IMP::container::AllPairContainer Class Reference

Return all unordered pairs of particles taken from the SingletonContainer. More...

#include <IMP/container/AllPairContainer.h>

Inheritance diagram for IMP::container::AllPairContainer:

Public Member Functions
	AllPairContainer (SingletonContainerAdaptor c, std::string name="AllPairContainer%1%")
	Get the individual particles from the passed SingletonContainer.
template<class F >
void	apply_generic (F *f) const
	IMP_IMPLEMENT_PAIR_CONTAINER (AllPairContainer)
Public Member Functions inherited from IMP::kernel::PairContainer
void	apply (const PairModifier *sm) const
	Apply a SingletonModifier to the contents.
void	apply_generic (const PairModifier *m) const
	Just use apply() in the base class.
bool	get_contains_particle_pair (ParticlePair v) const
	This function is very slow and you should think hard about using it. More...
virtual ParticleIndexPairs	get_indexes () const =0
unsigned int	get_number_of_particle_pairs () const
ParticlePair	get_particle_pair (unsigned int i) const
ParticlePairsTemp	get_particle_pairs () const
virtual ParticleIndexPairs	get_range_indexes () const =0
Public Member Functions inherited from IMP::kernel::Container
virtual void	do_after_evaluate (DerivativeAccumulator *accpt)
	Reset changed status.
ModelObjectsTemp	do_get_outputs () const
	containers don't have outputs
virtual ParticleIndexes	get_all_possible_indexes () const =0
	Get contained particles. More...
ParticlesTemp	get_all_possible_particles () const
bool	get_is_changed () const
virtual bool	get_is_decomposable () const
Public Member Functions inherited from IMP::kernel::ScoreState
	ScoreState (Model *m, std::string name="ScoreState %1%")
void	after_evaluate (DerivativeAccumulator *accpt)
	Do post evaluation work if needed.
void	before_evaluate ()
	Force update of the structure.
ContainersTemp	get_input_containers () const
ParticlesTemp	get_input_particles () const
ContainersTemp	get_output_containers () const
ParticlesTemp	get_output_particles () const
Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (Model *m, std::string name)
ModelObjectsTemp	get_inputs () const
ModelObjectsTemps	get_interactions () const
Model *	get_model () const
ModelObjectsTemp	get_outputs () const
Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Related Functions
(Note that these are not member functions.)
typedef IMP::base::Vector < IMP::base::WeakPointer < AllPairContainer > >	AllPairContainersTemp
Related Functions inherited from IMP::kernel::PairContainer
typedef IMP::base::Vector < IMP::base::WeakPointer < PairContainer > >	PairContainersTemp
Related Functions inherited from IMP::kernel::Container
typedef IMP::base::Vector < IMP::base::WeakPointer < Container > >	ContainersTemp
Related Functions inherited from IMP::kernel::ScoreState
typedef IMP::base::Vector < IMP::base::WeakPointer < ScoreState > >	ScoreStatesTemp
Related Functions inherited from IMP::kernel::ModelObject
typedef IMP::base::Vector < IMP::base::WeakPointer < ModelObject > >	ModelObjectsTemp
Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

Additional Inherited Members
Public Types inherited from IMP::kernel::PairContainer
typedef ParticleIndexPair	ContainedIndexType
typedef ParticleIndexPairs	ContainedIndexTypes
typedef ParticlePair	ContainedType
typedef ParticlePairsTemp	ContainedTypes
Protected Member Functions inherited from IMP::kernel::PairContainer
	PairContainer (Model *m, std::string name="PairContainer %1%")
virtual void	do_apply (const PairModifier *sm) const =0
virtual bool	do_get_provides_access () const

Detailed Description

Here is an example using this container to restrain all particles in a set to be within a a certain distance of one another.

## \example core/restrain_diameter.py
## An example restraining the diameter of a set of points. That is, the restraint penalizes conformations where there are two point more than a certain distance from one another.

import IMP
import IMP.core
import IMP.container

# This example restraints the diameter of a set of particles to be smaller than 10

diameter=10
m= IMP.Model()
lc= IMP.container.ListSingletonContainer(IMP.core.create_xyzr_particles(m, 50, 1.0))
h=IMP.core.HarmonicUpperBound(0,1)
r=IMP.core.DiameterRestraint(h, lc, diameter)
m.add_restraint(r)

# Set up optimizer
o= IMP.core.ConjugateGradients()
o.set_model(m)

max=0
for p0 in lc.get_particles():
    for p1 in lc.get_particles():
        d=IMP.core.get_distance(IMP.core.XYZ(p0),
                            IMP.core.XYZ(p1))
        if d > max: max=d
print "The maximim distance is "+str(max)

IMP.base.set_log_level(IMP.base.SILENT)
o.optimize(100)

max=0
for p0 in lc.get_particles():
    for p1 in lc.get_particles():
        d=IMP.core.get_distance(IMP.core.XYZ(p0),
                            IMP.core.XYZ(p1))
        if d > max: max=d
print "Afterwards, the maximim distance is "+str(max)

Note

Sequential access is much more efficient than random access which is suicidally slow for now. Complain if you want fast(er) random access. We might listen.

The maintenance of the invariant is done by an associated IMP::Constraint. As a result, the state is only guaranteed to be correct either during model evaluation, or immediately following model evaluation before any particles have been changed.

Definition at line 34 of file AllPairContainer.h.

Friends And Related Function Documentation

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

related

Pass a set of objects.

Definition at line 56 of file AllPairContainer.h.

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The documentation for this class was generated from the following file:

• AllPairContainer.h