protocols::multistate_design::MultiStateFitnessFunction Class Reference

#include <MultiStateFitnessFunction.hh>

Inheritance diagram for protocols::multistate_design::MultiStateFitnessFunction:

Collaboration diagram for protocols::multistate_design::MultiStateFitnessFunction:

Public Types
typedef utility::pointer::owning_ptr < MultiStateFitnessFunction >	OP
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 void	add_state (SingleStateOP state)
virtual void	add_state (core::pose::Pose const &pose, bool is_positive)
virtual core::Real	evaluate (protocols::genetic_algorithm::Entity &entity)
virtual core::Real	evaluate (protocols::genetic_algorithm::Entity &entity, core::Size single_state_num)=0
virtual core::Real	evaluate_positive_states (protocols::genetic_algorithm::Entity &entity)
virtual void	set_aggregate_function (MultiStateAggregateFunction::COP aggregate_function)
virtual MultiStateAggregateFunction::COP	aggregate_function () const
virtual void	set_scorefxn (core::scoring::ScoreFunctionCOP sf)
virtual core::scoring::ScoreFunctionCOP	scorefxn () const
virtual SingleStateCOPs	const_states (bool positive_only=false) const
	true const (read only) access to states More...
virtual SingleStateCOPs	positive_states () const
virtual core::Size	num_states () const
virtual core::Size	num_states (bool pos_neg) const
virtual core::Size	num_positive_states () const
virtual core::Size	num_negative_states () const
virtual void	add_metric_value_getter (std::string const &name, protocols::toolbox::pose_metric_calculators::MetricValueGetter const &metric_value_getter)
Public Member Functions inherited from protocols::genetic_algorithm::FitnessFunction
virtual	~FitnessFunction ()

Protected Types
typedef std::map< std::string, protocols::toolbox::pose_metric_calculators::MetricValueGetter >	MetricValueGetterMap

Protected Member Functions
virtual SingleStateOPs &	states ()
MetricValueGetterMap const &	metric_value_getters () const

Private Attributes
SingleStateOPs	states_
MultiStateAggregateFunction::COP	aggregate_function_
core::scoring::ScoreFunctionCOP	scorefxn_
utility::vector1 < core::pose::PoseOP >	best_entity_positive_states_
core::Real	best_fitness_
MetricValueGetterMap	metric_value_getters_

Detailed Description

Definition at line 47 of file MultiStateFitnessFunction.hh.

Member Typedef Documentation

typedef std::map<std::string, protocols::toolbox::pose_metric_calculators::MetricValueGetter> protocols::multistate_design::MultiStateFitnessFunction::MetricValueGetterMap

protected

Definition at line 83 of file MultiStateFitnessFunction.hh.

typedef utility::pointer::owning_ptr< MultiStateFitnessFunction > protocols::multistate_design::MultiStateFitnessFunction::OP

Definition at line 50 of file MultiStateFitnessFunction.hh.

Constructor & Destructor Documentation

protocols::multistate_design::MultiStateFitnessFunction::MultiStateFitnessFunction

(

)

Definition at line 32 of file MultiStateFitnessFunction.cc.

protocols::multistate_design::MultiStateFitnessFunction::~MultiStateFitnessFunction ( )

virtual

Definition at line 39 of file MultiStateFitnessFunction.cc.

Member Function Documentation

void protocols::multistate_design::MultiStateFitnessFunction::add_metric_value_getter ( std::string const &  name, protocols::toolbox::pose_metric_calculators::MetricValueGetter const &  metric_value_getter  )

virtual

Definition at line 153 of file MultiStateFitnessFunction.cc.

References metric_value_getters_.

void protocols::multistate_design::MultiStateFitnessFunction::add_state ( SingleStateOP  state)

virtual

Definition at line 48 of file MultiStateFitnessFunction.cc.

References best_entity_positive_states_, and states_.

Referenced by add_state().

void protocols::multistate_design::MultiStateFitnessFunction::add_state ( core::pose::Pose const &  pose, bool  is_positive  )

virtual

Definition at line 42 of file MultiStateFitnessFunction.cc.

References add_state().

MultiStateAggregateFunction::COP protocols::multistate_design::MultiStateFitnessFunction::aggregate_function ( ) const

virtual

Definition at line 113 of file MultiStateFitnessFunction.cc.

References aggregate_function_.

Referenced by set_aggregate_function().

SingleStateCOPs protocols::multistate_design::MultiStateFitnessFunction::const_states ( bool  positive_only = false) const

virtual

true const (read only) access to states

Definition at line 126 of file MultiStateFitnessFunction.cc.

References core::sequence::end, and states_.

Referenced by protocols::multistate_design::MultiStateAggregateFunction::evaluate(), protocols::multistate_design::PartitionAggregateFunction< T >::evaluate(), and positive_states().

core::Real protocols::multistate_design::MultiStateFitnessFunction::evaluate ( protocols::genetic_algorithm::Entity &  entity)

virtual

Implements protocols::genetic_algorithm::FitnessFunction.

Definition at line 62 of file MultiStateFitnessFunction.cc.

