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IMP Reference Guide  develop.1a04b19ae7,2021/11/27
The Integrative Modeling Platform
IMP::em2d::PCAFitRestraint Class Reference

Fast scoring of Particles against electron microscopy class averages. More...

#include <IMP/em2d/PCAFitRestraint.h>

+ Inheritance diagram for IMP::em2d::PCAFitRestraint:

Detailed Description

Fast scoring of Particles against electron microscopy class averages.

The restraint fits the particles into the 2D images by alignment of principal components of each of the particles' projections with principal components of the 2D class average. Therefore, the particle set should comprise all subunits that are in the image. The aligned projections are scored against 2D class averages using the cross correlation score. This is a fast alignment and score that works well for negative stain EM class averages.

Definition at line 31 of file d/PCAFitRestraint.h.

Public Member Functions

 PCAFitRestraint (Particles particles, const std::vector< std::string > &image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=false, unsigned int n_components=1)
 Constructor. More...
 
IMP::ModelObjectsTemp do_get_inputs () const
 
double get_cross_correlation_coefficient (unsigned int image_number) const
 Get cross correlation between the image and the best model projection. More...
 
RestraintInfoget_dynamic_info () const
 
unsigned int get_projection_number () const
 
RestraintInfoget_static_info () const
 
algebra::Transformation3D get_transformation (unsigned int image_number) const
 Get transformation that best places the model on the image. More...
 
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_projection_number (unsigned int n)
 
double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
void write_best_projections (std::string file_name, bool evaluate=false)
 
- 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...
 
void add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) 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
 Create a scoring function with only this restraint. More...
 
virtual double get_last_last_score () const
 Get the unweighted score from the last-but-one time it was evaluated. More...
 
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::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
 
virtual void do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 
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::PCAFitRestraint::PCAFitRestraint ( Particles  particles,
const std::vector< std::string > &  image_files,
double  pixel_size,
double  resolution = 10.0,
unsigned int  projection_number = 100,
bool  reuse_direction = false,
unsigned int  n_components = 1 
)

Constructor.

Parameters
[in]particlesThe particles participating in the score, which need to have XYZ, radius and mass
[in]image_files2D class average filenames in PGM text format
[in]pixel_sizePixel size in angstroms
[in]resolutionEstimated resolution of the images in angstroms
[in]projection_numberNumber of projections of the model to generate and fit to images. The lower the number, the faster the evaluation, but the lower the accuracy.
[in]reuse_directionSpeed up evaluation by only periodically recalculating projections
[in]n_componentsNumber of the largest components to be considered for the EM image

Member Function Documentation

IMP::ModelObjectsTemp IMP::em2d::PCAFitRestraint::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.

Definition at line 89 of file d/PCAFitRestraint.h.

double IMP::em2d::PCAFitRestraint::get_cross_correlation_coefficient ( unsigned int  image_number) const

Get cross correlation between the image and the best model projection.

This CCC is that calculated from the last scoring function evaluation; calling this function before the score is calculated results in undefined behavior.

RestraintInfo* IMP::em2d::PCAFitRestraint::get_dynamic_info ( ) const
virtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

RestraintInfo* IMP::em2d::PCAFitRestraint::get_static_info ( ) const
virtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

algebra::Transformation3D IMP::em2d::PCAFitRestraint::get_transformation ( unsigned int  image_number) const

Get transformation that best places the model on the image.

The transformation places the model such that if the image is placed on the xy plane with its lower left corner at the origin the model's projection along the z axis will coincide with the image. This transformation is that calculated from the last scoring function evaluation; calling this function before the score is calculated results in undefined behavior.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 90 of file d/PCAFitRestraint.h.


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