IMP Reference Guide
develop.63b38c487d,2024/12/24
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 |
class | AllPairContainer |
Return all unordered pairs of particles taken from the SingletonContainer. More... | |
class | CloseBipartitePairContainer |
Return all spatially-proximal pairs of particles (a,b) from the two SingletonContainers A and B, where a is in A and b is in B. 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 ParticleIndexPairs. More... | |
class | DynamicListQuadContainer |
Store a ParticleIndexQuads. More... | |
class | DynamicListSingletonContainer |
Store a ParticleIndexes. More... | |
class | DynamicListTripletContainer |
Store a ParticleIndexTriplets. More... | |
class | EventPairsOptimizerState |
class | EventQuadsOptimizerState |
class | EventSingletonsOptimizerState |
class | EventTripletsOptimizerState |
class | ExclusiveConsecutivePairContainer |
class | ExclusiveConsecutivePairFilter |
class | InContainerPairFilter |
A filter which returns true if a container contains the Pair. More... | |
class | InContainerQuadFilter |
A filter which returns true if a container contains the Quad. More... | |
class | InContainerSingletonFilter |
A filter which returns true if a container contains the Singleton. More... | |
class | InContainerTripletFilter |
A filter which returns true if a container contains the Triplet. More... | |
class | ListPairContainer |
Store a list of ParticleIndexPairs. More... | |
class | ListQuadContainer |
Store a list of ParticleIndexQuads. More... | |
class | ListSingletonContainer |
Store a list of ParticleIndexes. More... | |
class | ListTripletContainer |
Store a list of 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 > | |
Restraint * | create_restraint (Score *s, Container *c, std::string name=std::string()) |
double | get_slack_estimate (Model *m, ParticleIndexes ps, double upper_bound, double step, const RestraintsTemp &restraints, bool derivatives, Optimizer *opt, ClosePairContainer *cpc) |
Standard module functions | |
All | |
std::string | get_module_version () |
Return the version of this module, as a string. More... | |
std::string | get_module_name () |
std::string | get_data_path (std::string file_name) |
Return the full path to one of this module's data files. More... | |
std::string | get_example_path (std::string file_name) |
Return the full path to one of this module's example files. More... | |
typedef IMP::Vector<IMP::Pointer< AllBipartitePairContainer > > IMP::container::AllBipartitePairContainers |
A vector of reference-counting object pointers.
Definition at line 65 of file AllBipartitePairContainer.h.
typedef IMP::Vector<IMP::WeakPointer< AllBipartitePairContainer > > IMP::container::AllBipartitePairContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 65 of file AllBipartitePairContainer.h.
A vector of reference-counting object pointers.
Definition at line 54 of file AllPairContainer.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 54 of file AllPairContainer.h.
A vector of reference-counting object pointers.
Definition at line 140 of file ClosePairContainer.h.
typedef IMP::Vector<IMP::WeakPointer< ClosePairContainer > > IMP::container::ClosePairContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 140 of file ClosePairContainer.h.
typedef IMP::Vector<IMP::Pointer< ConnectingPairContainer > > IMP::container::ConnectingPairContainers |
A vector of reference-counting object pointers.
Definition at line 83 of file ConnectingPairContainer.h.
typedef IMP::Vector<IMP::WeakPointer< ConnectingPairContainer > > IMP::container::ConnectingPairContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 83 of file ConnectingPairContainer.h.
typedef IMP::Vector<IMP::Pointer< ConsecutivePairContainer > > IMP::container::ConsecutivePairContainers |
A vector of reference-counting object pointers.
Definition at line 71 of file ConsecutivePairContainer.h.
typedef IMP::Vector<IMP::WeakPointer< ConsecutivePairContainer > > IMP::container::ConsecutivePairContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 71 of file ConsecutivePairContainer.h.
typedef IMP::Vector<IMP::Pointer< DynamicListPairContainer > > IMP::container::DynamicListPairContainers |
A vector of reference-counting object pointers.
Definition at line 81 of file DynamicListPairContainer.h.
typedef IMP::Vector<IMP::WeakPointer< DynamicListPairContainer > > IMP::container::DynamicListPairContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 81 of file DynamicListPairContainer.h.
typedef IMP::Vector<IMP::Pointer< DynamicListQuadContainer > > IMP::container::DynamicListQuadContainers |
A vector of reference-counting object pointers.
Definition at line 81 of file DynamicListQuadContainer.h.
typedef IMP::Vector<IMP::WeakPointer< DynamicListQuadContainer > > IMP::container::DynamicListQuadContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 81 of file DynamicListQuadContainer.h.
typedef IMP::Vector<IMP::Pointer< DynamicListSingletonContainer > > IMP::container::DynamicListSingletonContainers |
A vector of reference-counting object pointers.
Definition at line 81 of file DynamicListSingletonContainer.h.
typedef IMP::Vector<IMP::WeakPointer< DynamicListSingletonContainer > > IMP::container::DynamicListSingletonContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 81 of file DynamicListSingletonContainer.h.
typedef IMP::Vector<IMP::Pointer< DynamicListTripletContainer > > IMP::container::DynamicListTripletContainers |
A vector of reference-counting object pointers.
Definition at line 81 of file DynamicListTripletContainer.h.
typedef IMP::Vector<IMP::WeakPointer< DynamicListTripletContainer > > IMP::container::DynamicListTripletContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 81 of file DynamicListTripletContainer.h.
A vector of reference-counting object pointers.
Definition at line 56 of file InContainerPairFilter.h.
typedef IMP::Vector<IMP::WeakPointer< InContainerPairFilter > > IMP::container::InContainerPairFiltersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 56 of file InContainerPairFilter.h.
A vector of reference-counting object pointers.
Definition at line 56 of file InContainerQuadFilter.h.
typedef IMP::Vector<IMP::WeakPointer< InContainerQuadFilter > > IMP::container::InContainerQuadFiltersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 56 of file InContainerQuadFilter.h.
typedef IMP::Vector<IMP::Pointer< InContainerSingletonFilter > > IMP::container::InContainerSingletonFilters |
A vector of reference-counting object pointers.
Definition at line 56 of file InContainerSingletonFilter.h.
typedef IMP::Vector<IMP::WeakPointer< InContainerSingletonFilter > > IMP::container::InContainerSingletonFiltersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 56 of file InContainerSingletonFilter.h.
typedef IMP::Vector<IMP::Pointer< InContainerTripletFilter > > IMP::container::InContainerTripletFilters |
A vector of reference-counting object pointers.
Definition at line 56 of file InContainerTripletFilter.h.
typedef IMP::Vector<IMP::WeakPointer< InContainerTripletFilter > > IMP::container::InContainerTripletFiltersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 56 of file InContainerTripletFilter.h.
A vector of reference-counting object pointers.
Definition at line 92 of file ListPairContainer.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 92 of file ListPairContainer.h.
A vector of reference-counting object pointers.
Definition at line 92 of file ListQuadContainer.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 92 of file ListQuadContainer.h.
typedef IMP::Vector<IMP::Pointer< ListSingletonContainer > > IMP::container::ListSingletonContainers |
A vector of reference-counting object pointers.
Definition at line 92 of file ListSingletonContainer.h.
typedef IMP::Vector<IMP::WeakPointer< ListSingletonContainer > > IMP::container::ListSingletonContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 92 of file ListSingletonContainer.h.
A vector of reference-counting object pointers.
Definition at line 92 of file ListTripletContainer.h.
typedef IMP::Vector<IMP::WeakPointer< ListTripletContainer > > IMP::container::ListTripletContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 92 of file ListTripletContainer.h.
A vector of reference-counting object pointers.
Definition at line 44 of file MinimumPairScore.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 44 of file MinimumPairScore.h.
A vector of reference-counting object pointers.
Definition at line 44 of file MinimumQuadScore.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 44 of file MinimumQuadScore.h.
A vector of reference-counting object pointers.
Definition at line 44 of file MinimumSingletonScore.h.
typedef IMP::Vector<IMP::WeakPointer< MinimumSingletonScore > > IMP::container::MinimumSingletonScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 44 of file MinimumSingletonScore.h.
A vector of reference-counting object pointers.
Definition at line 44 of file MinimumTripletScore.h.
typedef IMP::Vector<IMP::WeakPointer< MinimumTripletScore > > IMP::container::MinimumTripletScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 44 of file MinimumTripletScore.h.
A vector of reference-counting object pointers.
Definition at line 84 of file PairsConstraint.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 84 of file PairsConstraint.h.
A vector of reference-counting object pointers.
Definition at line 49 of file PairsOptimizerState.h.
typedef IMP::Vector<IMP::WeakPointer< PairsOptimizerState > > IMP::container::PairsOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 49 of file PairsOptimizerState.h.
A vector of reference-counting object pointers.
Definition at line 73 of file PairsRestraint.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 73 of file PairsRestraint.h.
A vector of reference-counting object pointers.
Definition at line 84 of file QuadsConstraint.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 84 of file QuadsConstraint.h.
A vector of reference-counting object pointers.
Definition at line 49 of file QuadsOptimizerState.h.
typedef IMP::Vector<IMP::WeakPointer< QuadsOptimizerState > > IMP::container::QuadsOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 49 of file QuadsOptimizerState.h.
A vector of reference-counting object pointers.
Definition at line 73 of file QuadsRestraint.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 73 of file QuadsRestraint.h.
A vector of reference-counting object pointers.
Definition at line 84 of file SingletonsConstraint.h.
typedef IMP::Vector<IMP::WeakPointer< SingletonsConstraint > > IMP::container::SingletonsConstraintsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 84 of file SingletonsConstraint.h.
typedef IMP::Vector<IMP::Pointer< SingletonsOptimizerState > > IMP::container::SingletonsOptimizerStates |
A vector of reference-counting object pointers.
Definition at line 49 of file SingletonsOptimizerState.h.
typedef IMP::Vector<IMP::WeakPointer< SingletonsOptimizerState > > IMP::container::SingletonsOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 49 of file SingletonsOptimizerState.h.
A vector of reference-counting object pointers.
Definition at line 73 of file SingletonsRestraint.h.
typedef IMP::Vector<IMP::WeakPointer< SingletonsRestraint > > IMP::container::SingletonsRestraintsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 73 of file SingletonsRestraint.h.
A vector of reference-counting object pointers.
Definition at line 84 of file TripletsConstraint.h.
typedef IMP::Vector<IMP::WeakPointer< TripletsConstraint > > IMP::container::TripletsConstraintsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 84 of file TripletsConstraint.h.
typedef IMP::Vector<IMP::Pointer< TripletsOptimizerState > > IMP::container::TripletsOptimizerStates |
A vector of reference-counting object pointers.
Definition at line 49 of file TripletsOptimizerState.h.
typedef IMP::Vector<IMP::WeakPointer< TripletsOptimizerState > > IMP::container::TripletsOptimizerStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 49 of file TripletsOptimizerState.h.
A vector of reference-counting object pointers.
Definition at line 73 of file TripletsRestraint.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 73 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.
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 one of this module's data files.
To read the data file "data_library" that was placed in the data
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::container::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::container::get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 5 of file EMageFit/__init__.py.
double IMP::container::get_slack_estimate | ( | Model * | m, |
ParticleIndexes | ps, | ||
double | upper_bound, | ||
double | step, | ||
const RestraintsTemp & | restraints, | ||
bool | derivatives, | ||
Optimizer * | opt, | ||
ClosePairContainer * | cpc | ||
) |
Estimate the proper slack based on
For best results, make the particles start in a configuration that is "typical" for the optimization.