protocols::pack_daemon::MultistateFitnessFunction Class Reference

#include <MultistateFitnessFunction.hh>

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

Public Member Functions
	MultistateFitnessFunction ()
	~MultistateFitnessFunction () override
core::Real	evaluate (Entity &entity) override
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< core::Size, PoseOP > >	recover_relevant_poses_for_entity (Entity const &)
Public Member Functions inherited from protocols::genetic_algorithm::FitnessFunction
	~FitnessFunction () override=default

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< core::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 ()
core::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_
TopEntitySet	top_entities_

Member Typedef Documentation

Entity

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

EntityAndScore

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

EntityHistory

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

EntityOP

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

parent

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

Pose

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

PoseOP

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

Real

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

Size

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

StateEnergies

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

StateEnergiesAndNPDs

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

Constructor & Destructor Documentation

MultistateFitnessFunction()

protocols::pack_daemon::MultistateFitnessFunction::MultistateFitnessFunction

(

)

References set_history_size().

~MultistateFitnessFunction()

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

overridedefault

Member Function Documentation

aggregate_function() [1/3]

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

protected

References aggregate_.

aggregate_function() [2/3]

MultistateAggregateFunctionCOP protocols::pack_daemon::MultistateFitnessFunction::aggregate_function

(

)

const

References aggregate_.

aggregate_function() [3/3]

void protocols::pack_daemon::MultistateFitnessFunction::aggregate_function

(

MultistateAggregateFunctionOP

func

)

References aggregate_.

clear_history()

void protocols::pack_daemon::MultistateFitnessFunction::clear_history

(

)

References protocols::pack_daemon::TopEntitySet::clear(), and top_entities_.

compute_aggregate_score()

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

protectedvirtual

References aggregate_, npd_properties_, and state_energies_.

Referenced by evaluate().

compute_state_energies()

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().

daemon_set() [1/3]

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

protected

References daemon_set_.

daemon_set() [2/3]

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().

daemon_set() [3/3]

void protocols::pack_daemon::MultistateFitnessFunction::daemon_set

(

DaemonSetOP

ds

)

References daemon_set_, npd_properties_, and state_energies_.

evaluate()

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

overridevirtual

Implements protocols::genetic_algorithm::FitnessFunction.

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

instruct_daemons_to_drop_entity()

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().

instruct_daemons_to_keep_last_entity()

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().

npd_properties() [1/2]

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

protected

References npd_properties_.

npd_properties() [2/2]

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().

recover_poses_from_states()

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().

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_, protocols::pack_daemon::TopEntitySet::index_of_entity(), recover_poses_from_states(), protocols::pack_daemon::TopEntitySet::size(), and top_entities_.

set_history_size()

void protocols::pack_daemon::MultistateFitnessFunction::set_history_size

(

core::Size

history_size

)

References protocols::pack_daemon::TopEntitySet::desired_entity_history_size(), and top_entities_.

Referenced by MultistateFitnessFunction().

state_energies() [1/2]

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

protected

References state_energies_.

state_energies() [2/2]

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().

update_entity_history()

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

protected

References instruct_daemons_to_drop_entity(), instruct_daemons_to_keep_last_entity(), npd_properties_, state_energies_, top_entities_, and protocols::pack_daemon::TopEntitySet::update_entity_history().

Referenced by evaluate().

which_top_entity()

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

protected

Member Data Documentation

aggregate_

MultistateAggregateFunctionOP protocols::pack_daemon::MultistateFitnessFunction::aggregate_

private

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

daemon_set_

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().

npd_properties_

StateEnergies protocols::pack_daemon::MultistateFitnessFunction::npd_properties_

private

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

state_energies_

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().

top_entities_

TopEntitySet protocols::pack_daemon::MultistateFitnessFunction::top_entities_

private

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

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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