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

#include <IMP/isd/TALOSRestraint.h>

Inheritance diagram for IMP::isd::TALOSRestraint:

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

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

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

	TALOSRestraint (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 void	do_show (std::ostream &out) const

double	get_chiexp () const

double	get_probability () const
	Call for probability.

double	get_R0 () const

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

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 (Model *m, std::string name)

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

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

virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.

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_current_decomposition () const

virtual Restraints	do_create_decomposition () const

ModelObjectsTemp	do_get_outputs () const

virtual void	do_update_dependencies ()

Related Functions inherited from IMP::kernel::Restraint
typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > >	RestraintsTemp

Detailed Description

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.

Constructor & Destructor Documentation

IMP::isd::TALOSRestraint::TALOSRestraint	(	Particles	p,
		Floats	data,
		Particle *	kappa
	)

Parameters

[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	(	Particle *	p1,
		Particle *	p2,
		Particle *	p3,
		Particle *	p4,
		Floats	data,
		Particle *	kappa
	)

Parameters

[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	(	Particles	p,
		unsigned	N,
		double	R0,
		double	chiexp,
		Particle *	kappa
	)

Parameters

[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	(	Particle *	p1,
		Particle *	p2,
		Particle *	p3,
		Particle *	p4,
		unsigned	N,
		double	R0,
		double	chiexp,
		Particle *	kappa
	)

Parameters

[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.

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

TALOSRestraint.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation