Base class for all optimizers. More...
#include <IMP/kernel/Optimizer.h>
Inheritance diagram for IMP::kernel::Optimizer:Public Member Functions | |
| Optimizer (Model *m, std::string name="Optimizer %1%") | |
| double | get_last_score () const |
| Return the score found in the last evaluate. | |
| Model * | get_model () const |
| Get the model being optimized. | |
| ScoringFunction * | get_scoring_function () const |
| Return the scoring function that is being used. | |
| bool | get_stop_on_good_score () const |
| double | optimize (unsigned int max_steps) |
| Optimize the model for up to max_steps iterations. More... | |
| void | set_model (Model *m) |
| Set the model being optimized. More... | |
| virtual void | set_scoring_function (ScoringFunctionAdaptor sf) |
| void | set_stop_on_good_score (bool tf) |
| virtual void | show (std::ostream &out=std::cout) const |
| Print info about the optimizer state. More... | |
| 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) |
Protected Member Functions | |
| virtual double | do_optimize (unsigned int ns)=0 |
| override this function to do actual optimization | |
| void | update_states () const |
| Update optimizer states, should be called at each successful step. More... | |
| double | width (FloatKey k) const |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
Related Functions | |
(Note that these are not member functions.) | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Optimizer > > | OptimizersTemp |
| Related Functions inherited from IMP::base::Object | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
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. | |
| 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 | reserve_optimizer_states (unsigned int sz) |
Methods for getting and setting optimized attributes | |
Optimizers don't have to go through the particles themselves looking for values to optimize unless they care about special properties of the optimized values. Instead they can iterate through the list of optimized attributes, each of which is identified by a FloatIndex. With these FloatIndex objects they can get and set the values and derivatives as needed. | |
| FloatIndexes | get_optimized_attributes () const |
| void | set_value (FloatIndex fi, double v) const |
| Float | get_value (FloatIndex fi) const |
| Float | get_derivative (FloatIndex fi) const |
Methods to get and set scaled optimizable values | |
Certain optimizers benefit from having all the optimized values scaled to vary over a similar range. These accessors use the Model::get_range ranges to scale the values before returning them and unscale them before setting them. | |
| void | set_scaled_value (FloatIndex fi, Float v) const |
| double | get_scaled_value (FloatIndex fi) const |
| double | get_scaled_derivative (FloatIndex fi) const |
| void | clear_range_cache () |
| Clear the cache of range information. Do this at the start of optimization. | |
Detailed Description
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:
- the optimizer calls Model::evaluate() to compute the score (and possibly the derivatives) of the current conformation of the Model.
- the optimizer uses this information to update the optimizeable parameters of the Particles contained in the Model.
- Implementors
- Developers who wish to implement a Optimizer should inherit from this class and use the IMP_OPTIMIZER() macro to help define the needed functions. Lamentably, we do not provide an example.
Definition at line 46 of file kernel/Optimizer.h.
Member Function Documentation
| double IMP::kernel::Optimizer::optimize | ( | unsigned int | max_steps | ) |
Optimize the model
- Parameters
-
[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.
- Returns
- The final score.
| void IMP::kernel::Optimizer::set_model | ( | Model * | m | ) |
- Note
- The model is not owned by the optimizer and so is not deleted when the optimizer is deleted. Further, the Optimizer does not prevent the model from being deleted when all Python references go away.
|
virtual |
By default, the Optimizer uses the scoring function provided by the model, but you can use another scoring function instead.
| void IMP::kernel::Optimizer::set_stop_on_good_score | ( | bool | tf | ) |
Optimization can be stopped if all the thresholds in the Model are satisfied.
Definition at line 78 of file kernel/Optimizer.h.
|
virtual |
It should end in a newline
Definition at line 110 of file kernel/Optimizer.h.
|
protected |
Make sure the scoring function restraints are up to date before this is called (eg by calling evaluate).
Friends And Related Function Documentation
|
related |
Pass a set of objects.
Definition at line 242 of file kernel/Optimizer.h.
The documentation for this class was generated from the following file: