See IMP.container Overview for more information.

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 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 list of ParticlePairsTemp. More...

class	DynamicListQuadContainer
	Store a list of ParticleQuadsTemp. More...

class	DynamicListSingletonContainer
	Store a list of ParticlesTemp. More...

class	DynamicListTripletContainer
	Store a list of ParticleTripletsTemp. 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	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::Pointer < AllPairContainer > >	AllPairContainers

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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...

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

	IMP_OBJECTS (DynamicListPairContainer, DynamicListPairContainers)

	IMP_OBJECTS (DynamicListQuadContainer, DynamicListQuadContainers)

	IMP_OBJECTS (DynamicListSingletonContainer, DynamicListSingletonContainers)

	IMP_OBJECTS (DynamicListTripletContainer, DynamicListTripletContainers)

	IMP_OBJECTS (ListTripletContainer, ListTripletContainers)

	IMP_OBJECTS (ListSingletonContainer, ListSingletonContainers)

	IMP_OBJECTS (ListPairContainer, ListPairContainers)

	IMP_OBJECTS (ListQuadContainer, ListQuadContainers)

	IMP_OBJECTS (SingletonsRestraint, SingletonsRestraints)

	IMP_OBJECTS (PairsRestraint, PairsRestraints)

	IMP_OBJECTS (TripletsRestraint, TripletsRestraints)

	IMP_OBJECTS (QuadsRestraint, QuadsRestraints)

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< AllBipartitePairContainer > > IMP::container::AllBipartitePairContainers

Store a set of objects.

Definition at line 53 of file AllBipartitePairContainer.h.

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

Store a set of objects.

Definition at line 56 of file AllPairContainer.h.

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

Store a set of objects.

Definition at line 98 of file ClosePairContainer.h.

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

Store a set of objects.

Definition at line 67 of file ConnectingPairContainer.h.

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

Store a set of objects.

Definition at line 64 of file ConsecutivePairContainer.h.

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

Store a set of objects.

Definition at line 54 of file InContainerPairFilter.h.

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

Store a set of objects.

Definition at line 54 of file InContainerQuadFilter.h.

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

Store a set of objects.

Definition at line 54 of file InContainerSingletonFilter.h.

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

Store a set of objects.

Definition at line 54 of file InContainerTripletFilter.h.

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

Store a set of objects.

Definition at line 40 of file MinimumPairScore.h.

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

Store a set of objects.

Definition at line 40 of file MinimumQuadScore.h.

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

Store a set of objects.

Definition at line 40 of file MinimumSingletonScore.h.

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

Store a set of objects.

Definition at line 40 of file MinimumTripletScore.h.

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

Store a set of objects.

Definition at line 79 of file PairsConstraint.h.

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

Store a set of objects.

Definition at line 48 of file PairsOptimizerState.h.

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

Store a set of objects.

Definition at line 79 of file QuadsConstraint.h.

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

Store a set of objects.

Definition at line 48 of file QuadsOptimizerState.h.

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

Store a set of objects.

Definition at line 79 of file SingletonsConstraint.h.

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

Store a set of objects.

Definition at line 48 of file SingletonsOptimizerState.h.

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

Store a set of objects.

Definition at line 79 of file TripletsConstraint.h.

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

Store a set of objects.

Definition at line 48 of file TripletsOptimizerState.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 46 of file container/generic.h.

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.

Definition at line 24 of file container/generic.h.

std::string IMP::container::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::container::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.

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.

Classes

Typedefs

Functions

Standard module methods

Typedef Documentation

Function Documentation