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 (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 void | do_show (std::ostream &out) const |
| bool | get_has_particles () |
| SampledDensityMap * | get_model_dens_map () const |
| unsigned int | get_number_of_particles () const |
| Particle * | get_particle (unsigned int i) const |
| Particles | get_particles () const |
| float | get_scale_factor () const |
| 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) |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. More... | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. More... | |
| virtual ScoringFunction * | create_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 |
| Model * | get_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 () |
| Related Functions inherited from IMP::kernel::Restraint | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
Detailed Description
Definition at line 32 of file FitRestraint.h.
Constructor & Destructor Documentation
| IMP::em::FitRestraint::FitRestraint | ( | ParticlesTemp | ps, |
| DensityMap * | em_map, | ||
| FloatPair | norm_factors = FloatPair(0., 0.), |
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| FloatKey | weight_key = atom::Mass::get_mass_key(), |
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| float | scale = 1, |
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| bool | use_rigid_bodies = true, |
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| KernelType | kt = GAUSSIAN |
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| ) |
- Parameters
-
[in] ps The particles participating in the fitting score [in] em_map The density map used in the fitting score [in] norm_factors if 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_key the name of the weight attribute of the particles [in] scale multiply the fitting restraint score and derivatives by this value [in] use_rigid_bodies if some of the particles are part of a rigid body, use the rigid body for faster calculations [in] kt KernelType 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
| SampledDensityMap* IMP::em::FitRestraint::get_model_dens_map | ( | ) | const |
- Returns
- the predicted density map of the model
Definition at line 63 of file FitRestraint.h.
The documentation for this class was generated from the following file: