protocols::pack_daemon::MultistateFitnessFunction Class Reference

#include <MultistateFitnessFunction.hh>

Inheritance diagram for protocols::pack_daemon::MultistateFitnessFunction:

Collaboration diagram for protocols::pack_daemon::MultistateFitnessFunction:

Public Types
typedef protocols::genetic_algorithm::FitnessFunction	parent
typedef protocols::genetic_algorithm::Entity	Entity
typedef protocols::genetic_algorithm::EntityOP	EntityOP
typedef utility::vector1 < core::Real >	StateEnergies
typedef std::pair < StateEnergies, StateEnergies >	StateEnergiesAndNPDs
typedef std::pair< EntityOP, StateEnergiesAndNPDs >	EntityAndScore
typedef utility::vector1 < EntityAndScore >	EntityHistory
typedef core::pose::PoseOP	PoseOP
typedef core::pose::Pose	Pose
typedef core::Real	Real
typedef core::Size	Size
Public Types inherited from protocols::genetic_algorithm::FitnessFunction
typedef utility::pointer::owning_ptr < FitnessFunction >	OP
typedef utility::pointer::owning_ptr < FitnessFunction const >	COP

Public Member Functions
	MultistateFitnessFunction ()
virtual	~MultistateFitnessFunction ()
virtual core::Real	evaluate (Entity &entity)
StateEnergies const &	state_energies () const
StateEnergies const &	npd_properties () const
void	daemon_set (DaemonSetOP ds)
void	aggregate_function (MultistateAggregateFunctionOP func)
DaemonSetCOP	daemon_set () const
MultistateAggregateFunctionCOP	aggregate_function () const
void	set_history_size (core::Size history_size)
void	clear_history ()
std::list< std::pair< Size, PoseOP > >	recover_relevant_poses_for_entity (Entity const &)
Public Member Functions inherited from protocols::genetic_algorithm::FitnessFunction
virtual	~FitnessFunction ()

Protected Member Functions
virtual void	compute_state_energies (Entity const &entity)
virtual core::Real	compute_aggregate_score (Entity const &entity)
virtual void	instruct_daemons_to_keep_last_entity ()
virtual void	instruct_daemons_to_drop_entity (Entity const &entity)
virtual std::list< std::pair < Size, PoseOP > >	recover_poses_from_states (Entity const &, utility::vector1< core::Size > const &which_states)
utility::vector1< core::Real > &	state_energies ()
utility::vector1< core::Real > &	npd_properties ()
DaemonSetOP	daemon_set ()
MultistateAggregateFunctionOP	aggregate_function ()
Size	which_top_entity (Entity const &ent) const
void	update_entity_history (Entity const &ent)

Private Attributes
DaemonSetOP	daemon_set_
StateEnergies	state_energies_
StateEnergies	npd_properties_
MultistateAggregateFunctionOP	aggregate_
Size	desired_entity_history_size_
Size	n_tied_for_worst_
EntityHistory	top_entities_

Member Typedef Documentation

typedef protocols::genetic_algorithm::Entity protocols::pack_daemon::MultistateFitnessFunction::Entity

typedef std::pair< EntityOP, StateEnergiesAndNPDs > protocols::pack_daemon::MultistateFitnessFunction::EntityAndScore

typedef utility::vector1< EntityAndScore > protocols::pack_daemon::MultistateFitnessFunction::EntityHistory

typedef protocols::genetic_algorithm::EntityOP protocols::pack_daemon::MultistateFitnessFunction::EntityOP

typedef protocols::genetic_algorithm::FitnessFunction protocols::pack_daemon::MultistateFitnessFunction::parent

typedef core::pose::Pose protocols::pack_daemon::MultistateFitnessFunction::Pose

typedef core::pose::PoseOP protocols::pack_daemon::MultistateFitnessFunction::PoseOP

typedef core::Real protocols::pack_daemon::MultistateFitnessFunction::Real

typedef core::Size protocols::pack_daemon::MultistateFitnessFunction::Size

typedef utility::vector1< core::Real > protocols::pack_daemon::MultistateFitnessFunction::StateEnergies

typedef std::pair< StateEnergies, StateEnergies > protocols::pack_daemon::MultistateFitnessFunction::StateEnergiesAndNPDs

