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.

Inheritance diagram for IMP::isd::TALOSRestraint:

List of all members.

Public Member Functions
	TALOSRestraint (Particles p, Floats data, Particle *kappa)
	Create restraint from a list of particles and the data.
	TALOSRestraint (Particle p1, Particle p2, Particle p3, Particle p4, Floats data, Particle *kappa)
	Create restraint from 4 particles and the data.
	TALOSRestraint (Particles p, unsigned N, double R0, double chiexp, Particle *kappa)
	Create restraint from a list of particles and the sufficient statistics.
	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.
double	get_chiexp () const
double	get_probability () const
	Call for probability.
double	get_R0 () const
Public Member Functions inherited from IMP::Restraint
	Restraint (Model *m, std::string name)
Restraint *	create_current_decomposition () const
	Decompose this restraint into constituent terms for the current conf.
Restraint *	create_decomposition () const
	Decompose this restraint into constituent terms.
double	evaluate (bool calc_derivs) const
	Return the score for this restraint for the current state of the model.
double	evaluate_if_below (bool calc_derivatives, double max) const
	See Model::evaluate_with_maximum()
double	evaluate_if_good (bool calc_derivatives) const
	See Model::evaluate_if_good()
double	get_last_score () const
bool	get_was_good () const
virtual double	unprotected_evaluate (DerivativeAccumulator *) const =0
virtual double	unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const
virtual double	unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
virtual ContainersTemp	get_input_containers () const =0
virtual ParticlesTemp	get_input_particles () const =0
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)
ModelObjectsTemp	get_inputs () const
Model *	get_model () const
ModelObjectsTemp	get_outputs () const
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
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.
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)

Static Public Member Functions
static TALOSRestraint *	get_from (IMP::base::Object *o)

Additional Inherited Members
Protected Member Functions inherited from IMP::Restraint
virtual Restraints	do_create_current_decomposition () const
virtual Restraints	do_create_decomposition () const
Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemp	do_get_inputs () const =0
virtual ModelObjectsTemp	do_get_outputs () const =0
virtual void	do_update_dependencies (const DependencyGraph &, const DependencyGraphVertexIndex &)
void	update_dependencies (const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)

Constructor & Destructor Documentation

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

Create restraint from a list of particles and the data.

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
	)

Create restraint from 4 particles and the data.

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
	)

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

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
	)

Create restraint from 4 particles and the sufficient statistics.

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.

Member Function Documentation

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

Call for probability.

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

TALOSRestraint.h
isd/__init__.py

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation