IMP::core::RigidClosePairsFinder Class Reference

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Detailed Description

Peform more efficient close pair finding when rigid bodies are involved.

The class finds all close pairs consisting of particles taken from the passed list(s) (if they are not rigid bodies) or members of rigid bodies passed as input. That is, given an input list l, for each pair of particles p, q taken from the list, that are closer than the distance threshold, it returns

• if neither p or q are RigidBody particles it returns (p,q)
• if bother p and q are RigidBody particles, it returns all (r,s) where r is a member of p and s is member of q and r and s are closer than the distance threshold
• pairs (p,s) or (r,q) as appropriate if only one of p or q is a rigid body.

Consequently, the user must ensure that the RigidBody are assigned a radius that encloses all of their RigidMember particles.

It uses another ClosePairsFinder to find which pairs of particles in the input list or lists are close. Your choice of this can be passed to the constructor.

Note:

The bipartite method will also not return any pairs where both members are in the same rigid body.

The bounding spheres are kept in internal coordinates for the rigid body and transformed on the fly. It would probably be faster to cache the tranformed results.

The particles are divided up using a grid. The number of grid cells to use should be explored. In addition, with highly excentric sets of points, there will be too many cells.

Do not reuse RigidClosePairsFinders for different sets of particles from the same rigid body.

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

# This example addes a restraint on nonbonded interactions
# Since it is between two rigid bodies, internal interactions are ignored

m= IMP.Model()
# The particles in the rigid bodies
rbps0= IMP.core.create_xyzr_particles(m, 3, 1)
rbps1= IMP.core.create_xyzr_particles(m, 3, 1)

rbp0= IMP.Particle(m)
rbp1= IMP.Particle(m)

rbss0 = IMP.core.RigidBody.setup_particle(rbp0, IMP.core.XYZs(rbps0))

rbss1 = IMP.core.RigidBody.setup_particle(rbp1, IMP.core.XYZs(rbps1))

lsc= IMP.container.ListSingletonContainer(m)
lsc.add_particles(rbps0)
lsc.add_particles(rbps1)

# Set up the nonbonded list
nbl= IMP.container.ClosePairContainer(lsc, 0, IMP.core.RigidClosePairsFinder(), 2.0)

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

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

done=False
while not done:
    try:
        o.optimize(1000)
    except IMP.base.ModelException:
        for d in [rbss0, rbss1]:
            d.set_transformation(IMP.algebra.Transformation3D(IMP.algebra.get_random_rotation_3d(),
                                                              IMP.algebra.get_random_vector_in(IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0,0,0),
                                                                                               IMP.algebra.Vector3D(10,10,10)))))
    else:
        done=True

The class RigidClosePairsFinder uses CGAL in order to improve its functionality. It will fall back on less good code without it.

See also:

ClosePairsScoreState

RigidBody

cover_members()

Examples: rigid collisions

Inheritance diagram for IMP::core::RigidClosePairsFinder:

List of all members.

Public Member Functions
	RigidClosePairsFinder (ClosePairsFinder *cpf=nullptr)
ParticlePairsTemp	get_close_pairs (Particle *a, Particle *b, const ParticleIndexes &pa, const ParticleIndexes &pb) const
void	set_distance (double d)
Public Member Functions inherited from IMP::core::ClosePairsFinder
	ClosePairsFinder (std::string name)
virtual ParticlePairsTemp	get_close_pairs (const ParticlesTemp &pc) const =0
virtual ParticlePairsTemp	get_close_pairs (const ParticlesTemp &pca, const ParticlesTemp &pcb) const =0
virtual ParticleIndexPairs	get_close_pairs (Model *m, const ParticleIndexes &pc) const
virtual ParticleIndexPairs	get_close_pairs (Model *m, const ParticleIndexes &pca, const ParticleIndexes &pcb) const
virtual IntPairs	get_close_pairs (const algebra::BoundingBox3Ds &bbs) const =0
virtual IntPairs	get_close_pairs (const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const =0
double	get_distance () const
virtual ParticlesTemp	get_input_particles (const ParticlesTemp &ps) const =0
virtual ContainersTemp	get_input_containers (const ParticlesTemp &ps) const =0
void	remove_pair_filter (PairPredicate *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 (PairPredicate *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
PairPredicate *	get_pair_filter (unsigned int i) const
PairPredicates	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
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
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.
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)

Static Public Member Functions
static RigidClosePairsFinder *	get_from (IMP::base::Object *o)

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

• RigidClosePairsFinder.h