References aggregate_function_, best_entity_positive_states_, best_fitness_, core::sequence::end, protocols::genetic_algorithm::Entity::set_fitness(), protocols::multistate_design::MultiStateEntity< T >::single_state_entity_data(), core::io::serialization::size(), states(), and states_.

Referenced by evaluate_positive_states().

virtual core::Real protocols::multistate_design::MultiStateFitnessFunction::evaluate ( protocols::genetic_algorithm::Entity &  entity, core::Size  single_state_num  )

pure virtual

Implemented in protocols::multistate_design::MultiStatePacker.

core::Real protocols::multistate_design::MultiStateFitnessFunction::evaluate_positive_states ( protocols::genetic_algorithm::Entity &  entity)

virtual

Definition at line 96 of file MultiStateFitnessFunction.cc.

References core::sequence::end, evaluate(), and states_.

std::map< std::string, protocols::toolbox::pose_metric_calculators::MetricValueGetter > const & protocols::multistate_design::MultiStateFitnessFunction::metric_value_getters ( ) const

protected

Definition at line 165 of file MultiStateFitnessFunction.cc.

References metric_value_getters_.

Referenced by protocols::multistate_design::MultiStatePacker::evaluate().

virtual core::Size protocols::multistate_design::MultiStateFitnessFunction::num_negative_states ( ) const

inlinevirtual

Definition at line 75 of file MultiStateFitnessFunction.hh.

References num_states().

virtual core::Size protocols::multistate_design::MultiStateFitnessFunction::num_positive_states ( ) const

inlinevirtual

Definition at line 74 of file MultiStateFitnessFunction.hh.

References num_states().

virtual core::Size protocols::multistate_design::MultiStateFitnessFunction::num_states ( ) const

inlinevirtual

Definition at line 72 of file MultiStateFitnessFunction.hh.

References states_.

Referenced by num_negative_states(), and num_positive_states().

core::Size protocols::multistate_design::MultiStateFitnessFunction::num_states ( bool  pos_neg) const

virtual

Definition at line 141 of file MultiStateFitnessFunction.cc.

References core::sequence::end, and states_.

SingleStateCOPs protocols::multistate_design::MultiStateFitnessFunction::positive_states ( ) const

virtual

Definition at line 138 of file MultiStateFitnessFunction.cc.

References const_states().

core::scoring::ScoreFunctionCOP protocols::multistate_design::MultiStateFitnessFunction::scorefxn ( ) const

virtual

Definition at line 122 of file MultiStateFitnessFunction.cc.

References scorefxn_.

Referenced by protocols::multistate_design::MultiStatePacker::evaluate(), and protocols::multistate_design::MultiStatePacker::single_state_design().

void protocols::multistate_design::MultiStateFitnessFunction::set_aggregate_function ( MultiStateAggregateFunction::COP  aggregate_function)

virtual

Definition at line 107 of file MultiStateFitnessFunction.cc.

References aggregate_function(), and aggregate_function_.

void protocols::multistate_design::MultiStateFitnessFunction::set_scorefxn ( core::scoring::ScoreFunctionCOP  sf)

virtual

Definition at line 119 of file MultiStateFitnessFunction.cc.

References scorefxn_.

SingleStateOPs & protocols::multistate_design::MultiStateFitnessFunction::states ( )

protectedvirtual

Definition at line 162 of file MultiStateFitnessFunction.cc.

References states_.

Referenced by evaluate(), protocols::multistate_design::MultiStatePacker::evaluate(), and protocols::multistate_design::MultiStatePacker::single_state_design().

Member Data Documentation

MultiStateAggregateFunction::COP protocols::multistate_design::MultiStateFitnessFunction::aggregate_function_

private

Definition at line 90 of file MultiStateFitnessFunction.hh.

Referenced by aggregate_function(), evaluate(), and set_aggregate_function().

utility::vector1< core::pose::PoseOP > protocols::multistate_design::MultiStateFitnessFunction::best_entity_positive_states_

private

Definition at line 93 of file MultiStateFitnessFunction.hh.

Referenced by add_state(), and evaluate().

core::Real protocols::multistate_design::MultiStateFitnessFunction::best_fitness_

private

Definition at line 94 of file MultiStateFitnessFunction.hh.

Referenced by evaluate().

MetricValueGetterMap protocols::multistate_design::MultiStateFitnessFunction::metric_value_getters_

private

Definition at line 95 of file MultiStateFitnessFunction.hh.

Referenced by add_metric_value_getter(), and metric_value_getters().

core::scoring::ScoreFunctionCOP protocols::multistate_design::MultiStateFitnessFunction::scorefxn_

private

Definition at line 91 of file MultiStateFitnessFunction.hh.

Referenced by scorefxn(), and set_scorefxn().

SingleStateOPs protocols::multistate_design::MultiStateFitnessFunction::states_

private

Definition at line 89 of file MultiStateFitnessFunction.hh.

Referenced by add_state(), const_states(), evaluate(), evaluate_positive_states(), num_states(), and states().

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

• src/protocols/multistate_design/MultiStateFitnessFunction.hh
• src/protocols/multistate_design/MultiStateFitnessFunction.cc