IMP  2.0.0
The Integrative Modeling Platform
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
 
Modelget_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
 

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

Pass a set of objects.

Definition at line 56 of file AllPairContainer.h.


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