Ensure that a set of particles remains connected with one another. More...

#include <IMP/core/ConnectivityRestraint.h>

Inheritance diagram for IMP::core::ConnectivityRestraint:

Public Member Functions
	ConnectivityRestraint (PairScore ps, SingletonContainer sc)
	Use the given PairScore.

	ConnectivityRestraint (PairScore *ps)

kernel::Restraints	do_create_current_decomposition () const

IMP::kernel::ModelObjectsTemp	do_get_inputs () const

kernel::ParticlePairsTemp	get_connected_pairs () const
	Return the set of pairs which are connected by the restraint. More...

PairScore *	get_pair_score () const
	Return the pair score used for scoring.

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.

double	unprotected_evaluate (IMP::DerivativeAccumulator *accum) const

Public Member Functions inherited from IMP::kernel::Restraint
	Restraint (kernel::Model *m, std::string name)

	Restraint (std::string name="Restraint %1%")

void	add_score_and_derivatives (ScoreAccumulator sa) const

Restraint *	create_current_decomposition () const
	Decompose this restraint into constituent terms for the current conf. More...

Restraint *	create_decomposition () const
	Decompose this restraint into constituent terms. More...

virtual ScoringFunction *	create_scoring_function (double weight=1.0, double max=NO_MAX) const

ContainersTemp	get_input_containers () const

ParticlesTemp	get_input_particles () const

virtual double	get_last_score () const

double	get_score () const

bool	get_was_good () const

void	set_weight (Float weight)

Float	get_weight () const

double	get_maximum_score () const

void	set_maximum_score (double s)

Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (kernel::Model *m, std::string name)

	ModelObject (std::string name)

virtual void	do_set_model (kernel::Model *)

bool	get_has_dependencies () const
	Return whether this object has dependencies computed.

bool	get_has_required_score_states () const

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

bool	get_is_part_of_model () const

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const

void	set_has_dependencies (bool tf)

void	set_has_required_score_states (bool tf)

virtual void	set_model (kernel::Model *m)

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

virtual void	do_destroy ()

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::kernel::Restraint
virtual void	do_add_score_and_derivatives (ScoreAccumulator sa) const

virtual Restraints	do_create_decomposition () const

ModelObjectsTemp	do_get_outputs () const

Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

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

	Object ()

Detailed Description

The restraint implements ambiguous connectivity. That is, it takes several particles and ensures that they remain connected, but allows how they are connected to change. If you wish to restraint the connectivity of sets of particles (i.e. each protein is represented using a set of balls) use an appropriate PairScore which calls a Refiner (such as ClosePairsPairScore).

 ## \example core/connectivity_restraint.py
 # This example shows how to use the ConnectivityRestraint to ensure that
 # all the particles end up in a connected conformation following the
 # optimization. One should also check out the
 # IMP::atom::create_connectivity_restraint() helper functions.
 
 import IMP
 import IMP.core
 import IMP.algebra
 import IMP.atom
 
 m = IMP.kernel.Model()
 
 # Put the parent particles for each molecule
 hs = []
 
 # create the molecules, with 5 particles for each of 10 molecules
 for i in range(0, 10):
     pr = IMP.kernel.Particle(m)
     pr.set_name("root " + str(i))
     d = IMP.atom.Hierarchy.setup_particle(pr)
     for j in range(0, 5):
         p = IMP.kernel.Particle(m)
         p.set_name("fragment " + str(i) + " " + str(j))
         cd = IMP.atom.Fragment.setup_particle(p)
         d.add_child(cd)
         xd = IMP.core.XYZR.setup_particle(
             p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(3 * i, j, 0), 1))
     hs.append(pr)
 
 
 ps = IMP.core.SphereDistancePairScore(IMP.core.HarmonicUpperBound(0, 1))
 cps = IMP.core.ChildrenRefiner(IMP.atom.Hierarchy.get_traits())
 
 # score based on the one closest particle from each set of balls
 lrps = IMP.core.KClosePairsPairScore(ps, cps, 1)
 # connect all 10 molecules together
 cr = IMP.core.ConnectivityRestraint(lrps)
 cr.set_particles(hs)
 m.add_restraint(cr)
 
 m.evaluate(False)

More precisely, the restraint scores by computing the MST on the complete graph connecting all the particles. The edge weights are given by the value of the PairScore for the two endpoints of the edge.

Definition at line 38 of file ConnectivityRestraint.h.

Constructor & Destructor Documentation

IMP::core::ConnectivityRestraint::ConnectivityRestraint ( PairScore * ps )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use constructor that takes a container instead.

Member Function Documentation

kernel::Restraints IMP::core::ConnectivityRestraint::do_create_current_decomposition ( ) const

virtual

A Restraint should override this if they want to decompose themselves for display and other purposes. The returned restraints will be made in to a RestraintSet, if needed and the weight and maximum score set for the restraint set.

The returned restraints should be only the non-zero terms and should have their last scores set appropriately;

Reimplemented from IMP::kernel::Restraint.

IMP::kernel::ModelObjectsTemp IMP::core::ConnectivityRestraint::do_get_inputs ( ) const

virtual

Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.

Implements IMP::kernel::ModelObject.

kernel::ParticlePairsTemp IMP::core::ConnectivityRestraint::get_connected_pairs ( ) const

This set of pairs reflects the current configuration at the time of the get_connected_pairs() call, not the set at the time of the last evaluate() call.

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

ConnectivityRestraint.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation