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This restraint ensures that a set of particles are similar to a set of EM images
This restraint generates projections of the model that are compared with the EM images. The projections are generated from the radius of its particles. In the case of atoms, the radius is generated automatically. For other particles the radius has to be provided.
Examples: optimize em2d with montecarlo
Inheritance diagram for IMP::em2d::Em2DRestraint:Public Member Functions | |
| Em2DRestraint () | |
| Create the restraint. | |
| RegistrationResults | get_registration_results () const |
| void | set_coarse_registration_mode (bool opt) |
| void | set_fast_mode (unsigned int n) |
| void | set_images (const em2d::Images em_images) |
| Sets the EM images to use as restraints. | |
| void | set_particles (SingletonContainer *particles_container) |
| Sets the particles that should correspond to the EM images. | |
| void | set_variance_images (const em2d::Images variance_images) |
| void | setup (ScoreFunction *score_function, const Em2DRestraintParameters ¶ms) |
| This function initializes the restraint with the required parameters. | |
| Public Member Functions inherited from IMP::Restraint | |
| Restraint (Model *m, std::string name) | |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. | |
| double | evaluate (bool calc_derivs) const |
| Return the score for this restraint for the current state of the model. | |
| double | evaluate_if_below (bool calc_derivatives, double max) const |
| See Model::evaluate_with_maximum() | |
| double | evaluate_if_good (bool calc_derivatives) const |
| See Model::evaluate_if_good() | |
| double | get_last_score () const |
| bool | get_was_good () const |
| virtual double | unprotected_evaluate (DerivativeAccumulator *) const =0 |
| virtual double | unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const |
| virtual double | unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const |
| virtual ContainersTemp | get_input_containers () const =0 |
| virtual ParticlesTemp | get_input_particles () const =0 |
| 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) | |
| ModelObjectsTemp | get_inputs () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| Public Member Functions inherited from IMP::base::Object | |
| std::size_t | __hash__ () const |
| virtual std::string | get_type_name () const =0 |
| Return a string identifying the type of the object. | |
| 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. | |
| 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) |
Static Public Member Functions | |
| static Em2DRestraint * | get_from (IMP::base::Object *o) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::Restraint | |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| Protected Member Functions inherited from IMP::ModelObject | |
| virtual ModelObjectsTemp | do_get_inputs () const =0 |
| virtual ModelObjectsTemp | do_get_outputs () const =0 |
| virtual void | do_update_dependencies (const DependencyGraph &, const DependencyGraphVertexIndex &) |
| void | update_dependencies (const DependencyGraph &dg, const DependencyGraphVertexIndex &index) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| IMP::em2d::Em2DRestraint::Em2DRestraint | ( | ) |
Create the restraint.
| void IMP::em2d::Em2DRestraint::set_coarse_registration_mode | ( | bool | opt | ) |
If the value provided to this function is true, restraint operates only using a coarse registration scheme (maximizing the CCC). This option (which is set to false by default) can speed the evaluation of the restraint by a order of magnitude, but the values obtained are not going to be optimum. You could wnat to activate it at the beginning of an optimization.
| void IMP::em2d::Em2DRestraint::set_fast_mode | ( | unsigned int | n | ) |
Sets fast mode for computing the restraint. This mode only makes sense it the set_coarse_registration_mode option is false. This option only optimizes some coarse results (those given by the argument) to get the refined value. This option is very fast compared to a full optimization, and almost always is a good idea to use it with 1-5 results. This mode is still significantly slow compared to set_coarse_registration_mode(), but the values optimized are optimum.
| void IMP::em2d::Em2DRestraint::set_images | ( | const em2d::Images | em_images | ) |
Sets the EM images to use as restraints.
| void IMP::em2d::Em2DRestraint::set_particles | ( | SingletonContainer * | particles_container | ) |
Sets the particles that should correspond to the EM images.
| void IMP::em2d::Em2DRestraint::set_variance_images | ( | const em2d::Images | variance_images | ) |
Sets the variance images of EM images. This is useful if the image is a class average Note: Not all the scoring function use this data
| void IMP::em2d::Em2DRestraint::setup | ( | ScoreFunction * | score_function, |
| const Em2DRestraintParameters & | params | ||
| ) |
This function initializes the restraint with the required parameters.
| [in] | apix | Angstroms per pixel in the images |
| [in] | resolution | resolution to use when generating projections |
| [in] | n_projections | number of projections to generate to perform the initial coarse registration. |
