IMP logo
IMP Reference Guide  develop.731656d855,2020/02/17
The Integrative Modeling Platform
IMP::isd::GaussianProcessInterpolationRestraint Class Reference

gaussian process restraint More...

#include <IMP/isd/GaussianProcessInterpolationRestraint.h>

+ Inheritance diagram for IMP::isd::GaussianProcessInterpolationRestraint:

Detailed Description

gaussian process restraint

Definition at line 31 of file GaussianProcessInterpolationRestraint.h.

Public Member Functions

 GaussianProcessInterpolationRestraint (Model *m, GaussianProcessInterpolation *gpi)
 
IMP::ModelObjectsTemp do_get_inputs () const
 
Eigen::MatrixXd get_hessian () const
 Get hessian of the minus log likelihood. More...
 
FloatsList get_hessian (bool unused) const
 call this one from Python More...
 
double get_logdet_hessian () const
 Get log determinant of hessian. More...
 
double get_minus_exponent () const
 
double get_minus_log_normalization () const
 Get minus log normalization and minus exponent separately. More...
 
double get_probability () 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...
 
void set_use_cg (bool use, double tol)
 Use conjugate gradients when possible (default false) More...
 
double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. More...
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
 Create a scoring function with only this restraint. More...
 
virtual RestraintInfoget_dynamic_info () const
 
virtual double get_last_score () const
 
double get_score () const
 
virtual RestraintInfoget_static_info () 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::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...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_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
 A restraint should override this to compute the score and derivatives. More...
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- 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 ()
 

Constructor & Destructor Documentation

IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint ( Model m,
GaussianProcessInterpolation gpi 
)

This is a restraint on other restraints. It first constructs the necessary vectors from GaussianProcessInterpolation, then creates a multivariate normal distribution around it. Upon evaluation, it checks if parameters have changed, reconstructs the matrix if necessary, changes the DA weight and passes it to the functions.

Member Function Documentation

IMP::ModelObjectsTemp IMP::isd::GaussianProcessInterpolationRestraint::do_get_inputs ( ) const
virtual

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.

Eigen::MatrixXd IMP::isd::GaussianProcessInterpolationRestraint::get_hessian ( ) const

Get hessian of the minus log likelihood.

FloatsList IMP::isd::GaussianProcessInterpolationRestraint::get_hessian ( bool  unused) const

call this one from Python

double IMP::isd::GaussianProcessInterpolationRestraint::get_logdet_hessian ( ) const

Get log determinant of hessian.

double IMP::isd::GaussianProcessInterpolationRestraint::get_minus_log_normalization ( ) const

Get minus log normalization and minus exponent separately.

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

To call this, you need to update the scorestate before. calling model.evaluate(False) is enough.

Definition at line 55 of file GaussianProcessInterpolationRestraint.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 77 of file GaussianProcessInterpolationRestraint.h.

+ Here is the call graph for this function:

void IMP::isd::GaussianProcessInterpolationRestraint::set_use_cg ( bool  use,
double  tol 
)

Use conjugate gradients when possible (default false)

Definition at line 58 of file GaussianProcessInterpolationRestraint.h.


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