protocols::multistate_design Namespace Reference

Classes
class	MetricCalculatorFitnessFunction
class	MultiStateAggregateFunction
class	MultiStateEntity
class	MultiStateFitnessFunction
class	PosType
class	PosTypeCreator
class	MultiStatePacker
class	PackingState
class	PartitionAggregateFunction
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::shared_ptr< MultiStateAggregateFunction >	MultiStateAggregateFunctionOP
typedef utility::pointer::shared_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 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

MetricCalculatorFitnessFunctionCOP

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

MetricCalculatorFitnessFunctionOP

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

MultiStateAggregateFunctionCOP

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

MultiStateAggregateFunctionOP

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

MultiStatePackerCOP

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

MultiStatePackerOP

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

PackingStateCOP

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

PackingStateOP

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

PosTypeCOP

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

PosTypeOP

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

SingleStateCOP

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

SingleStateCOPs

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

SingleStateFitnessFunctionCOP

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

SingleStateFitnessFunctionOP

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

SingleStateOP

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

SingleStateOPs

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

Function Documentation

entity_elements_from_1letterstring()

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.

limit_rotamer_set()

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_unk, core::pack::rotamer_set::RotamerSets::nrotamers(), protocols::multistate_design::SingleState::pose(), core::pack::rotamer_set::RotamerSets::res_for_rotamer(), core::pose::Pose::residue_type(), core::pack::rotamer_set::RotamerSets::rotamer(), and protocols::multistate_design::PackingState::rotamersets().

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

list_amino_acid_options()

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

References protocols::cluster::calibur::aa, core::pack::task::ResidueLevelTask::allowed_residue_types(), and protocols::hybridization::t.

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

restrict_to_canonical_aas()

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

References core::chemical::ResidueTypeBase::name3(), core::pack::rotamer_set::RotamerSets::nrotamers(), core::chemical::num_canonical_aas, protocols::multistate_design::SingleState::pose(), core::pack::rotamer_set::RotamerSets::res_for_rotamer(), core::pose::Pose::residue(), rot(), core::pack::rotamer_set::RotamerSets::rotamer(), protocols::multistate_design::PackingState::rotamersets(), and core::conformation::Residue::type().

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

TR()

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

static

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

Variable Documentation

pt_registrator

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