Perform more efficient close pair finding when rigid bodies are involved. More...

#include <IMP/core/RigidClosePairsFinder.h>

Inheritance diagram for IMP::core::RigidClosePairsFinder:

Detailed Description

Perform 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 transformed results.; The particles are divided up using a grid. The number of grid cells to use should be explored. In addition, with highly eccentric sets of points, there will be too many cells.; Do not reuse RigidClosePairsFinders for different sets of particles from the same rigid body.

 ## \example core/rigid_collisions.py
 # Collision detection and building of a non-bonded list can be sped up when rigid bodies are used.
 # To do this, use a RigidClosePairsFinder.
 
 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.kernel.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.kernel.Particle(m)
 rbp1 = IMP.kernel.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(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()

Definition at line 60 of file RigidClosePairsFinder.h.

Public Member Functions
	RigidClosePairsFinder (ClosePairsFinder *cpf=nullptr)

virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

kernel::ParticleIndexPairs	get_close_pairs (kernel::Model *m, kernel::ParticleIndex a, kernel::ParticleIndex b, const kernel::ParticleIndexes &pa, const kernel::ParticleIndexes &pb) const

virtual IntPairs	get_close_pairs (const algebra::BoundingBox3Ds &bbs) const

virtual IntPairs	get_close_pairs (const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const

virtual kernel::ParticleIndexPairs	get_close_pairs (kernel::Model *m, const kernel::ParticleIndexes &pc) const

virtual kernel::ParticleIndexPairs	get_close_pairs (kernel::Model *m, const kernel::ParticleIndexes &pca, const kernel::ParticleIndexes &pcb) const

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

void	set_distance (double d)

Public Member Functions inherited from IMP::core::ClosePairsFinder
	ClosePairsFinder (std::string name)

kernel::ParticlePairsTemp	get_close_pairs (const kernel::ParticlesTemp &pc) const

kernel::ParticlePairsTemp	get_close_pairs (const kernel::ParticlesTemp &pca, const kernel::ParticlesTemp &pcb) const

double	get_distance () const

void	remove_pair_filter (PairPredicate *d)

void	remove_pair_filters (const PairPredicates &d)

void	set_pair_filters (const PairPredicates &ps)

void	set_pair_filters_order (const PairPredicates &objs)

unsigned int	add_pair_filter (PairPredicate *obj)

void	add_pair_filters (const PairPredicates &objs)

void	clear_pair_filters ()

unsigned int	get_number_of_pair_filters () const

bool	get_has_pair_filters ()

PairPredicate *	get_pair_filter (unsigned int i) const

PairPredicates	get_pair_filters () const

void	reserve_pair_filters (unsigned int sz)

Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp	get_input_containers (Particle *p) const

virtual ParticlesTemp	get_input_particles (Particle *p) const

ModelObjectsTemp	get_inputs (kernel::Model *m, const ParticleIndexes &pis) const

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

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)

Additional Inherited Members
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Member Function Documentation

virtual kernel::ModelObjectsTemp IMP::core::RigidClosePairsFinder::do_get_inputs	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	pis
	)		const

virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

virtual ::IMP::base::VersionInfo IMP::core::RigidClosePairsFinder::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 103 of file RigidClosePairsFinder.h.

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

RigidClosePairsFinder.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation