainer > >	ListQuadContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < ListSingletonContainer > >	ListSingletonContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < ListSingletonContainer > >	ListSingletonContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < ListTripletContainer > >	ListTripletContainers

typedef IMP::base::Vector < IMP::base::WeakPointer < ListTripletContainer > >	ListTripletContainersTemp

typedef IMP::base::Vector < IMP::base::Pointer < MinimumPairScore > >	MinimumPairScores

typedef IMP::base::Vector < IMP::base::WeakPointer < MinimumPairScore > >	MinimumPairScoresTemp

typedef IMP::base::Vector < IMP::base::Pointer < MinimumQuadScore > >	MinimumQuadScores

typedef IMP::base::Vector < IMP::base::WeakPointer < MinimumQuadScore > >	MinimumQuadScoresTemp

typedef IMP::base::Vector < IMP::base::Pointer < MinimumSingletonScore > >	MinimumSingletonScores

typedef IMP::base::Vector < IMP::base::WeakPointer < MinimumSingletonScore > >	MinimumSingletonScoresTemp

typedef IMP::base::Vector < IMP::base::Pointer < MinimumTripletScore > >	MinimumTripletScores

typedef IMP::base::Vector < IMP::base::WeakPointer < MinimumTripletScore > >	MinimumTripletScoresTemp

typedef IMP::base::Vector < IMP::base::Pointer < PairsConstraint > >	PairsConstraints

typedef IMP::base::Vector < IMP::base::WeakPointer < PairsConstraint > >	PairsConstraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < PairsOptimizerState > >	PairsOptimizerStates

typedef IMP::base::Vector < IMP::base::WeakPointer < PairsOptimizerState > >	PairsOptimizerStatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < PairsRestraint > >	PairsRestraints

typedef IMP::base::Vector < IMP::base::WeakPointer < PairsRestraint > >	PairsRestraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < QuadsConstraint > >	QuadsConstraints

typedef IMP::base::Vector < IMP::base::WeakPointer < QuadsConstraint > >	QuadsConstraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < QuadsOptimizerState > >	QuadsOptimizerStates

typedef IMP::base::Vector < IMP::base::WeakPointer < QuadsOptimizerState > >	QuadsOptimizerStatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < QuadsRestraint > >	QuadsRestraints

typedef IMP::base::Vector < IMP::base::WeakPointer < QuadsRestraint > >	QuadsRestraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < SingletonsConstraint > >	SingletonsConstraints

typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonsConstraint > >	SingletonsConstraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < SingletonsOptimizerState > >	SingletonsOptimizerStates

typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonsOptimizerState > >	SingletonsOptimizerStatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < SingletonsRestraint > >	SingletonsRestraints

typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonsRestraint > >	SingletonsRestraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < TripletsConstraint > >	TripletsConstraints

typedef IMP::base::Vector < IMP::base::WeakPointer < TripletsConstraint > >	TripletsConstraintsTemp

typedef IMP::base::Vector < IMP::base::Pointer < TripletsOptimizerState > >	TripletsOptimizerStates

typedef IMP::base::Vector < IMP::base::WeakPointer < TripletsOptimizerState > >	TripletsOptimizerStatesTemp

typedef IMP::base::Vector < IMP::base::Pointer < TripletsRestraint > >	TripletsRestraints

typedef IMP::base::Vector < IMP::base::WeakPointer < TripletsRestraint > >	TripletsRestraintsTemp

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 >
PairPredicate *	create_in_container_filter (Container *c, std::string name=std::string())

template<class Score , class Container >
kernel::Restraint *	create_restraint (Score s, Container c, std::string name=std::string())

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

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

typedef IMP::base::Vector<IMP::base::Pointer< AllBipartitePairContainer > > IMP::container::AllBipartitePairContainers

Store a set of objects.

Definition at line 61 of file AllBipartitePairContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< AllBipartitePairContainer > > IMP::container::AllBipartitePairContainersTemp

Pass a set of objects.

