protocols::multistate_design Namespace Reference

Classes
class	MetricCalculatorFitnessFunction
class	MultiStateAggregateFunction
class	MultiStateEntity
class	MultiStateFitnessFunction
class	MultiStatePacker
class	PackingState
class	PartitionAggregateFunction
class	PosType
class	PosTypeCreator
class	SingleState
class	SingleStateEntityData
class	SingleStateFitnessFunction

Typedefs
typedef utility::pointer::shared_ptr < MetricCalculatorFitnessFunction >	MetricCalculatorFitnessFunctionOP
typedef utility::pointer::shared_ptr < MetricCalculatorFitnessFunction const >	MetricCalculatorFitnessFunctionCOP
typedef utility::pointer::owning_ptr < MultiStateAggregateFunction >	MultiStateAggregateFunctionOP
typedef utility::pointer::owning_ptr < MultiStateAggregateFunction const >	MultiStateAggregateFunctionCOP
typedef utility::pointer::shared_ptr < PosType >	PosTypeOP
typedef utility::pointer::shared_ptr < PosType const >	PosTypeCOP
typedef utility::pointer::shared_ptr < MultiStatePacker >	MultiStatePackerOP
typedef utility::pointer::shared_ptr < MultiStatePacker const >	MultiStatePackerCOP
typedef utility::pointer::shared_ptr < PackingState >	PackingStateOP
typedef utility::pointer::shared_ptr < PackingState const >	PackingStateCOP
typedef utility::pointer::shared_ptr < SingleState >	SingleStateOP
typedef utility::pointer::shared_ptr < SingleState const >	SingleStateCOP
typedef utility::vector1 < SingleStateOP >	SingleStateOPs
typedef utility::vector1 < SingleStateCOP >	SingleStateCOPs
typedef utility::pointer::shared_ptr < SingleStateFitnessFunction >	SingleStateFitnessFunctionOP
typedef utility::pointer::shared_ptr < SingleStateFitnessFunction const >	SingleStateFitnessFunctionCOP

Functions
void	limit_rotamer_set (utility::vector0< int > &rot_to_pack, PackingState const &state, genetic_algorithm::EntityElements const &seq)
void	restrict_to_canonical_aas (PackingState const &state, utility::vector0< int > &rot_to_pack)
static thread_local basic::Tracer	TR ("protocols.multistate_design.PartitionAggregateFunction")
protocols::genetic_algorithm::EntityElements	list_amino_acid_options (core::Size i, core::pack::task::ResidueLevelTask const &rtask)
protocols::genetic_algorithm::EntityElements	entity_elements_from_1letterstring (std::string const &input)
	Creates a set of PosType entity-elements from a string of 1-letter AA codes. More...

Variables
genetic_algorithm::EntityElementRegistrator < PosTypeCreator >	pt_registrator

Typedef Documentation

typedef utility::pointer::shared_ptr< MetricCalculatorFitnessFunction const > protocols::multistate_design::MetricCalculatorFitnessFunctionCOP

typedef utility::pointer::shared_ptr< MetricCalculatorFitnessFunction > protocols::multistate_design::MetricCalculatorFitnessFunctionOP

typedef utility::pointer::owning_ptr< MultiStateAggregateFunction const > protocols::multistate_design::MultiStateAggregateFunctionCOP

typedef utility::pointer::owning_ptr< MultiStateAggregateFunction > protocols::multistate_design::MultiStateAggregateFunctionOP

typedef utility::pointer::shared_ptr< MultiStatePacker const > protocols::multistate_design::MultiStatePackerCOP

typedef utility::pointer::shared_ptr< MultiStatePacker > protocols::multistate_design::MultiStatePackerOP

typedef utility::pointer::shared_ptr< PackingState const > protocols::multistate_design::PackingStateCOP

typedef utility::pointer::shared_ptr< PackingState > protocols::multistate_design::PackingStateOP

typedef utility::pointer::shared_ptr< PosType const > protocols::multistate_design::PosTypeCOP

typedef utility::pointer::shared_ptr< PosType > protocols::multistate_design::PosTypeOP

typedef utility::pointer::shared_ptr< SingleState const > protocols::multistate_design::SingleStateCOP

typedef utility::vector1< SingleStateCOP > protocols::multistate_design::SingleStateCOPs

typedef utility::pointer::shared_ptr< SingleStateFitnessFunction const > protocols::multistate_design::SingleStateFitnessFunctionCOP

typedef utility::pointer::shared_ptr< SingleStateFitnessFunction > protocols::multistate_design::SingleStateFitnessFunctionOP

typedef utility::pointer::shared_ptr< SingleState > protocols::multistate_design::SingleStateOP

typedef utility::vector1< SingleStateOP > protocols::multistate_design::SingleStateOPs

Function Documentation

protocols::genetic_algorithm::EntityElements protocols::multistate_design::entity_elements_from_1letterstring

(

std::string const &

input

)

Creates a set of PosType entity-elements from a string of 1-letter AA codes.

References protocols::genetic_algorithm::EntityElementFactory::element_from_string(), and utility::SingletonBase< EntityElementFactory >::get_instance().

void protocols::multistate_design::limit_rotamer_set	(	utility::vector0< int > &	rot_to_pack,
		PackingState const &	state,
		genetic_algorithm::EntityElements const &	seq
	)

References core::chemical::ResidueType::aa(), core::chemical::aa_unk, end, protocols::multistate_design::SingleState::pose(), core::pose::Pose::residue_type(), protocols::multistate_design::PackingState::rotamersets(), and utility_exit_with_message.

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

protocols::genetic_algorithm::EntityElements protocols::multistate_design::list_amino_acid_options	(	core::Size	i,
		core::pack::task::ResidueLevelTask const &	rtask
	)

References core::pack::task::ResidueLevelTask::allowed_residue_types(), and end.

Referenced by protocols::pack_daemon::initialize_ga_randomizer_from_entity_task().

void protocols::multistate_design::restrict_to_canonical_aas	(	PackingState const &	state,
		utility::vector0< int > &	rot_to_pack
	)

References core::conformation::Residue::name3(), core::chemical::num_canonical_aas, protocols::multistate_design::SingleState::pose(), core::pose::Pose::residue(), rot(), and protocols::multistate_design::PackingState::rotamersets().

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

static thread_local basic::Tracer protocols::multistate_design::TR ( "protocols.multistate_design.PartitionAggregateFunction"  )

static

Referenced by protocols::multistate_design::PartitionAggregateFunction< T >::evaluate(), and protocols::multistate_design::MultiStatePacker::single_state_design().

Variable Documentation

genetic_algorithm::EntityElementRegistrator< PosTypeCreator > protocols::multistate_design::pt_registrator