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

bools

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

EvolutionaryDynamicsMoverCOP

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

EvolutionaryDynamicsMoverOP

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

EvolutionaryDynamicsMoverTrigger

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

Trigger API definition.

NucleotideMutationCOP

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

NucleotideMutationOP

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

PoseCommentCOP

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

PoseCommentOP

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

Function Documentation

TR() [1/4]

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::AASynthesisFitnessCost::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::evolution::AASynthesisFitnessCost::compute(), protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag(), and protocols::evolution::AlignmentGapInserter::parse_my_tag().

TR() [2/4]

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

static

TR() [3/4]

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

static

TR() [4/4]

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

static