See Also: AllBipartitePairContainer

Definition at line 61 of file AllBipartitePairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< AllPairContainer > > IMP::container::AllPairContainers

Store a set of objects.

Definition at line 57 of file AllPairContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< AllPairContainer > > IMP::container::AllPairContainersTemp

Pass a set of objects.

See Also: AllPairContainer

Definition at line 57 of file AllPairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< ClosePairContainer > > IMP::container::ClosePairContainers

Store a set of objects.

Definition at line 130 of file ClosePairContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ClosePairContainer > > IMP::container::ClosePairContainersTemp

Pass a set of objects.

See Also: ClosePairContainer

Definition at line 130 of file ClosePairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< ConnectingPairContainer > > IMP::container::ConnectingPairContainers

Store a set of objects.

Definition at line 83 of file ConnectingPairContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ConnectingPairContainer > > IMP::container::ConnectingPairContainersTemp

Pass a set of objects.

See Also: ConnectingPairContainer

Definition at line 83 of file ConnectingPairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< ConsecutivePairContainer > > IMP::container::ConsecutivePairContainers

Store a set of objects.

Definition at line 70 of file ConsecutivePairContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ConsecutivePairContainer > > IMP::container::ConsecutivePairContainersTemp

Pass a set of objects.

See Also: ConsecutivePairContainer

Definition at line 70 of file ConsecutivePairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< DynamicListPairContainer > > IMP::container::DynamicListPairContainers

Store a set of objects.

Definition at line 70 of file DynamicListPairContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DynamicListPairContainer > > IMP::container::DynamicListPairContainersTemp

Pass a set of objects.

See Also: DynamicListPairContainer

Definition at line 70 of file DynamicListPairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< DynamicListQuadContainer > > IMP::container::DynamicListQuadContainers

Store a set of objects.

Definition at line 70 of file DynamicListQuadContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DynamicListQuadContainer > > IMP::container::DynamicListQuadContainersTemp

Pass a set of objects.

See Also: DynamicListQuadContainer

Definition at line 70 of file DynamicListQuadContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< DynamicListSingletonContainer > > IMP::container::DynamicListSingletonContainers

Store a set of objects.

Definition at line 70 of file DynamicListSingletonContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DynamicListSingletonContainer > > IMP::container::DynamicListSingletonContainersTemp

Pass a set of objects.

See Also: DynamicListSingletonContainer

Definition at line 70 of file DynamicListSingletonContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< DynamicListTripletContainer > > IMP::container::DynamicListTripletContainers

Store a set of objects.

Definition at line 70 of file DynamicListTripletContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DynamicListTripletContainer > > IMP::container::DynamicListTripletContainersTemp

Pass a set of objects.

See Also: DynamicListTripletContainer

Definition at line 70 of file DynamicListTripletContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< InContainerPairFilter > > IMP::container::InContainerPairFilters

Store a set of objects.

Definition at line 55 of file InContainerPairFilter.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< InContainerPairFilter > > IMP::container::InContainerPairFiltersTemp

Pass a set of objects.

See Also: InContainerPairFilter

Definition at line 55 of file InContainerPairFilter.h.

typedef IMP::base::Vector<IMP::base::Pointer< InContainerQuadFilter > > IMP::container::InContainerQuadFilters

Store a set of objects.

Definition at line 55 of file InContainerQuadFilter.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< InContainerQuadFilter > > IMP::container::InContainerQuadFiltersTemp

Pass a set of objects.

See Also: InContainerQuadFilter

Definition at line 55 of file InContainerQuadFilter.h.

typedef IMP::base::Vector<IMP::base::Pointer< InContainerSingletonFilter > > IMP::container::InContainerSingletonFilters

Store a set of objects.

Definition at line 55 of file InContainerSingletonFilter.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< InContainerSingletonFilter > > IMP::container::InContainerSingletonFiltersTemp

Pass a set of objects.

See Also: InContainerSingletonFilter

Definition at line 55 of file InContainerSingletonFilter.h.

typedef IMP::base::Vector<IMP::base::Pointer< InContainerTripletFilter > > IMP::container::InContainerTripletFilters

Store a set of objects.

Definition at line 55 of file InContainerTripletFilter.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< InContainerTripletFilter > > IMP::container::InContainerTripletFiltersTemp

Pass a set of objects.

See Also: InContainerTripletFilter

Definition at line 55 of file InContainerTripletFilter.h.

typedef IMP::base::Vector<IMP::base::Pointer< ListPairContainer > > IMP::container::ListPairContainers

Store a set of objects.

Definition at line 75 of file ListPairContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ListPairContainer > > IMP::container::ListPairContainersTemp

Pass a set of objects.

See Also: ListPairContainer

Definition at line 75 of file ListPairContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< ListQuadContainer > > IMP::container::ListQuadContainers

Store a set of objects.

Definition at line 75 of file ListQuadContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ListQuadContainer > > IMP::container::ListQuadContainersTemp

Pass a set of objects.

See Also: ListQuadContainer

Definition at line 75 of file ListQuadContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< ListSingletonContainer > > IMP::container::ListSingletonContainers

Store a set of objects.

Definition at line 75 of file ListSingletonContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ListSingletonContainer > > IMP::container::ListSingletonContainersTemp

Pass a set of objects.

See Also: ListSingletonContainer

Definition at line 75 of file ListSingletonContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< ListTripletContainer > > IMP::container::ListTripletContainers

Store a set of objects.

Definition at line 75 of file ListTripletContainer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ListTripletContainer > > IMP::container::ListTripletContainersTemp

Pass a set of objects.

See Also: ListTripletContainer

Definition at line 75 of file ListTripletContainer.h.

typedef IMP::base::Vector<IMP::base::Pointer< MinimumPairScore > > IMP::container::MinimumPairScores

Store a set of objects.

Definition at line 43 of file MinimumPairScore.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< MinimumPairScore > > IMP::container::MinimumPairScoresTemp

Pass a set of objects.

See Also: MinimumPairScore

Definition at line 43 of file MinimumPairScore.h.

typedef IMP::base::Vector<IMP::base::Pointer< MinimumQuadScore > > IMP::container::MinimumQuadScores

Store a set of objects.

Definition at line 43 of file MinimumQuadScore.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< MinimumQuadScore > > IMP::container::MinimumQuadScoresTemp

Pass a set of objects.

See Also: MinimumQuadScore

Definition at line 43 of file MinimumQuadScore.h.

typedef IMP::base::Vector<IMP::base::Pointer< MinimumSingletonScore > > IMP::container::MinimumSingletonScores

Store a set of objects.

Definition at line 43 of file MinimumSingletonScore.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< MinimumSingletonScore > > IMP::container::MinimumSingletonScoresTemp

Pass a set of objects.

See Also: MinimumSingletonScore

Definition at line 43 of file MinimumSingletonScore.h.

typedef IMP::base::Vector<IMP::base::Pointer< MinimumTripletScore > > IMP::container::MinimumTripletScores

Store a set of objects.

Definition at line 43 of file MinimumTripletScore.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< MinimumTripletScore > > IMP::container::MinimumTripletScoresTemp

Pass a set of objects.

See Also: MinimumTripletScore

Definition at line 43 of file MinimumTripletScore.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairsConstraint > > IMP::container::PairsConstraints

Store a set of objects.

Definition at line 72 of file PairsConstraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< PairsConstraint > > IMP::container::PairsConstraintsTemp

Pass a set of objects.

See Also: PairsConstraint

Definition at line 72 of file PairsConstraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairsOptimizerState > > IMP::container::PairsOptimizerStates

Store a set of objects.

Definition at line 49 of file PairsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< PairsOptimizerState > > IMP::container::PairsOptimizerStatesTemp

Pass a set of objects.

See Also: PairsOptimizerState

Definition at line 49 of file PairsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairsRestraint > > IMP::container::PairsRestraints

Store a set of objects.

Definition at line 64 of file PairsRestraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< PairsRestraint > > IMP::container::PairsRestraintsTemp

Pass a set of objects.

See Also: PairsRestraint

Definition at line 64 of file PairsRestraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< QuadsConstraint > > IMP::container::QuadsConstraints

Store a set of objects.

Definition at line 72 of file QuadsConstraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< QuadsConstraint > > IMP::container::QuadsConstraintsTemp

Pass a set of objects.

See Also: QuadsConstraint

Definition at line 72 of file QuadsConstraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< QuadsOptimizerState > > IMP::container::QuadsOptimizerStates

Store a set of objects.

Definition at line 49 of file QuadsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< QuadsOptimizerState > > IMP::container::QuadsOptimizerStatesTemp

Pass a set of objects.

See Also: QuadsOptimizerState

Definition at line 49 of file QuadsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< QuadsRestraint > > IMP::container::QuadsRestraints

Store a set of objects.

Definition at line 64 of file QuadsRestraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< QuadsRestraint > > IMP::container::QuadsRestraintsTemp

Pass a set of objects.

See Also: QuadsRestraint

Definition at line 64 of file QuadsRestraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< SingletonsConstraint > > IMP::container::SingletonsConstraints

Store a set of objects.

Definition at line 72 of file SingletonsConstraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SingletonsConstraint > > IMP::container::SingletonsConstraintsTemp

Pass a set of objects.

See Also: SingletonsConstraint

Definition at line 72 of file SingletonsConstraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< SingletonsOptimizerState > > IMP::container::SingletonsOptimizerStates

Store a set of objects.

Definition at line 49 of file SingletonsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SingletonsOptimizerState > > IMP::container::SingletonsOptimizerStatesTemp

Pass a set of objects.

See Also: SingletonsOptimizerState

Definition at line 49 of file SingletonsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< SingletonsRestraint > > IMP::container::SingletonsRestraints

Store a set of objects.

Definition at line 64 of file SingletonsRestraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< SingletonsRestraint > > IMP::container::SingletonsRestraintsTemp

Pass a set of objects.

See Also: SingletonsRestraint

Definition at line 64 of file SingletonsRestraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< TripletsConstraint > > IMP::container::TripletsConstraints

Store a set of objects.

Definition at line 72 of file TripletsConstraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TripletsConstraint > > IMP::container::TripletsConstraintsTemp

Pass a set of objects.

See Also: TripletsConstraint

Definition at line 72 of file TripletsConstraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< TripletsOptimizerState > > IMP::container::TripletsOptimizerStates

Store a set of objects.

Definition at line 49 of file TripletsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TripletsOptimizerState > > IMP::container::TripletsOptimizerStatesTemp

Pass a set of objects.

See Also: TripletsOptimizerState

Definition at line 49 of file TripletsOptimizerState.h.

typedef IMP::base::Vector<IMP::base::Pointer< TripletsRestraint > > IMP::container::TripletsRestraints

Store a set of objects.

Definition at line 64 of file TripletsRestraint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TripletsRestraint > > IMP::container::TripletsRestraintsTemp

Pass a set of objects.

See Also: TripletsRestraint

Definition at line 64 of file TripletsRestraint.h.

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.

Definition at line 34 of file container/generic.h.

template<class Container >

PairPredicate* 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.

Note: This is different than the InContainerPairFilter.

Definition at line 44 of file container/generic.h.

template<class Score , class Container >

kernel::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.

A Python version of this is provided, but it produces a slightly less efficient restraint.

Definition at line 26 of file container/generic.h.

std::string IMP::container::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::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 setup_environment.sh script.

double IMP::container::get_slack_estimate	(	const kernel::ParticlesTemp &	ps,
		double	upper_bound,
		double	step,
		const kernel::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

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