IMP  2.0.1
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:

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
 
double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
- 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)
 

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

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 works well for low resolution density maps.

Definition at line 32 of file EnvelopeFitRestraint.h.

Constructor & Destructor Documentation

IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint ( Particles  particles,
DensityMap em_map,
double  density_threshold,
double  penetration_threshold 
)
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

Override if this reads other objects during evaluate.

Implements IMP::kernel::ModelObject.

Definition at line 59 of file EnvelopeFitRestraint.h.


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