IMP::container::SingletonsRestraint Class Reference

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Detailed Description

Applies a SingletonScore to each Singleton in a list.

This restraint stores the used particles in a ParticlesTemp. The container used can be set so that the list can be shared with other containers (or a nonbonded list can be used). By default a ListSingletonContainer is used and the {add_, set_, clear_}particle{s} methodas can be used.

Examples using various multiplicity containers:

import IMP.example
radius=10
stiffness=2
center= IMP.algebra.Vector3D(1,2,3)
(m,c)=IMP.example.create_model_and_particles()
ub= IMP.core.HarmonicUpperBound(radius, stiffness)

# Restrain based on the distance to a single point (hence a ball
ss= IMP.core.DistanceToSingletonScore(ub, center)

r= IMP.container.SingletonsRestraint(ss, c)
m.add_restraint(r)
m.evaluate(False)

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)

See also:

SingletonRestraint

Examples: charmm forcefield verbose, initialize chains, optimize balls, restrain in sphere, load protein restrain bonds

Inheritance diagram for IMP::container::SingletonsRestraint:

List of all members.

Public Member Functions
	SingletonsRestraint (SingletonScore *ss, SingletonContainer *pc, std::string name="SingletonsRestraint %1%")
	Create the restraint with a shared container.
ParticlesTemp	get_arguments () const
	Get the container used to store Particles.
SingletonContainer *	get_container () const
SingletonScore *	get_score () const
Static Public Member Functions
static SingletonsRestraint *	get_from (IMP::base::Object *o)

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Constructor & Destructor Documentation

IMP::container::SingletonsRestraint::SingletonsRestraint	(	SingletonScore *	ss,
		SingletonContainer *	pc,
		std::string	name = "SingletonsRestraint %1%"
	)

Create the restraint with a shared container.

Parameters:

[in]	ss	The function to apply to each particle.
[in]	pc	The container containing the stored particles. This container is not copied.
[in]	name	The object name

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Member Function Documentation

ParticlesTemp IMP::container::SingletonsRestraint::get_arguments

(

)

const

Get the container used to store Particles.

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

• SingletonsRestraint.h