Constructor & Destructor Documentation

protocols::pack_daemon::MultistateFitnessFunction::MultistateFitnessFunction

(

)

References set_history_size().

protocols::pack_daemon::MultistateFitnessFunction::~MultistateFitnessFunction ( )

virtual

Member Function Documentation

void protocols::pack_daemon::MultistateFitnessFunction::aggregate_function

(

MultistateAggregateFunctionOP

func)

References aggregate_.

MultistateAggregateFunctionCOP protocols::pack_daemon::MultistateFitnessFunction::aggregate_function

(

)

const

References aggregate_.

MultistateAggregateFunctionOP protocols::pack_daemon::MultistateFitnessFunction::aggregate_function ( )

protected

References aggregate_.

void protocols::pack_daemon::MultistateFitnessFunction::clear_history

(

)

References n_tied_for_worst_, and top_entities_.

core::Real protocols::pack_daemon::MultistateFitnessFunction::compute_aggregate_score ( Entity const &  entity)

protectedvirtual

References aggregate_, npd_properties_, and state_energies_.

Referenced by evaluate().

void protocols::pack_daemon::MultistateFitnessFunction::compute_state_energies ( Entity const &  entity)

protectedvirtual

Reimplemented in protocols::pack_daemon::MPIMultistateFitnessFunction.

References daemon_set_, npd_properties_, and state_energies_.

Referenced by evaluate().

void protocols::pack_daemon::MultistateFitnessFunction::daemon_set

(

DaemonSetOP

ds)

References daemon_set_, npd_properties_, and state_energies_.

DaemonSetCOP protocols::pack_daemon::MultistateFitnessFunction::daemon_set

(

)

const

References daemon_set_.

Referenced by protocols::pack_daemon::MPIMultistateFitnessFunction::compute_state_energies(), protocols::pack_daemon::MPIMultistateFitnessFunction::instruct_daemons_to_drop_entity(), protocols::pack_daemon::MPIMultistateFitnessFunction::instruct_daemons_to_keep_last_entity(), and protocols::pack_daemon::MPIMultistateFitnessFunction::recover_poses_from_states().

DaemonSetOP protocols::pack_daemon::MultistateFitnessFunction::daemon_set ( )

protected

References daemon_set_.

core::Real protocols::pack_daemon::MultistateFitnessFunction::evaluate ( Entity &  entity)

virtual

Implements protocols::genetic_algorithm::FitnessFunction.

References compute_aggregate_score(), compute_state_energies(), protocols::genetic_algorithm::Entity::set_fitness(), state_energies_, protocols::pack_daemon::TR(), and update_entity_history().

void protocols::pack_daemon::MultistateFitnessFunction::instruct_daemons_to_drop_entity ( Entity const &  entity)

protectedvirtual

Reimplemented in protocols::pack_daemon::MPIMultistateFitnessFunction.

References daemon_set_.

Referenced by update_entity_history().

void protocols::pack_daemon::MultistateFitnessFunction::instruct_daemons_to_keep_last_entity ( )

protectedvirtual

Reimplemented in protocols::pack_daemon::MPIMultistateFitnessFunction.

References daemon_set_.

Referenced by update_entity_history().

utility::vector1< core::Real > const & protocols::pack_daemon::MultistateFitnessFunction::npd_properties

(

)

const

References npd_properties_.

