IMP::core::RigidClosePairsFinder Class Reference

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
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 60 of file RigidClosePairsFinder.h.

Public Member Functions
	RigidClosePairsFinder (ClosePairsFinder *cpf=nullptr)
virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const
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
virtual ParticleIndexPairs	get_close_pairs (Model *m, const ParticleIndexes &pca, const ParticleIndexes &pcb) const
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
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 ::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 94 of file RigidClosePairsFinder.h.

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

• RigidClosePairsFinder.h