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IMP Reference Guide
2.7.0
The Integrative Modeling Platform
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Calculate score based on fit to EM map. More...
#include <IMP/em/FitRestraint.h>
Inheritance diagram for IMP::em::FitRestraint: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.
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 () |
| SampledDensityMap * | get_model_dens_map () const |
| Return the predicted density map of the model. More... | |
| unsigned int | get_number_of_particles () const |
| Particle * | get_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... | |
| 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 |
| Create a scoring function with only this restraint. More... | |
| 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::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... | |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_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 () |
| 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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| ) |
Constructor.
| [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 |
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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.
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 73 of file FitRestraint.h.