Referenced by protocols::pack_daemon::MPIMultistateFitnessFunction::compute_state_energies(), and protocols::pack_daemon::MPIMultistateFitnessFunction::set_num_npd_properties().

utility::vector1< core::Real > & protocols::pack_daemon::MultistateFitnessFunction::npd_properties ( )

protected

References npd_properties_.

std::list< std::pair< MultistateFitnessFunction::Size, MultistateFitnessFunction::PoseOP > > protocols::pack_daemon::MultistateFitnessFunction::recover_poses_from_states ( Entity const &  ent, utility::vector1< core::Size > const &  which_states  )

protectedvirtual

Reimplemented in protocols::pack_daemon::MPIMultistateFitnessFunction.

References daemon_set_.

Referenced by recover_relevant_poses_for_entity().

std::list< std::pair< MultistateFitnessFunction::Size, MultistateFitnessFunction::PoseOP > > protocols::pack_daemon::MultistateFitnessFunction::recover_relevant_poses_for_entity

(

Entity const &

ent)

References aggregate_, recover_poses_from_states(), top_entities_, and which_top_entity().

void protocols::pack_daemon::MultistateFitnessFunction::set_history_size

(

core::Size

history_size)

References desired_entity_history_size_, n_tied_for_worst_, and top_entities_.

Referenced by MultistateFitnessFunction().

utility::vector1< core::Real > const & protocols::pack_daemon::MultistateFitnessFunction::state_energies

(

)

const

References state_energies_.

Referenced by protocols::pack_daemon::MPIMultistateFitnessFunction::compute_state_energies(), and protocols::pack_daemon::MPIMultistateFitnessFunction::set_num_pack_daemons().

utility::vector1< core::Real > & protocols::pack_daemon::MultistateFitnessFunction::state_energies ( )

protected

References state_energies_.

void protocols::pack_daemon::MultistateFitnessFunction::update_entity_history ( Entity const &  ent)

protected

References desired_entity_history_size_, protocols::genetic_algorithm::Entity::fitness(), instruct_daemons_to_drop_entity(), instruct_daemons_to_keep_last_entity(), n_tied_for_worst_, npd_properties_, state_energies_, and top_entities_.

Referenced by evaluate().

core::Size protocols::pack_daemon::MultistateFitnessFunction::which_top_entity ( Entity const &  ent) const

protected

References top_entities_.

Referenced by recover_relevant_poses_for_entity().

Member Data Documentation

MultistateAggregateFunctionOP protocols::pack_daemon::MultistateFitnessFunction::aggregate_

private

Referenced by aggregate_function(), compute_aggregate_score(), and recover_relevant_poses_for_entity().

DaemonSetOP protocols::pack_daemon::MultistateFitnessFunction::daemon_set_

private

Referenced by compute_state_energies(), daemon_set(), instruct_daemons_to_drop_entity(), instruct_daemons_to_keep_last_entity(), and recover_poses_from_states().

Size protocols::pack_daemon::MultistateFitnessFunction::desired_entity_history_size_

private

Referenced by set_history_size(), and update_entity_history().

Size protocols::pack_daemon::MultistateFitnessFunction::n_tied_for_worst_

private

Referenced by clear_history(), set_history_size(), and update_entity_history().

StateEnergies protocols::pack_daemon::MultistateFitnessFunction::npd_properties_

private

Referenced by compute_aggregate_score(), compute_state_energies(), daemon_set(), npd_properties(), and update_entity_history().

StateEnergies protocols::pack_daemon::MultistateFitnessFunction::state_energies_

private

Referenced by compute_aggregate_score(), compute_state_energies(), daemon_set(), evaluate(), state_energies(), and update_entity_history().

EntityHistory protocols::pack_daemon::MultistateFitnessFunction::top_entities_

private

Referenced by clear_history(), recover_relevant_poses_for_entity(), set_history_size(), update_entity_history(), and which_top_entity().

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

• src/protocols/pack_daemon/MultistateFitnessFunction.hh
• src/protocols/pack_daemon/MultistateFitnessFunction.cc