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IMP Reference Guide  develop.d247202c1c,2019/10/23
The Integrative Modeling Platform
IMP::em::FitRestraint Class Reference

Calculate score based on fit to EM map. More...

#include <IMP/em/FitRestraint.h>

+ Inheritance diagram for IMP::em::FitRestraint:

Detailed Description

Calculate score based on fit to EM map.

The score is a function of the cross correlation between the EM map and the map simulated from the particles. This is calculated by means of a double sum over the two sets of voxels.

Note
In most cases it is faster to approximate the two maps with a Gaussian Mixture Model and to use that for the scoring, with isd::GaussianEMRestraint.

Definition at line 39 of file FitRestraint.h.

Public Member Functions

 FitRestraint (ParticlesTemp ps, DensityMap *em_map, FloatPair norm_factors=FloatPair(0., 0.), FloatKey weight_key=atom::Mass::get_mass_key(), float scale=1, bool use_rigid_bodies=true, KernelType kt=GAUSSIAN)
 Constructor. More...
 
unsigned int add_particle (Particle *obj)
 
void add_particles (const Particles &objs)
 
void clear_particles ()
 
virtual IMP::ModelObjectsTemp do_get_inputs () const
 
bool get_has_particles ()
 
SampledDensityMapget_model_dens_map () const
 Return the predicted density map of the model. More...
 
unsigned int get_number_of_particles () const
 
Particleget_particle (unsigned int i) const
 
Particles get_particles () const
 
float get_scale_factor () 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 remove_particle (Particle *d)
 
void remove_particles (const Particles &d)
 
void reserve_particles (unsigned int sz)
 
void set_particles (const Particles &ps)
 
void set_particles_order (const Particles &objs)
 
void set_scale_factor (float scale)
 
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::em::FitRestraint::FitRestraint ( ParticlesTemp  ps,
DensityMap em_map,
FloatPair  norm_factors = FloatPair(0., 0.),
FloatKey  weight_key = atom::Mass::get_mass_key(),
float  scale = 1,
bool  use_rigid_bodies = true,
KernelType  kt = GAUSSIAN 
)

Constructor.

Parameters
[in]psThe particles participating in the fitting score
[in]em_mapThe density map used in the fitting score
[in]norm_factorsif set, they are used as normalization factors for the cross correlation calculations. This is relevant when the cross-correlation score of the entire system is decomposed.
[in]weight_keythe name of the weight attribute of the particles
[in]scalemultiply the fitting restraint score and derivatives by this value
[in]use_rigid_bodiesif some of the particles are part of a rigid body, use the rigid body for faster calculations
[in]ktKernelType to use for simulating density from particles
Note
Rigid-bodies are interpolated and not resampled if use_rigid_bodies option is selected. This significantly reduces the running time but is less accurate. If the user prefers to get more accurate results, provide its members as input particles and not the rigid body.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::em::FitRestraint::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.

SampledDensityMap* IMP::em::FitRestraint::get_model_dens_map ( ) const

Return the predicted density map of the model.

Definition at line 67 of file FitRestraint.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 73 of file FitRestraint.h.


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