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.SoftSpherePairScore(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

Examples: chain, filter close pairs, nonbonded interactions, charmm forcefield verbose, initialize chains, basic optimization, rigid collisions, charmm forcefield, assess dope, excluded volume

Inheritance diagram for IMP::container::ClosePairContainer:

List of all members.

Public Member Functions
	ClosePairContainer (SingletonContainer *c, double distance, double slack=1)
	Get the individual particles from the passed SingletonContainer.
	ClosePairContainer (SingletonContainer *c, double distance, core::ClosePairsFinder *cpf, double slack=1)
	Get the individual particles from the passed SingletonContainer.
bool	get_is_up_to_date () const
double	get_slack () const
	IMP_IMPLEMENT_PAIR_CONTAINER (ClosePairContainer)
void	set_slack (double s)
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.
void	remove_pair_filter (PairFilter *d)
template<class F >
void	remove_pair_filters_if (const F &f)
template<class List >
void	remove_pair_filters (List d)
template<class List >
void	set_pair_filters (List ps)
template<class List >
void	set_pair_filters_order (List ps)
unsigned int	add_pair_filter (PairFilter *obj)
template<class List >
void	add_pair_filters (List objs)
void	clear_pair_filters ()
unsigned int	get_number_of_pair_filters () const
bool	get_has_pair_filters () const
PairFilter *	get_pair_filter (unsigned int i) const
PairFilters	get_pair_filters () const
void	reserve_pair_filters (unsigned int sz)
PairFilterIterator	pair_filters_begin ()
PairFilterIterator	pair_filters_end ()
PairFilterConstIterator	pair_filters_begin () const
PairFilterConstIterator	pair_filters_end () const

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Constructor & Destructor Documentation

IMP::container::ClosePairContainer::ClosePairContainer	(	SingletonContainer *	c,
		double	distance,
		double	slack = 1
	)

Get the individual particles from the passed SingletonContainer.

IMP::container::ClosePairContainer::ClosePairContainer	(	SingletonContainer *	c,
		double	distance,
		core::ClosePairsFinder *	cpf,
		double	slack = 1
	)

Get the individual particles from the passed SingletonContainer.

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

• ClosePairContainer.h