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Class for storing model, its restraints, constraints, and particles.
The Model maintains a standard IMP container for each of Particle, ScoreState and Restraint object types.
Each Float attribute has an associated range which reflects the range of values that it is expected to take on during optimization. The optimizer can use these ranges to make the optimization process more efficient. By default, the range estimates are simply the range of values for that attribute in the various particles, but it can be set to another value. For example, an attribute storing an angle could have the range set to (0,PI).
The ranges are not enforced; they are just guidelines. In order to enforce ranges, see, for example, IMP::example::ExampleSingletonModifier.
Inheritance diagram for IMP::Model:Public Member Functions | |
| Model (std::string name="Model %1%") | |
| void | clear_particle_caches (ParticleIndex pi) |
| ScoringFunction * | create_model_scoring_function () |
| ModelObjectsTemp | get_model_objects () const |
| void | remove_particle (Particle *p) |
| void | update () |
| Sometimes it is useful to be able to make sure the model is up to date. | |
| Public Member Functions inherited from IMP::RestraintSet | |
| RestraintSet (Model *m, double weight, const std::string &name="RestraintSet %1%") | |
| Create an empty set that is registered with the model. | |
| ContainersTemp | get_input_containers () const |
| ParticlesTemp | get_input_particles () const |
| std::pair< RestraintsTemp, RestraintSetsTemp > | get_non_sets_and_sets () const |
| double | unprotected_evaluate (DerivativeAccumulator *accum) const |
| double | unprotected_evaluate_if_below (DerivativeAccumulator *accum, double max) const |
| double | unprotected_evaluate_if_good (DerivativeAccumulator *accum, double max) const |
| void | remove_restraint (Restraint *d) |
| template<class F > | |
| void | remove_restraints_if (const F &f) |
| template<class List > | |
| void | remove_restraints (List d) |
| template<class List > | |
| void | set_restraints (List ps) |
| template<class List > | |
| void | set_restraints_order (List ps) |
| unsigned int | add_restraint (Restraint *obj) |
| template<class List > | |
| void | add_restraints (List objs) |
| void | clear_restraints () |
| unsigned int | get_number_of_restraints () const |
| bool | get_has_restraints () const |
| Restraint * | get_restraint (unsigned int i) const |
| Restraints | get_restraints () const |
| void | reserve_restraints (unsigned int sz) |
| RestraintIterator | restraints_begin () |
| RestraintIterator | restraints_end () |
| RestraintConstIterator | restraints_begin () const |
| RestraintConstIterator | restraints_end () const |
| 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 |
| 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 Model * | get_from (IMP::base::Object *o) |
States | |
The Model stores a list of ScoreStates which are given an opportunity to update the stored Particles and their internal state before and after the restraints are evaluated. Use the methods below to manipulate the list of ScoreState objects. The value type for the iterators is a ScoreState*.
| |
| void | remove_score_state (ScoreState *d) |
| template<class F > | |
| void | remove_score_states_if (const F &f) |
| template<class List > | |
| void | remove_score_states (List d) |
| template<class List > | |
| void | set_score_states (List ps) |
| template<class List > | |
| void | set_score_states_order (List ps) |
| unsigned int | add_score_state (ScoreState *obj) |
| template<class List > | |
| void | add_score_states (List objs) |
| void | clear_score_states () |
| unsigned int | get_number_of_score_states () const |
| bool | get_has_score_states () const |
| ScoreState * | get_score_state (unsigned int i) const |
| ScoreStates | get_score_states () const |
| void | reserve_score_states (unsigned int sz) |
| ScoreStateIterator | score_states_begin () |
| ScoreStateIterator | score_states_end () |
| ScoreStateConstIterator | score_states_begin () const |
| ScoreStateConstIterator | score_states_end () const |
Restraints | |
The Model scores the current configuration using the stored Restraint objects. Use the methods below to manipulate the list. The value type for the iterators is a Restraint*. | |
| RestraintSet * | get_root_restraint_set () |
Statistics | |
The Model can gather various statistics about the restraints and score states used. To use this feature, first turn on statistics gather and then run your optimization (or just call evaluate).
| |
| void | clear_all_statistics () |
| void | set_gather_statistics (bool tf) |
| bool | get_gather_statistics () const |
| void | show_all_statistics (std::ostream &out=std::cout) const |
| void | show_restraint_time_statistics (std::ostream &out=std::cout) const |
| void | show_restraint_score_statistics (std::ostream &out=std::cout) const |
| RestraintStatistics | get_restraint_statistics (Restraint *r) const |
| void | show_score_state_time_statistics (std::ostream &out=std::cout) const |
Model Data | |
Arbitrary non-particle data can be associated with the Model. This can be used for Model-level caches and such. | |
| void | add_data (ModelKey mk, base::Object *o) |
| base::Object * | get_data (ModelKey mk) const |
| void | remove_data (ModelKey mk) |
| bool | get_has_data (ModelKey mk) const |
Methods to debug particles | |
It is sometimes useful to inspect the list of all particles when debugging. These methods allow you to do that.
The value type for the iterators is a Particle*. | |
| unsigned int | get_number_of_particles () const |
| ParticlesTemp | get_particles () const |
| Particle * | get_particle (ParticleIndex p) const |
| ParticleIterator | particles_begin () const |
| ParticleIterator | particles_end () const |
Additional Inherited Members |
| IMP::Model::Model | ( | std::string | name = "Model %1%" | ) |
Construct an empty model
| ScoringFunction* IMP::Model::create_model_scoring_function | ( | ) |
Create a scoring function from the model restraints.
| ModelObjectsTemp IMP::Model::get_model_objects | ( | ) | const |
Get all the ModelObjects associated with this Model.
| void IMP::Model::remove_particle | ( | Particle * | p | ) |
Remove a particle from the Model. The particle will then be inactive and cannot be used for anything and all data stored in the particle is lost.
| void IMP::Model::update | ( | ) |
Sometimes it is useful to be able to make sure the model is up to date.
This method updates all the state but does not necessarily compute the score. Use this to make sure that your containers and rigid bodies are up to date.
