phi/psi dihedral restraint between four particles, using data from TALOS. More...

#include <IMP/isd/TALOSRestraint.h>

Inheritance diagram for IMP::isd::TALOSRestraint:

Detailed Description

phi/psi dihedral restraint between four particles, using data from TALOS.

The likelihood is

\[ f(\chi_{exp}^1,\cdots,\chi_{exp}^N|\chi(X),\kappa,I) = \frac{1}{2\pi I_0(\kappa)^N} \exp \left(R_0 \kappa \cos (\chi_{exp}-\chi(X)) \right) \]

where the sufficient statistics are \(N\) the number of observations, \(R\) and \(\chi_{exp}\).

See Also: vonMisesSufficient.h for further detail.

Definition at line 32 of file TALOSRestraint.h.

Public Member Functions
	TALOSRestraint (Model m, Particles p, Floats data, Particle kappa)
	Create restraint from a list of particles and the data. More...

	TALOSRestraint (Model m, Particle p1, Particle p2, Particle p3, Particle p4, Floats data, Particle kappa)
	Create restraint from 4 particles and the data. More...

	TALOSRestraint (Model m, Particles p, unsigned N, double R0, double chiexp, Particle kappa)
	Create restraint from a list of particles and the sufficient statistics. More...

	TALOSRestraint (Model m, Particle p1, Particle p2, Particle p3, Particle p4, unsigned N, double R0, double chiexp, Particle kappa)
	Create restraint from 4 particles and the sufficient statistics. More...

virtual IMP::ModelObjectsTemp	do_get_inputs () const override

double	get_chiexp () const

double	get_probability () const
	Call for probability. More...

double	get_R0 () const

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...

virtual 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)

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_current_decomposition () 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::isd::TALOSRestraint::TALOSRestraint	(	Model *	m,
		Particles	p,
		Floats	data,
		Particle *	kappa
	)

Create restraint from a list of particles and the data.

Parameters

[in]	m	the Model
[in]	p	list of 4 particles that make the dihedral angle.
[in]	data	list of observations for that angle.
[in]	kappa	Pointer to the \(\kappa\) concentration particle.

IMP::isd::TALOSRestraint::TALOSRestraint	(	Model *	m,
		Particle *	p1,
		Particle *	p2,
		Particle *	p3,
		Particle *	p4,
		Floats	data,
		Particle *	kappa
	)

Create restraint from 4 particles and the data.

Parameters

[in]	m	the Model
[in]	p1	Pointer to first particle in dihedral restraint.
[in]	p2	Pointer to second particle in dihedral restraint.
[in]	p3	Pointer to third particle in dihedral restraint.
[in]	p4	Pointer to fourth particle in dihedral restraint.
[in]	data	list of observations for that angle.
[in]	kappa	Pointer to the \(\kappa\) concentration particle.

IMP::isd::TALOSRestraint::TALOSRestraint	(	Model *	m,
		Particles	p,
		unsigned	N,
		double	R0,
		double	chiexp,
		Particle *	kappa
	)

Create restraint from a list of particles and the sufficient statistics.

Parameters

[in]	m	the Model
[in]	p	list of 4 particles that make the dihedral angle.
[in]	N	Number of observations
[in]	R0	component on the x axis
[in]	chiexp	average observed angle.
[in]	kappa	Pointer to the \(\kappa\) concentration particle.

IMP::isd::TALOSRestraint::TALOSRestraint	(	Model *	m,
		Particle *	p1,
		Particle *	p2,
		Particle *	p3,
		Particle *	p4,
		unsigned	N,
		double	R0,
		double	chiexp,
		Particle *	kappa
	)

Create restraint from 4 particles and the sufficient statistics.

Parameters

[in]	m	the Model
[in]	p1	Pointer to first particle in dihedral restraint.
[in]	p2	Pointer to second particle in dihedral restraint.
[in]	p3	Pointer to third particle in dihedral restraint.
[in]	p4	Pointer to fourth particle in dihedral restraint.
[in]	N	Number of observations
[in]	R0	component on the x axis
[in]	chiexp	average observed angle.
[in]	kappa	Pointer to the \(\kappa\) concentration particle.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::isd::TALOSRestraint::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.

double IMP::isd::TALOSRestraint::get_probability ( ) const

Call for probability.

Definition at line 83 of file TALOSRestraint.h.

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virtual ::IMP::VersionInfo IMP::isd::TALOSRestraint::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 92 of file TALOSRestraint.h.

virtual double IMP::isd::TALOSRestraint::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:

TALOSRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation