IMP  2.1.1
The Integrative Modeling Platform
IMP::em::FitRestraint Class Reference

Calculate score based on fit to EM map.

#include <IMP/em/FitRestraint.h>

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

Public Member Functions

 FitRestraint (kernel::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 (kernel::Particle *obj)
 
void add_particles (const kernel::Particles &objs)
 
void clear_particles ()
 
virtual
IMP::kernel::ModelObjectsTemp 
do_get_inputs () const
 
bool get_has_particles ()
 
SampledDensityMapget_model_dens_map () const
 
unsigned int get_number_of_particles () const
 
kernel::Particleget_particle (unsigned int i) const
 
kernel::Particles get_particles () const
 
float get_scale_factor () const
 
virtual std::string get_type_name () const
 
virtual ::IMP::base::VersionInfo get_version_info () const
 Get information about the module and version of the object.
 
void remove_particle (kernel::Particle *d)
 
void remove_particles (const kernel::Particles &d)
 
void reserve_particles (unsigned int sz)
 
void set_particles (const kernel::Particles &ps)
 
void set_particles_order (const kernel::Particles &objs)
 
void set_scale_factor (float scale)
 
- Public Member Functions inherited from IMP::kernel::Restraint
 Restraint (kernel::Model *m, std::string name)
 
 Restraint (std::string name="Restraint %1%")
 
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 (kernel::Model *m, std::string name)
 
 ModelObject (std::string name)
 
virtual void do_set_model (kernel::Model *)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed.
 
bool get_has_required_score_states () const
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
bool get_is_part_of_model () const
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_required_score_states () const
 
void set_has_dependencies (bool tf)
 
void set_has_required_score_states (bool tf)
 
virtual void set_model (kernel::Model *m)
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual void do_destroy ()
 
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)
 

Public Attributes

virtual double const
 

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
 
- Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
 Object ()
 

Detailed Description

Definition at line 31 of file FitRestraint.h.

Constructor & Destructor Documentation

IMP::em::FitRestraint::FitRestraint ( kernel::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 
)
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::kernel::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::kernel::ModelObject.

SampledDensityMap* IMP::em::FitRestraint::get_model_dens_map ( ) const
Returns
the predicted density map of the model

Definition at line 62 of file FitRestraint.h.


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