Base class for all optimizers. More...

#include <IMP/kernel/Optimizer.h>

Inheritance diagram for IMP::kernel::Optimizer:

Public Member Functions
	Optimizer (kernel::Model *m, std::string name="Optimizer %1%")

	Optimizer ()

void	clear_range_cache ()

Float	get_derivative (FloatIndex fi) const

double	get_last_score () const
	Return the score found in the last evaluate.

FloatIndexes	get_optimized_attributes () const

Restraints	get_restraints () const

double	get_scaled_derivative (FloatIndex fi) const

double	get_scaled_value (FloatIndex fi) const

double	get_score_threshold () const

ScoringFunction *	get_scoring_function () const
	Return the scoring function that is being used.

bool	get_stop_on_good_score () const

Float	get_value (FloatIndex fi) const

double	get_width (FloatKey k) const

double	optimize (unsigned int max_steps)
	Optimize the model for up to max_steps iterations. More...

void	set_restraints (const RestraintsTemp &rs)

void	set_scaled_value (FloatIndex fi, Float v) const

void	set_score_threshold (double s)

virtual void	set_scoring_function (ScoringFunctionAdaptor sf)

void	set_stop_on_good_score (bool tf)

void	set_value (FloatIndex fi, double v) const

double	width (FloatKey k) const

Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (kernel::Model *m, std::string name)

	ModelObject (std::string name)

bool	get_has_dependencies () const
	Return whether this object has dependencies computed.

bool	get_has_required_score_states () const

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

bool	get_is_part_of_model () const

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const

void	set_has_dependencies (bool tf)

void	set_has_required_score_states (bool tf)

virtual void	set_model (kernel::Model *m)

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

virtual void	do_destroy ()

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.

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

virtual double	do_optimize (unsigned int ns)=0
	override this function to do actual optimization

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...

	Object ()

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)

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.

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

Constructor & Destructor Documentation

IMP::kernel::Optimizer::Optimizer ( )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the constructor with a Model and a name.

Member Function Documentation

void IMP::kernel::Optimizer::clear_range_cache ( )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

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 60 of file kernel/Optimizer.h.

Float IMP::kernel::Optimizer::get_derivative ( FloatIndex fi ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

FloatIndexes IMP::kernel::Optimizer::get_optimized_attributes ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

Restraints IMP::kernel::Optimizer::get_restraints ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use Optimizer::get_scoring_function() instead.

double IMP::kernel::Optimizer::get_scaled_derivative ( FloatIndex fi ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

double IMP::kernel::Optimizer::get_scaled_value ( FloatIndex fi ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

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

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do not use as it is not reliably supported.

Float IMP::kernel::Optimizer::get_value ( FloatIndex fi ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

double IMP::kernel::Optimizer::get_width ( FloatKey k ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

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_restraints ( const RestraintsTemp & rs )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_scoring_function() instead.

void IMP::kernel::Optimizer::set_scaled_value	(	FloatIndex	fi,
		Float	v
	)		const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

void IMP::kernel::Optimizer::set_score_threshold ( double s )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Do not use as it is not reliably supported.

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 83 of file kernel/Optimizer.h.

void IMP::kernel::Optimizer::set_value	(	FloatIndex	fi,
		double	v
	)		const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

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

protected

Make sure the scoring function restraints are up to date before this is called (eg by calling evaluate).

double IMP::kernel::Optimizer::width ( FloatKey k ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AttributeOptimizer instead.

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

kernel/Optimizer.h

Public Member Functions

Protected Member Functions

States

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation