protocols::evolution Namespace Reference

Namespaces
	AlignmentCleanerTools

Classes
class	AASynthesisFitnessCost
	test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...
class	AASynthesisFitnessCostFilterCreator
class	AlignmentAAFinder
	test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...
class	AlignmentAAFinderFilterCreator
class	AlignmentGapInserter
	test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts. More...
class	AlignmentGapInserterFilterCreator
class	EvolutionaryDynamicsMover
class	EvolutionaryDynamicsMoverCreator
class	NucleotideMutation
	designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...
class	NucleotideMutationCreator

Typedefs
typedef utility::pointer::shared_ptr < PoseComment >	PoseCommentOP
typedef utility::pointer::shared_ptr < PoseComment const >	PoseCommentCOP
using	bools = utility::vector1< bool >
typedef utility::pointer::shared_ptr < EvolutionaryDynamicsMover >	EvolutionaryDynamicsMoverOP
typedef utility::pointer::shared_ptr < EvolutionaryDynamicsMover const >	EvolutionaryDynamicsMoverCOP
typedef std::function< bool(core::Size, core::Size, const core::pose::Pose &, core::scoring::ScoreFunctionOP)>	EvolutionaryDynamicsMoverTrigger
	Trigger API definition. More...
typedef utility::pointer::shared_ptr < NucleotideMutation >	NucleotideMutationOP
typedef utility::pointer::shared_ptr < NucleotideMutation const >	NucleotideMutationCOP

Functions
static basic::Tracer	TR ("protocols.evolution.AASynthesisFitnessCost")
static basic::Tracer	TR ("protocols.evolution.AlignmentAAFinder")
static basic::Tracer	TR ("protocols.evolution.AlignmentGapInserter")
static basic::Tracer	TR ("protocols.evolution.NucleotideMutation")

Typedef Documentation

typedef utility::vector1< bool > protocols::evolution::bools

typedef utility::pointer::shared_ptr< EvolutionaryDynamicsMover const > protocols::evolution::EvolutionaryDynamicsMoverCOP

typedef utility::pointer::shared_ptr< EvolutionaryDynamicsMover > protocols::evolution::EvolutionaryDynamicsMoverOP

typedef std::function<bool(core::Size, core::Size, const core::pose::Pose&, core::scoring::ScoreFunctionOP)> protocols::evolution::EvolutionaryDynamicsMoverTrigger

Trigger API definition.

typedef utility::pointer::shared_ptr< NucleotideMutation const > protocols::evolution::NucleotideMutationCOP

typedef utility::pointer::shared_ptr< NucleotideMutation > protocols::evolution::NucleotideMutationOP

typedef utility::pointer::shared_ptr< PoseComment const > protocols::evolution::PoseCommentCOP

typedef utility::pointer::shared_ptr< PoseComment > protocols::evolution::PoseCommentOP

Function Documentation

static basic::Tracer protocols::evolution::TR ( "protocols.evolution.AASynthesisFitnessCost"  )

static

Referenced by protocols::evolution::NucleotideMutation::add_nt_seq_to_pose(), protocols::evolution::AlignmentAAFinder::apply(), protocols::evolution::AlignmentGapInserter::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::evolution::AlignmentGapInserter::parse_my_tag(), and protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag().

static basic::Tracer protocols::evolution::TR ( "protocols.evolution.AlignmentAAFinder"  )

static

static basic::Tracer protocols::evolution::TR ( "protocols.evolution.AlignmentGapInserter"  )

static

static basic::Tracer protocols::evolution::TR ( "protocols.evolution.NucleotideMutation"  )

static