A restraint is a term in an IMP ScoringFunction. More...

#include "IMP/Restraint.h"

Detailed Description

A restraint is a term in an IMP ScoringFunction.

To implement a new restraint, just implement the two methods:

IMP::Restraint::unprotected_evaluate()
IMP::ModelObject::do_get_inputs(); and use the macro to handle IMP::Object
IMP_OBJECT_METHODS()

Note: When logging is VERBOSE, restraints should print enough information in evaluate to reproduce the entire flow of data in evaluate. When logging is TERSE the restraint should print out only a constant number of lines per evaluate call.; Physical restraints should use the units of kcal/mol for restraint values and kcal/mol/A for derivatives.

When implementing an expensive restraint it makes sense to support early abort of evaluation if the user is only interested in good scores or scores below a threshold. To do this, look at the fields of the ScoreAccumulator object such as

See IMP::example::ExampleRestraint for an example.

Definition at line 56 of file Restraint.h.

Public Member Functions
	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

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

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

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)

virtual std::string	get_type_name () const

Protected Member Functions
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_current_decomposition () const

virtual Restraints	do_create_decomposition () const

ModelObjectsTemp	do_get_outputs () const override

Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemp	do_get_inputs () const =0

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
bool	is_aggregate_

Evaluation convenience methods
These are convenience methods to get the score of just this restraint; each just calls the equivalent method in the ScoringFunction class.
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

Evaluation implementation
These methods are called in order to perform the actual restraint scoring. The restraints should assume that all appropriate ScoreState objects have been updated and so that the input particles and containers are up to date. The returned score should be the unweighted score. Note These functions probably should be called `do_evaluate`, but were grandfathered in. Although the returned score is unweighted, the DerivativeAccumulator passed in should be properly weighted.
virtual double	unprotected_evaluate (DerivativeAccumulator *da) const
	Return the unweighted score for the restraint. More...

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

Weights
Each restraint's contribution to the model score is weighted. The total weight for the restraint is the some over all the paths containing it. That is, if a restraint is in a RestraintSet with weight .5 and another with weight 2, and the restraint itself has weight 3, then the total weight of the restraint is \(.5 \cdot 3 + 2 \cdot 3 = 7.5 \).
void	set_weight (Float weight)

Float	get_weight () const

Filtering
We are typically only interested in "good" conformations of the model. These are described by specifying maximum scores per restraint (or RestraintSet). Samplers, optimizers etc are free to ignore configurations they encounter which go outside these bounds. Note The maximum score is for the unweighted restraint. That is, the restraint evaluation is bad if the value is greater than the maximum score divided by the weight.
double	get_maximum_score () const

void	set_maximum_score (double s)

Constructor & Destructor Documentation

IMP::Restraint::Restraint	(	Model *	m,
		std::string	name
	)

Create a restraint and register it with the model.

IMP::Restraint::Restraint ( )

Default constructor.

Default-constructed restraints cannot be evaluated.

Member Function Documentation

Restraint* IMP::Restraint::create_current_decomposition ( ) const

Decompose this restraint into constituent terms for the current conf.

Returns: a decomposition that is value for the current conformation, but will not necessarily be valid if any of the particles are changed. This is the same as create_decomposition() for non-conditional restraints.

The restraints returned have had set_model() called and so can be evaluated.

Restraint* IMP::Restraint::create_decomposition ( ) const

Decompose this restraint into constituent terms.

Given the set of input particles, decompose the restraint into parts that are as simple as possible. For many restraints, the simplest part is simply the restraint itself.

If a restraint can be decomposed, it should return a RestraintSet so that the maximum score and weight can be passed properly.

The restraints returned have had set_model() called and so can be evaluated.

virtual ScoringFunction* IMP::Restraint::create_scoring_function	(	double	weight = `1.0`,
		double	max = `NO_MAX`
	)		const

virtual

Create a scoring function with only this restraint.

Note: This method cannot be implemented in Python due to memory management issues (and the question of why you would ever want to).

virtual Restraints IMP::Restraint::do_create_current_decomposition ( ) const

protectedvirtual

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 in IMP::core::ExcludedVolumeRestraint, IMP::core::MSConnectivityRestraint, and IMP::core::ConnectivityRestraint.

Definition at line 315 of file Restraint.h.

virtual Restraints IMP::Restraint::do_create_decomposition ( ) const

protectedvirtual

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

Reimplemented in IMP::core::ExcludedVolumeRestraint.

Definition at line 305 of file Restraint.h.

