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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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Base class for all optimizers. More...
#include <IMP/Optimizer.h>
Inheritance diagram for IMP::Optimizer:Base class for all optimizers.
An optimizer attempts to improve the current configuration of the Model by moving particles around so as to lower the score.
The Optimizer maintains a list of OptimizerStates which are updated each time the conformation is changed.
The optimizers have one key method Optimizer::optimize() which takes the number of steps to perform. The optimizers can have other stopping conditions as appropriate.
A typical optimization loop proceeds by:
Definition at line 48 of file Optimizer.h.
Public Member Functions | |
| Optimizer (Model *m, std::string name="Optimizer %1%") | |
| double | get_last_score () const |
| Return the score found in the last evaluate. More... | |
| ScoringFunction * | get_scoring_function () const |
| Return the scoring function that is being used. More... | |
| bool | get_stop_on_good_score () const |
| double | optimize (unsigned int max_steps) |
| Optimize the model for up to max_steps iterations. More... | |
| virtual void | set_scoring_function (ScoringFunctionAdaptor sf) |
| Set the scoring function to use. More... | |
| void | set_stop_on_good_score (bool tf) |
| 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 |
| virtual VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| 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) |
| virtual std::string | get_type_name () const |
Protected Member Functions | |
| virtual ModelObjectsTemp | do_get_inputs () const override |
| virtual ModelObjectsTemp | do_get_outputs () const override |
| don't return anything here to avoid pointless dependencies More... | |
| virtual double | do_optimize (unsigned int ns)=0 |
| override this function to do actual optimization More... | |
| ModelObjectsTemp | get_optimizer_state_inputs () const |
| void | update_states () const |
| Update optimizer states, should be called at each successful step. More... | |
| 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 () |
States | |
The stored OptimizerState objects are updated each time the Optimizer decides to accept a new configuration of the Model. To manipulate the list of optimizer states use the methods below. | |
| list | optimizer_states |
| A Python list of OptimizerStates More... | |
| void | remove_optimizer_state (OptimizerState *d) |
| void | remove_optimizer_states (const OptimizerStates &d) |
| void | set_optimizer_states (const OptimizerStates &ps) |
| void | set_optimizer_states_order (const OptimizerStates &objs) |
| unsigned int | add_optimizer_state (OptimizerState *obj) |
| void | add_optimizer_states (const OptimizerStates &objs) |
| void | clear_optimizer_states () |
| unsigned int | get_number_of_optimizer_states () const |
| bool | get_has_optimizer_states () |
| OptimizerState * | get_optimizer_state (unsigned int i) const |
| OptimizerStates | get_optimizer_states () const |
| void | erase_optimizer_state (unsigned int i) |
| void | reserve_optimizer_states (unsigned int sz) |
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overrideprotectedvirtual |
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.
Definition at line 71 of file Optimizer.h.
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overrideprotectedvirtual |
don't return anything here to avoid pointless dependencies
Implements IMP::ModelObject.
Definition at line 76 of file Optimizer.h.
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protectedpure virtual |
override this function to do actual optimization
Implemented in IMP::atom::Simulator, IMP::gsl::Simplex, IMP::core::MonteCarlo, IMP::core::ConjugateGradients, IMP::gsl::QuasiNewton, IMP::gsl::ConjugateGradients, and IMP::core::SteepestDescent.
| double IMP::Optimizer::get_last_score | ( | ) | const |
Return the score found in the last evaluate.
Definition at line 101 of file Optimizer.h.
| ScoringFunction* IMP::Optimizer::get_scoring_function | ( | ) | const |
Return the scoring function that is being used.
| ValueException | if no scoring function was set |
Definition at line 106 of file Optimizer.h.
| double IMP::Optimizer::optimize | ( | unsigned int | max_steps | ) |
Optimize the model for up to max_steps iterations.
Optimize the model
| [in] | max_steps | The maximum number of iterations of the optimizer to perform. Increasing this number will generally make the optimizer spend more time searching for a solution, but beyond that, the details of what changes will vary. |
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virtual |
Set the scoring function to use.
| void IMP::Optimizer::set_stop_on_good_score | ( | bool | tf | ) |
Optimization can be stopped if all the thresholds in the Model are satisfied.
Definition at line 98 of file Optimizer.h.
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protected |
Update optimizer states, should be called at each successful step.
Make sure the scoring function restraints are up to date before this is called (eg by calling evaluate).
| list IMP::Optimizer::optimizer_states |
A Python list of OptimizerStates
Definition at line 127 of file Optimizer.h.