IMP  2.0.0
The Integrative Modeling Platform
IMP::container Namespace Reference

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 >
Constraintcreate_constraint (Before *b, After *a, Container *c, std::string name=std::string())
 
template<class Container >
PairPredicatecreate_in_container_filter (Container *c, std::string name=std::string())
 
template<class Score , class Container >
Restraintcreate_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

Store a set of objects.

Definition at line 56 of file AllPairContainer.h.

Store a set of objects.

Definition at line 40 of file MinimumPairScore.h.

Store a set of objects.

Definition at line 40 of file MinimumQuadScore.h.

Store a set of objects.

Definition at line 79 of file PairsConstraint.h.

Store a set of objects.

Definition at line 79 of file QuadsConstraint.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.