IMP  2.0.1
The Integrative Modeling Platform
IMP::em2d::Em2DRestraint Class Reference

#include <IMP/em2d/Em2DRestraint.h>

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

Public Member Functions

 Em2DRestraint ()
 
virtual void do_show (std::ostream &out) const
 
RegistrationResults get_registration_results () const
 
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)
 
- Public Member Functions inherited from IMP::kernel::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 
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
 
ContainersTemp get_input_containers () const
 
ParticlesTemp get_input_particles () const
 
virtual double get_last_score () const
 
double get_score () 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::kernel::ModelObject
 ModelObject (Model *m, std::string name)
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
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. 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)
 

Related Functions

(Note that these are not member functions.)

typedef IMP::base::Vector
< IMP::base::WeakPointer
< Em2DRestraint > > 
Em2DRestraintsTemp
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::kernel::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
virtual void do_update_dependencies ()
 

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 Em2DRestraint.h.

Constructor & Destructor Documentation

IMP::em2d::Em2DRestraint::Em2DRestraint ( )

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

Definition at line 53 of file Em2DRestraint.h.

Member Function Documentation

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 132 of file 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 122 of file 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 evalute the similarity between particles and projections
paramsAll the parameters required for the restraint

Definition at line 61 of file Em2DRestraint.h.

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Friends And Related Function Documentation

Pass a set of objects.

Definition at line 139 of file Em2DRestraint.h.


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