Detailed Description

Covariance function.

Definition at line 119 of file bivariate_functions.h.

Public Member Functions
	Covariance1DFunction (kernel::Particle tau, kernel::Particle ilambda, double alpha=2.0, double jitter=0.0, double cutoff=1e-7)

void	add_to_derivatives (const Floats &x1, const Floats &x2, DerivativeAccumulator &accum) const
	update derivatives of particles More...

void	add_to_particle_derivative (unsigned particle_no, double value, DerivativeAccumulator &accum) const
	update derivatives of particles More...

IMP_Eigen::MatrixXd	get_derivative_matrix (unsigned particle_no, const FloatsList &xlist) const
	return derivative matrix More...

FloatsList	get_derivative_matrix (unsigned particle_no, const FloatsList &xlist, bool) const

ContainersTemp	get_input_containers () const

kernel::ParticlesTemp	get_input_particles () const
	particle manipulation More...

unsigned	get_ndims_x1 () const
	returns the number of input dimensions More...

unsigned	get_ndims_x2 () const

unsigned	get_ndims_y () const
	returns the number of output dimensions More...

unsigned	get_number_of_optimized_particles () const
	returns the number of particles that are optimized More...

unsigned	get_number_of_particles () const
	returns the number of particles that this function uses More...

bool	get_particle_is_optimized (unsigned particle_no) const
	returns true if the particle whose index is provided is optimized More...

IMP_Eigen::MatrixXd	get_second_derivative_matrix (unsigned particle_a, unsigned particle_b, const FloatsList &xlist) const
	return second derivative matrix More...

FloatsList	get_second_derivative_matrix (unsigned particle_a, unsigned particle_b, const FloatsList &xlist, bool) const

virtual std::string	get_type_name () const

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

bool	has_changed () const
	return true if internal parameters have changed. More...

Floats	operator() (const Floats &x1, const Floats &x2) const
	evaluate the function at a certain point More...

IMP_Eigen::MatrixXd	operator() (const IMP::FloatsList &xlist) const
	evaluate the function at a list of points More...

FloatsList	operator() (const IMP::FloatsList &xlist, bool) const
	used for testing only More...

void	update ()
	update internal parameters More...

Public Member Functions inherited from IMP::isd::BivariateFunction
	BivariateFunction (std::string str)

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

virtual void	do_destroy ()

Member Function Documentation

void IMP::isd::Covariance1DFunction::add_to_derivatives	(	const Floats &	x1,
		const Floats &	x2,
		DerivativeAccumulator &	accum
	)		const

virtual

update derivatives of particles

Implements IMP::isd::BivariateFunction.

Definition at line 199 of file bivariate_functions.h.

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void IMP::isd::Covariance1DFunction::add_to_particle_derivative	(	unsigned	particle_no,
		double	value,
		DerivativeAccumulator &	accum
	)		const

virtual

update derivatives of particles

Implements IMP::isd::BivariateFunction.

Definition at line 216 of file bivariate_functions.h.

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IMP_Eigen::MatrixXd IMP::isd::Covariance1DFunction::get_derivative_matrix	(	unsigned	particle_no,
		const FloatsList &	xlist
	)		const

virtual

return derivative matrix

Implements IMP::isd::BivariateFunction.

Definition at line 232 of file bivariate_functions.h.

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kernel::ParticlesTemp IMP::isd::Covariance1DFunction::get_input_particles ( ) const

virtual

particle manipulation

Implements IMP::isd::BivariateFunction.

Definition at line 411 of file bivariate_functions.h.

unsigned IMP::isd::Covariance1DFunction::get_ndims_x1 ( ) const

virtual

returns the number of input dimensions

Implements IMP::isd::BivariateFunction.

Definition at line 387 of file bivariate_functions.h.

unsigned IMP::isd::Covariance1DFunction::get_ndims_y ( ) const

virtual

returns the number of output dimensions

Implements IMP::isd::BivariateFunction.

Definition at line 389 of file bivariate_functions.h.

unsigned IMP::isd::Covariance1DFunction::get_number_of_optimized_particles ( ) const

virtual

returns the number of particles that are optimized

Implements IMP::isd::BivariateFunction.

Definition at line 404 of file bivariate_functions.h.

unsigned IMP::isd::Covariance1DFunction::get_number_of_particles ( ) const

virtual

returns the number of particles that this function uses

Implements IMP::isd::BivariateFunction.

Definition at line 391 of file bivariate_functions.h.

bool IMP::isd::Covariance1DFunction::get_particle_is_optimized ( unsigned particle_no ) const

virtual

returns true if the particle whose index is provided is optimized

Implements IMP::isd::BivariateFunction.

Definition at line 393 of file bivariate_functions.h.

IMP_Eigen::MatrixXd IMP::isd::Covariance1DFunction::get_second_derivative_matrix	(	unsigned	particle_a,
		unsigned	particle_b,
		const FloatsList &	xlist
	)		const