Detailed Description

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

The restraint implements ambiguous connectivity. That is, it takes several particles including multiple copies and ensures that they remain connected, but allows how they are connected to change. If you wish to restrain 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/ms_connectivity_restraint.py
 # This example shows how to use the MSConnectivityRestraint to ensure that
 # all the particles that are part of complexes end up in a connected
 # conformation following the optimization. It allows multiple copies of
 # particles and takes an experimental tree as an input.
 #
 
 # -- File: ms_connectivity_restraint.py --#
 
 import IMP
 import IMP.core
 import IMP.algebra
 import sys
 
 IMP.setup_from_argv(sys.argv, "ms connectivity restraint")
 
 # Setup model
 
 m = IMP.Model()
 ps = [IMP.Particle(m) for x in range(6)]
 ds = []
 ds.append(IMP.core.XYZ.setup_particle(
     ps[0], IMP.algebra.Vector3D(0.0, 0.0, 0.0)))
 ds.append(IMP.core.XYZ.setup_particle(
     ps[1], IMP.algebra.Vector3D(1.0, 1.0, 0.0)))
 ds.append(IMP.core.XYZ.setup_particle(
     ps[2], IMP.algebra.Vector3D(2.0, 0.0, 0.0)))
 ds.append(IMP.core.XYZ.setup_particle(
     ps[3], IMP.algebra.Vector3D(3.0, 0.0, 0.0)))
 ds.append(IMP.core.XYZ.setup_particle(
     ps[4], IMP.algebra.Vector3D(4.0, -1.0, 0.0)))
 ds.append(IMP.core.XYZ.setup_particle(
     ps[5], IMP.algebra.Vector3D(1000, 1000, 1000)))
 
 # Create MS connectivity restraint
 
 ub = IMP.core.HarmonicUpperBound(1.0, 0.1)
 ss = IMP.core.DistancePairScore(ub)
 r = IMP.core.MSConnectivityRestraint(m, ss)
 
 # Add particle types to the restraint
 # add_type() returns a unique type handle that can be used as an argument
 # to add_composite() later on.
 
 pa = r.add_type([ds[0], ds[1]])
 pb = r.add_type([ds[2], ds[3]])
 pc = r.add_type([ds[4]])
 pd = r.add_type([ds[5]])
 
 # Enter experimental tree data into restraint
 # In add_composite(), the first argument is node label and the second
 # argument is the parent.
 
 i1 = r.add_composite([pa, pa, pb, pb, pc])
 i2 = r.add_composite([pa, pb, pb, pc], i1)
 i3 = r.add_composite([pa, pa, pb, pb], i1)
 i4 = r.add_composite([pa, pb], i1)
 i5 = r.add_composite([pa, pb, pb], i2)
 i6 = r.add_composite([pb, pc], i2)
 i7 = r.add_composite([pa, pa, pb], i3)
 i8 = r.add_composite([pa, pb], i5)
 
 # Evaluate the restraint score
 r.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 54 of file MSConnectivityRestraint.h.

Public Member Functions
	MSConnectivityRestraint (Model m, PairScore ps, double eps=0.1)
	Use the given PairScore. More...

Restraints	do_create_current_decomposition () const override

ModelObjectsTemp	do_get_inputs () const override

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. More...

virtual std::string	get_type_name () const override

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

double	unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override
	Return the unweighted score for the restraint. More...

Public Member Functions inherited from IMP::Restraint
	Restraint (Model *m, std::string name)
	Create a restraint and register it with the model. More...

	Restraint ()
	Default constructor. More...

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
	Create a scoring function with only this restraint. More...

virtual RestraintInfo *	get_dynamic_info () const

bool	get_is_aggregate () const
	Return whether this restraint wraps a number of other restraints. More...

double	get_last_last_score () const
	Get the unweighted score from the last-but-one time it was evaluated. More...

virtual double	get_last_score () const

double	get_score () const

virtual RestraintInfo *	get_static_info () const

bool	get_was_good () const

double	evaluate (bool calc_derivs) const

double	evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double	evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

double	evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double	evaluate_if_good (bool calc_derivatives) const

double	evaluate_if_below (bool calc_derivatives, double max) const

virtual double	unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
	Return the unweighted score, taking moving particles into account. More...

virtual double	unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const

virtual double	unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
	The function calling this will treat any score >= max as bad. More...

virtual double	unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

virtual double	unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) 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::ModelObject
	ModelObject (Model *m, std::string name)

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

bool	get_has_required_score_states () const
	Return whether score states are computed. More...

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const
	Get the interacting sets induced by this ModelObject. More...

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const
	Get the score states that are ancestors of this in the dependency graph. More...

void	set_has_dependencies (bool tf)
	Either invalidate the dependencies or ensure they are correct. More...

void	set_has_required_score_states (bool tf)
	Compute the required score states. 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)

Particles to be connected
The following methods are used to manipulate the list of particles that are to be connected. Each particle should have all the attributes expected by the PairScore used. Ideally, one should pass a singleton container instead. These can only be used if none is passed.
unsigned int	add_type (const ParticlesTemp &ps)

unsigned int	add_composite (const Ints &components)

unsigned int	add_composite (const Ints &components, unsigned int parent)

Additional Inherited Members
Protected Member Functions inherited from IMP::Restraint
virtual void	do_add_score_and_derivatives (ScoreAccumulator sa) const

virtual void	do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

virtual Restraints	do_create_decomposition () const

ModelObjectsTemp	do_get_outputs () const override

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

virtual void	handle_set_has_required_score_states (bool)

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

virtual void	do_destroy ()

Protected Attributes inherited from IMP::Restraint
bool	is_aggregate_

Constructor & Destructor Documentation

IMP::core::MSConnectivityRestraint::MSConnectivityRestraint	(	Model *	m,
		PairScore *	ps,
		double	eps = `0.1`
	)

Use the given PairScore.

If sc is nullptr, a ListSingletonContainer is created internally. eps is set to 0.1 by default.

Member Function Documentation

Restraints IMP::core::MSConnectivityRestraint::do_create_current_decomposition ( ) const

overridevirtual

A Restraint should override this if it wants to decompose itself for display and other purposes. The returned restraints will be made into a RestraintSet if needed, with suitable weight and maximum score.

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

Reimplemented from IMP::Restraint.

ModelObjectsTemp IMP::core::MSConnectivityRestraint::do_get_inputs ( ) const

overridevirtual

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::ModelObject.

ParticlePairsTemp IMP::core::MSConnectivityRestraint::get_connected_pairs ( ) const

Return the set of pairs which are connected by the restraint.

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.

PairScore* IMP::core::MSConnectivityRestraint::get_pair_score ( ) const

Return the pair score used for scoring.

Definition at line 91 of file MSConnectivityRestraint.h.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 100 of file MSConnectivityRestraint.h.

double IMP::core::MSConnectivityRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator * da ) const

overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

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

MSConnectivityRestraint.h

Detailed Description

Public Member Functions

Particles to be connected

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation