IMP::container::ClosePairContainer Class Reference

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Detailed Description

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

This maintains a list of particles whose inter-sphere distance is smaller than the distance parameter.

In order to do this efficiently the class actually computes all pairs within distance+slack of one another. As long as the particles don't move more than the slack amount, the list is still valid and doesn't need to be recomputed. The container keeps track internally of how far the particles have moved using a score state, and is also updated via a score state.

Note:

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.

Here is a simple example of using this for a nonbonded list

import IMP
import IMP.core
import IMP.atom
import IMP.container

# This example addes a restraint on nonbonded interactions
# after excluding a set of bonded interactions.

m= IMP.Model()
# The set of particles
ps = IMP.container.ListSingletonContainer(IMP.core.create_xyzr_particles(m, 20, 1.0))

# create a bond between two particles
bd0= IMP.atom.Bonded.setup_particle(ps.get_particle(0))
bd1= IMP.atom.Bonded.setup_particle(ps.get_particle(1))
IMP.atom.create_custom_bond(bd0, bd1, 2.0)

# Set up the nonbonded list for all pairs at are touching
# and let things move 3 before updating the list
nbl= IMP.container.ClosePairContainer(ps, 0.0, 3.0)
nbl.add_pair_filter(IMP.atom.BondedPairFilter())

# Set up excluded volume
sdps= IMP.core.SphereDistancePairScore(IMP.core.HarmonicLowerBound(0,1))
evr= IMP.container.PairsRestraint(sdps, nbl)
m.add_restraint(evr)

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

o.optimize(1000)

Note:

This class uses the IMP::core::BoxSweepClosePairsFinder by default if CGAL is available.

See also:

CloseBipartitePairContainer

ClosePairsFinder

Inheritance diagram for IMP::container::ClosePairContainer:

[legend]

Public Member Functions
void	apply (const PairModifier *sm, DerivativeAccumulator &da)
void	apply (const PairModifier *sm)
	ClosePairContainer (SingletonContainer *c, Model *m, double distance, core::ClosePairsFinder *cpf, double slack=1)
	If the container is empty, you can pass the model explicitly.
	ClosePairContainer (SingletonContainer *c, double distance, core::ClosePairsFinder *cpf, double slack=1)
	Get the individual particles from the passed SingletonContainer.
	ClosePairContainer (SingletonContainer *c, Model *m, double distance, double slack=1)
	If the container is empty, you can pass the model explicitly.
	ClosePairContainer (SingletonContainer *c, double distance, double slack=1)
	Get the individual particles from the passed SingletonContainer.
double	evaluate (const PairScore *s, DerivativeAccumulator *da) const
double	evaluate_change (const PairScore *s, DerivativeAccumulator *da) const
double	evaluate_prechange (const PairScore *s, DerivativeAccumulator *da) const
ParticlesTemp	get_contained_particles () const
bool	get_contained_particles_changed () const
bool	get_contains_particle_pair (const ParticlePair &p) const
ContainersTemp	get_input_containers () const
unsigned int	get_number_of_particle_pairs () const
ParticlePair	get_particle_pair (unsigned int i) const
virtual std::string	get_type_name () const
virtual ::IMP::VersionInfo	get_version_info () const
Methods to control the set of filters
PairContainer objects can be used as filters to prevent the addition of pairs to the containeroutput list. Pairs which are contained in any container added to this list will be excluded from the close pairs list.
unsigned int	add_pair_filter (PairFilter *obj)
void	add_pair_filters (const PairFilters &obj)
void	clear_pair_filters ()
bool	get_has_pair_filters () const
	return true if there are any objects in the container
unsigned int	get_number_of_pair_filters () const
PairFilter *	get_pair_filter (unsigned int i) const
PairFilterConstIterator	pair_filters_begin () const
PairFilterIterator	pair_filters_begin ()
PairFilterConstIterator	pair_filters_end () const
PairFilterIterator	pair_filters_end ()
void	remove_pair_filter (PairFilter *d)
	Remove any occurences of d from the container.
void	remove_pair_filters (const PairFilters &d)
	Remove any occurences of each item in d.
template<class F >
void	remove_pair_filters_if (const F &f)
	Remove any occurrences for which f is true.
void	reserve_pair_filters (unsigned int sz)
void	set_pair_filters (const PairFilters &ps)
Friends
template<class T >
void	IMP::internal::unref (T *)

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Member Function Documentation

unsigned int IMP::container::ClosePairContainer::add_pair_filter

(

PairFilter *

obj

)

Returns:

index of object within the object

void IMP::container::ClosePairContainer::add_pair_filters

(

const PairFilters &

obj

)

Add several objects to the container. They are not necessarily added at the end.

PairFilter* IMP::container::ClosePairContainer::get_pair_filter

(

unsigned int

i

)

const

Get the object refered to by the index

Exceptions:

IndexException

in Python if the index is out of range

void IMP::container::ClosePairContainer::set_pair_filters

(

const PairFilters &

ps

)

Set the contents of the container to ps removing all its current contents.

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

• ClosePairContainer.h
• container/__init__.py