IMP
2.3.1
The Integrative Modeling Platform
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Various classes to hold sets of particles. More...
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.
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:
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... | |
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 | |
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 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.
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::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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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::Pointer< ListQuadContainer > > IMP::container::ListQuadContainers |
Store a set of objects.
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.
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.
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::Pointer< MinimumQuadScore > > IMP::container::MinimumQuadScores |
Store a set of objects.
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.
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.
Definition at line 43 of file MinimumTripletScore.h.
Store a set of objects.
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.
Definition at line 49 of file PairsOptimizerState.h.
Store a set of objects.
Definition at line 64 of file PairsRestraint.h.
Store a set of objects.
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.
Definition at line 49 of file QuadsOptimizerState.h.
Store a set of objects.
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.
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.
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.
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.
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.
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.
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.
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.
Definition at line 44 of file container/generic.h.
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
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
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
For best results, make the particles start in a that is "typical" for the optimization.