Base class for optimizers that act on individual attributes. More...

#include <IMP/kernel/AttributeOptimizer.h>

Inheritance diagram for IMP::kernel::AttributeOptimizer:

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

	AttributeOptimizer ()

Public Member Functions inherited from IMP::kernel::Optimizer
	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

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)

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
double	get_width (FloatKey k) const

Protected Member Functions inherited from IMP::kernel::Optimizer
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 ()

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.

Detailed Description

AttributeOptimizers optimize the collection of optimized attributes (see Model::set_is_optimized()) in contrast to, say molecular dynamics where the fundamental entity is a Particle.

Definition at line 22 of file kernel/AttributeOptimizer.h.

Constructor & Destructor Documentation

IMP::kernel::AttributeOptimizer::AttributeOptimizer ( )

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.

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

kernel/AttributeOptimizer.h

Public Member Functions

Protected Member Functions

Methods for getting and setting optimized attributes

Methods to get and set scaled optimizable values

Detailed Description

Constructor & Destructor Documentation