#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_

Detailed Description

Definition at line 42 of file MultistateFitnessFunction.hh.

Member Typedef Documentation

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

Definition at line 46 of file MultistateFitnessFunction.hh.

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

Definition at line 50 of file MultistateFitnessFunction.hh.

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

Definition at line 51 of file MultistateFitnessFunction.hh.

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

Definition at line 47 of file MultistateFitnessFunction.hh.

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

Definition at line 45 of file MultistateFitnessFunction.hh.

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

Definition at line 53 of file MultistateFitnessFunction.hh.

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

Definition at line 52 of file MultistateFitnessFunction.hh.

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

Definition at line 54 of file MultistateFitnessFunction.hh.

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

Definition at line 55 of file MultistateFitnessFunction.hh.

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

Definition at line 48 of file MultistateFitnessFunction.hh.

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

Definition at line 49 of file MultistateFitnessFunction.hh.

Constructor & Destructor Documentation

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

Definition at line 65 of file MultistateFitnessFunction.cc.

References set_history_size().

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

virtual

Definition at line 71 of file MultistateFitnessFunction.cc.

Member Function Documentation

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

Definition at line 104 of file MultistateFitnessFunction.cc.

References aggregate_.

MultistateAggregateFunctionCOP protocols::pack_daemon::MultistateFitnessFunction::aggregate_function ( ) const

Definition at line 125 of file MultistateFitnessFunction.cc.

References aggregate_.

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

protected

Definition at line 236 of file MultistateFitnessFunction.cc.

References aggregate_.

void protocols::pack_daemon::MultistateFitnessFunction::clear_history ( )

Definition at line 139 of file MultistateFitnessFunction.cc.

References n_tied_for_worst_, and top_entities_.

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

protectedvirtual

Definition at line 195 of file MultistateFitnessFunction.cc.

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.

Definition at line 166 of file MultistateFitnessFunction.cc.

References daemon_set_, npd_properties_, and state_energies_.

Referenced by evaluate().

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

Definition at line 95 of file MultistateFitnessFunction.cc.

References daemon_set_, npd_properties_, and state_energies_.

DaemonSetCOP protocols::pack_daemon::MultistateFitnessFunction::daemon_set ( ) const

Definition at line 109 of file MultistateFitnessFunction.cc.

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

Definition at line 231 of file MultistateFitnessFunction.cc.

References daemon_set_.

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

virtual

Implements protocols::genetic_algorithm::FitnessFunction.

Definition at line 73 of file MultistateFitnessFunction.cc.

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.

Definition at line 205 of file MultistateFitnessFunction.cc.

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.

Definition at line 200 of file MultistateFitnessFunction.cc.

References daemon_set_.

Referenced by update_entity_history().

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

Definition at line 119 of file MultistateFitnessFunction.cc.

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

Definition at line 226 of file MultistateFitnessFunction.cc.

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.

Definition at line 211 of file MultistateFitnessFunction.cc.

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)

Definition at line 146 of file MultistateFitnessFunction.cc.

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

void protocols::pack_daemon::MultistateFitnessFunction::set_history_size ( core::Size history_size)

Definition at line 130 of file MultistateFitnessFunction.cc.

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

Definition at line 114 of file MultistateFitnessFunction.cc.

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