Detailed Description

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:

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.

Definition at line 44 of file kernel/Optimizer.h.

Public Member Functions
	Optimizer (kernel::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)

void	set_stop_on_good_score (bool tf)

Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (kernel::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::base::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

virtual ModelObjectsTemp	do_get_outputs () const
	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::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::base::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.
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)

Member Function Documentation

virtual ModelObjectsTemp IMP::kernel::Optimizer::do_get_inputs ( ) const

protectedvirtual

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::kernel::ModelObject.

Definition at line 58 of file kernel/Optimizer.h.

virtual ModelObjectsTemp IMP::kernel::Optimizer::do_get_outputs ( ) const

protectedvirtual

don't return anything here to avoid pointless dependencies

Implements IMP::kernel::ModelObject.

Definition at line 62 of file kernel/Optimizer.h.

virtual double IMP::kernel::Optimizer::do_optimize ( unsigned int ns )

protectedpure virtual

override this function to do actual optimization

Implemented in IMP::atom::Simulator, and IMP::core::MonteCarlo.

double IMP::kernel::Optimizer::get_last_score ( ) const

Return the score found in the last evaluate.

Definition at line 84 of file kernel/Optimizer.h.

ScoringFunction* IMP::kernel::Optimizer::get_scoring_function ( ) const

Return the scoring function that is being used.

Definition at line 87 of file kernel/Optimizer.h.

double IMP::kernel::Optimizer::optimize ( unsigned int max_steps )

Optimize the model for up to max_steps iterations.

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.

virtual void IMP::kernel::Optimizer::set_scoring_function ( ScoringFunctionAdaptor sf )

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 81 of file kernel/Optimizer.h.

void IMP::kernel::Optimizer::update_states ( ) const

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).

The documentation for this class was generated from the following file:

kernel/Optimizer.h

Detailed Description

Public Member Functions

Protected Member Functions

States

Member Function Documentation