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IMP Reference Guide  develop.0ea7f7a4db,2020/10/23
The Integrative Modeling Platform
IMP::isd::Covariance1DFunction Class Reference

Covariance function. More...

#include <IMP/isd/bivariate_functions.h>

+ Inheritance diagram for IMP::isd::Covariance1DFunction:

Detailed Description

Covariance function.

Definition at line 118 of file bivariate_functions.h.

Public Member Functions

 Covariance1DFunction (Particle *tau, 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...
 
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
 
ModelObjectsTemp get_inputs () 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...
 
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::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...
 
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::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::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 198 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 215 of file bivariate_functions.h.

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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 231 of file bivariate_functions.h.

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ModelObjectsTemp IMP::isd::Covariance1DFunction::get_inputs ( ) const
virtual

particle manipulation

Implements IMP::isd::BivariateFunction.

Definition at line 410 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 386 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 388 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 403 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 390 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 392 of file bivariate_functions.h.

Eigen::MatrixXd IMP::isd::Covariance1DFunction::get_second_derivative_matrix ( unsigned  particle_a,
unsigned  particle_b,
const FloatsList xlist 
) const
virtual

return second derivative matrix

Implements IMP::isd::BivariateFunction.

Definition at line 329 of file bivariate_functions.h.

virtual ::IMP::VersionInfo IMP::isd::Covariance1DFunction::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 420 of file bivariate_functions.h.

bool IMP::isd::Covariance1DFunction::has_changed ( ) const
virtual

return true if internal parameters have changed.

Implements IMP::isd::BivariateFunction.

Definition at line 137 of file bivariate_functions.h.

Floats IMP::isd::Covariance1DFunction::operator() ( const Floats x1,
const Floats x2 
) const
virtual

evaluate the function at a certain point

Implements IMP::isd::BivariateFunction.

Definition at line 165 of file bivariate_functions.h.

Eigen::MatrixXd IMP::isd::Covariance1DFunction::operator() ( const IMP::FloatsList xlist) const
virtual

evaluate the function at a list of points

Implements IMP::isd::BivariateFunction.

Definition at line 172 of file bivariate_functions.h.

FloatsList IMP::isd::Covariance1DFunction::operator() ( const IMP::FloatsList xlist,
bool  stupid 
) const
virtual

used for testing only

Implements IMP::isd::BivariateFunction.

Definition at line 189 of file bivariate_functions.h.

void IMP::isd::Covariance1DFunction::update ( )
virtual

update internal parameters

Implements IMP::isd::BivariateFunction.

Definition at line 153 of file bivariate_functions.h.

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