ModelObjectsTemp IMP::Restraint::do_get_outputs ( ) const

overrideprotectedvirtual

No outputs.

Implements IMP::ModelObject.

Definition at line 326 of file Restraint.h.

double IMP::Restraint::evaluate ( bool calc_derivs ) const

See Also: ScoringFunction::evaluate

double IMP::Restraint::evaluate_if_below	(	bool	calc_derivatives,
		double	max
	)		const

See Also: ScoringFunction::evaluate_if_below

double IMP::Restraint::evaluate_if_good ( bool calc_derivatives ) const

See Also: ScoringFunction::evaluate_if_good

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

See Also: ScoringFunction::evaluate_moved

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

See Also: ScoringFunction::evaluate_moved_if_below

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

See Also: ScoringFunction::evaluate_moved_if_good

virtual RestraintInfo* IMP::Restraint::get_dynamic_info ( ) const

virtual

Returns: dynamic key:value information about this restraint, or null.; a set of key:value pairs that contain dynamic information about this restraint (i.e. information that changes during a sampling run, such as scores or cross correlations). If no such information is available, a null pointer is returned. This information is used when writing restraints to files, e.g. by the IMP.rmf module.

Reimplemented in IMP::bayesianem::GaussianEMRestraint, IMP::isd::GaussianEMRestraint, IMP::em2d::PCAFitRestraint, and IMP::isd::UniformPrior.

Definition at line 190 of file Restraint.h.

bool IMP::Restraint::get_is_aggregate ( ) const

Return whether this restraint wraps a number of other restraints.

Definition at line 291 of file Restraint.h.

double IMP::Restraint::get_last_last_score ( ) const

Get the unweighted score from the last-but-one time it was evaluated.

See Also: get_last_score

Definition at line 288 of file Restraint.h.

virtual double IMP::Restraint::get_last_score ( ) const

virtual

Return the (unweighted) score for this restraint last time it was evaluated.

Note: If some sort of special evaluation (eg Model::evaluate_if_good()) was the last call, the score, if larger than the max, is not accurate.

Reimplemented in IMP::RestraintSet.

Definition at line 283 of file Restraint.h.

double IMP::Restraint::get_score ( ) const

Compute and return the current score for the restraint.

virtual RestraintInfo* IMP::Restraint::get_static_info ( ) const

virtual

Returns: static key:value information about this restraint, or null.; a set of key:value pairs that contain static information about this restraint (i.e. information that doesn't change during a sampling run, such as the type of restraint or filename from which information is read). Usually this includes a "type" key with the fully qualified classname (e.g. IMP.mymodule.MyRestraint). If no such information is available, a null pointer is returned. This information is used when writing restraints to files, e.g. by the IMP.rmf module.

Definition at line 178 of file Restraint.h.

bool IMP::Restraint::get_was_good ( ) const

Return whether this restraint violated its maximum last time it was evaluated.

Definition at line 296 of file Restraint.h.

virtual double IMP::Restraint::unprotected_evaluate ( DerivativeAccumulator * da ) const

virtual

Return the unweighted score for the restraint.

virtual double IMP::Restraint::unprotected_evaluate_if_below	(	DerivativeAccumulator *	da,
		double	max
	)		const

virtual

The function calling this will treat any score >= max as bad.

Definition at line 146 of file Restraint.h.

virtual double IMP::Restraint::unprotected_evaluate_if_good	(	DerivativeAccumulator *	da,
		double	max
	)		const

virtual

The function calling this will treat any score >= get_maximum_score as bad and so can return early as soon as such a situation is found.

Definition at line 139 of file Restraint.h.

virtual double IMP::Restraint::unprotected_evaluate_moved	(	DerivativeAccumulator *	da,
		const ParticleIndexes &	moved_pis,
		const ParticleIndexes &	reset_pis
	)		const

virtual

Return the unweighted score, taking moving particles into account.

By default this just calls regular unprotected_evaluate(), but may be overridden by restraints to be more efficient, e.g. by skipping terms that involve unchanged particles.

Parameters

da	Object to accumulate derivatives, or nullptr.
moved_pis	Particles that have moved since the last scoring function evaluation.
reset_pis	Particles that have moved, but back to the positions they had at the last-but-one evaluation (e.g. due to a rejected Monte Carlo move).

Returns: Current score.

Reimplemented in IMP::isd::LogWrapper.

Definition at line 129 of file Restraint.h.

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

Restraint.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Evaluation convenience methods

Evaluation implementation

Weights

Filtering

Constructor & Destructor Documentation

Member Function Documentation