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

(p,q) if neither p or q are RigidBody particles
all (r,s) where r is a member of p, s is a member of q, and r and s are closer than the distance threshold if both p and q are RigidBody particles
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 each RigidBody is assigned a radius that encloses all of its 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
 import sys
 
 IMP.setup_from_argv(sys.argv, "rigid collisions")
 
 # 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(rbps0)
 lsc.add(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)
 sf = IMP.core.RestraintsScoringFunction([evr])
 
 # Set up optimizer
 o = IMP.core.ConjugateGradients(m)
 o.set_scoring_function(sf)
 
 done = False
 while not done:
     try:
         o.optimize(1000)
     except IMP.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 59 of file RigidClosePairsFinder.h.

Public Member Functions
	RigidClosePairsFinder (ClosePairsFinder *cpf=nullptr)

virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const
	Overload this method to specify the inputs. More...

ParticleIndexPairs	get_close_pairs (Model *m, ParticleIndex a, ParticleIndex b, const ParticleIndexes &pa, const 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 ParticleIndexPairs	get_close_pairs (Model *m, const ParticleIndexes &pc) const
	return all close pairs among pc in model m More...

virtual ParticleIndexPairs	get_close_pairs (Model *m, const ParticleIndexes &pca, const ParticleIndexes &pcb) const
	return all close pairs among pc in model m More...

virtual std::string	get_type_name () const

virtual ::IMP::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)

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::ParticleInputs
ModelObjectsTemp	get_inputs (Model *m, const ParticleIndexes &pis) const
	Get the ModelObjects read when the given list of particles is used. More...

Public Member Functions inherited from IMP::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::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Member Function Documentation

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

virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

virtual ParticleIndexPairs IMP::core::RigidClosePairsFinder::get_close_pairs	(	Model *	m,
		const ParticleIndexes &	pc
	)		const

virtual

return all close pairs among pc in model m

Implements IMP::core::ClosePairsFinder.

virtual ParticleIndexPairs IMP::core::RigidClosePairsFinder::get_close_pairs	(	Model *	m,
		const ParticleIndexes &	pca,
		const ParticleIndexes &	pcb
	)		const

virtual

return all close pairs among pc in model m

Implements IMP::core::ClosePairsFinder.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 93 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