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IMP Reference Guide  develop.660a833c7e,2021/01/16
The Integrative Modeling Platform
IMP::em::EnvelopeFitRestraint Class Reference

A restraint for envelope-based scoring of particles in the density map. More...

#include <IMP/em/EnvelopeFitRestraint.h>

+ Inheritance diagram for IMP::em::EnvelopeFitRestraint:

Detailed Description

A restraint for envelope-based scoring of particles in the density map.

The restraint fits the particles into the density map by alignment of principal components of the particles with principal components of the map. Therefore, the particle set should comprise all subunits that fill the map. The aligned particles are scored using EnvelopeScore. This is a fast alignment and scoring that can work well for low resolution density maps.

Note
In most cases it is more appropriate to use isd::GaussianEMRestraint.

Definition at line 34 of file EnvelopeFitRestraint.h.

Public Member Functions

 EnvelopeFitRestraint (Particles particles, DensityMap *em_map, double density_threshold, double penetration_threshold)
 Constructor. More...
 
void apply_transformation ()
 
IMP::ModelObjectsTemp do_get_inputs () const
 
algebra::Transformation3D get_transformation () 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...
 
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::em::EnvelopeFitRestraint::EnvelopeFitRestraint ( Particles  particles,
DensityMap em_map,
double  density_threshold,
double  penetration_threshold 
)

Constructor.

Parameters
[in]particlesThe particles participating in the score
[in]em_mapThe density map used in the fitting score
[in]density_thresholdDensity map threshold
[in]penetration_thresholdA distance for which penetration of particles out of the map envelope (as defined by density_threshold) is allowed. Recommended value is approximately map resolution

Member Function Documentation

IMP::ModelObjectsTemp IMP::em::EnvelopeFitRestraint::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 59 of file EnvelopeFitRestraint.h.

virtual ::IMP::VersionInfo IMP::em::EnvelopeFitRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 60 of file EnvelopeFitRestraint.h.


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