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IMP Reference Guide  develop.716bca0a46,2020/04/04
The Integrative Modeling Platform
IMP::em2d::Em2DRestraint Class Reference

#include <IMP/em2d/Em2DRestraint.h>

+ Inheritance diagram for IMP::em2d::Em2DRestraint:

Detailed Description

This restraint ensures that a set of particles are similar to a set of EM images. The restraint generates projections of the model that are then compared with the EM images. The projections are generated from the radius of its particles. In the case of atoms, the radius is generated automatically. For other particles the radius has to be provided.

Definition at line 32 of file em2d/Em2DRestraint.h.

Public Member Functions

 Em2DRestraint (Model *m)
 
virtual IMP::ModelObjectsTemp do_get_inputs () const
 
RegistrationResults get_registration_results () 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_coarse_registration_mode (bool opt)
 
void set_fast_mode (unsigned int n)
 
void set_images (const em2d::Images em_images)
 
void set_particles (SingletonContainer *particles_container)
 
void set_variance_images (const em2d::Images variance_images)
 
void setup (ScoreFunction *score_function, const Em2DRestraintParameters &params)
 
virtual 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::em2d::Em2DRestraint::Em2DRestraint ( Model m)

Creates the restraint. You are not done yet by creating the restraint. After creating it, you need to call the setup() function

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::em2d::Em2DRestraint::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.

RegistrationResults IMP::em2d::Em2DRestraint::get_registration_results ( ) const

Get the registration results for each of the images after finishing the optimization. Obviously, requesting the results before optimizing is an error

Returns
A list of registration results

Definition at line 131 of file em2d/Em2DRestraint.h.

virtual ::IMP::VersionInfo IMP::em2d::Em2DRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 138 of file em2d/Em2DRestraint.h.

void IMP::em2d::Em2DRestraint::set_coarse_registration_mode ( bool  opt)

If the value provided to this function is true, restraint operates only using a coarse registration scheme (maximizing the cross correlation coefficient). This option (which is set to false by default) can speed the evaluation of the restraint by a order of magnitude, but the values obtained are not going to be less accurate. You could want to activate it at the beginning of an optimization.

Parameters
opttrue if you want to use the coarse mode

Definition at line 121 of file em2d/Em2DRestraint.h.

void IMP::em2d::Em2DRestraint::set_fast_mode ( unsigned int  n)

Sets fast mode for computing the restraint. This mode only makes sense it the set_coarse_registration_mode option is false. This option only optimizes some coarse results (those given by the argument) to get the refined value. This option is very fast compared to a full optimization, and almost always is a good idea to use it with 1-5 results. This mode is still significantly slow compared to set_coarse_registration_mode(), but the values optimized are optimum.

Parameters
nThe number of images to optimize
void IMP::em2d::Em2DRestraint::set_images ( const em2d::Images  em_images)

Sets the EM images to use as restraints

Parameters
em_imagesThe images
void IMP::em2d::Em2DRestraint::set_particles ( SingletonContainer particles_container)

Sets the particles used to compute projections.

Parameters
particles_containerAll the particles must be in the container
void IMP::em2d::Em2DRestraint::set_variance_images ( const em2d::Images  variance_images)

Sets the variance images of EM images. This is useful if the image is a class average Note: Not all the scoring function use this data Sets the variance images for class averages. If class averages are used as restraints, it is possible to use the variance images to assign a standard deviation (error) for each of the pixels in a class average.

Parameters
variance_images
Note
Not all the scoring functions use the variance images
This function is functional as is tested, but has not been tested in a real application yet.
void IMP::em2d::Em2DRestraint::setup ( ScoreFunction score_function,
const Em2DRestraintParameters params 
)

Initializes the restraint

Parameters
score_functionScoring function to use to evaluate the similarity between particles and projections
paramsAll the parameters required for the restraint

Definition at line 60 of file em2d/Em2DRestraint.h.

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