protocols::evaluation Namespace Reference

Classes
class	AlignEvaluator
class	EvaluatorCreator
	The Creator class is responsible for creating a particular mover class. More...
class	EvaluatorFactory
	Create Evaluator Reporters. More...
class	EvaluatorRegistrator
	This templated class will register an instance of an EvaluatorCreator (class T) with the EvaluatorFactory. It will ensure that no EvaluatorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	PCA
class	SingleValuePoseEvaluator
class	PoseEvaluator
class	MetaPoseEvaluator
class	SingleValuePoseEvaluator_Size
class	SingleValuePoseEvaluator_SSize
class	TimeEvaluator

Typedefs
typedef utility::pointer::shared_ptr< AlignEvaluator >	AlignEvaluatorOP
typedef utility::pointer::shared_ptr< AlignEvaluator const >	AlignEvaluatorCOP
typedef utility::pointer::shared_ptr< EvaluatorCreator >	EvaluatorCreatorOP
typedef utility::pointer::shared_ptr< EvaluatorCreator const >	EvaluatorCreatorCOP
typedef utility::pointer::shared_ptr< PCA >	PCA_OP
typedef MetaPoseEvaluator	PoseEvaluators
typedef utility::pointer::shared_ptr< PoseEvaluator >	PoseEvaluatorOP
typedef utility::pointer::shared_ptr< PoseEvaluator const >	PoseEvaluatorCOP
typedef utility::pointer::shared_ptr< MetaPoseEvaluator >	MetaPoseEvaluatorOP
typedef MetaPoseEvaluatorOP	PoseEvaluatorsOP
typedef utility::pointer::shared_ptr< MetaPoseEvaluator const >	MetaPoseEvaluatorCOP
typedef MetaPoseEvaluatorCOP	PoseEvaluatorsCOP
typedef utility::pointer::shared_ptr< TimeEvaluator >	TimeEvaluatorOP
typedef utility::pointer::shared_ptr< TimeEvaluator const >	TimeEvaluatorCOP

Functions
static basic::Tracer	tr ("protocols.evaluator.EvaluatorFactory")
static basic::Tracer	tr ("protocols.evaluation.PCA", basic::t_info)
template<class T >
void	dump_matrix (core::Size, T const &, basic::Tracer &)
	A function (not a macro) that will not print a square matrix to tr.Debug. More...
template<class T >
void	dump_matrix_no (core::Size nr, T const &a, basic::Tracer &tracer)
	A function (not a macro) that will print a square matrix to tr.Debug. More...
template<class T >
void	ROTATE (T &a, int i, int j, int k, int l, core::Real s, core::Real tau)
void	register_options ()
	register cmd-line options relevant for evaluators... More...
void	invert_include_residues (core::Size nres, core::scoring::ResidueSelectionVector const &include_list, core::scoring::ResidueSelectionVector &exclude_list)
void	find_existing_residues (core::pose::PoseCOP pose, std::string const &tag, core::scoring::ResidueSelection &selection)
void	evaluate_pose (core::pose::Pose &pose, PoseEvaluator &eval, std::ostream &os)

Variables
constexpr int	DIM6 = 6
constexpr int	XX = 0
constexpr int	YY = 1
constexpr int	ZZ = 2
static bool	options_registered_ =false

Typedef Documentation

AlignEvaluatorCOP

typedef utility::pointer::shared_ptr< AlignEvaluator const > protocols::evaluation::AlignEvaluatorCOP

AlignEvaluatorOP

typedef utility::pointer::shared_ptr< AlignEvaluator > protocols::evaluation::AlignEvaluatorOP

EvaluatorCreatorCOP

typedef utility::pointer::shared_ptr< EvaluatorCreator const > protocols::evaluation::EvaluatorCreatorCOP

EvaluatorCreatorOP

typedef utility::pointer::shared_ptr< EvaluatorCreator > protocols::evaluation::EvaluatorCreatorOP

MetaPoseEvaluatorCOP

typedef utility::pointer::shared_ptr< MetaPoseEvaluator const > protocols::evaluation::MetaPoseEvaluatorCOP

MetaPoseEvaluatorOP

typedef utility::pointer::shared_ptr< MetaPoseEvaluator > protocols::evaluation::MetaPoseEvaluatorOP

PCA_OP

typedef utility::pointer::shared_ptr< PCA > protocols::evaluation::PCA_OP

PoseEvaluatorCOP

typedef utility::pointer::shared_ptr< PoseEvaluator const > protocols::evaluation::PoseEvaluatorCOP

PoseEvaluatorOP

typedef utility::pointer::shared_ptr< PoseEvaluator > protocols::evaluation::PoseEvaluatorOP

PoseEvaluators

typedef MetaPoseEvaluator protocols::evaluation::PoseEvaluators

PoseEvaluatorsCOP

typedef MetaPoseEvaluatorCOP protocols::evaluation::PoseEvaluatorsCOP

PoseEvaluatorsOP

typedef MetaPoseEvaluatorOP protocols::evaluation::PoseEvaluatorsOP

TimeEvaluatorCOP

typedef utility::pointer::shared_ptr< TimeEvaluator const > protocols::evaluation::TimeEvaluatorCOP

TimeEvaluatorOP

typedef utility::pointer::shared_ptr< TimeEvaluator > protocols::evaluation::TimeEvaluatorOP

Function Documentation

dump_matrix()

template<class T >

void protocols::evaluation::dump_matrix	(	core::Size	,
		T const &	,
		basic::Tracer &
	)

A function (not a macro) that will not print a square matrix to tr.Debug.

Referenced by protocols::evaluation::PCA::calc_fit_R(), and protocols::evaluation::PCA::eval().

dump_matrix_no()

template<class T >

void protocols::evaluation::dump_matrix_no	(	core::Size	nr,
		T const &	a,
		basic::Tracer &	tracer
	)

A function (not a macro) that will print a square matrix to tr.Debug.

References core::pose::motif::a(), and protocols::frag_picker::tracer().

evaluate_pose()

void protocols::evaluation::evaluate_pose	(	core::pose::Pose &	pose,
		PoseEvaluator &	eval,
		std::ostream &	os
	)

References core::energy_methods::eval().

Referenced by protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops().

find_existing_residues()

void protocols::evaluation::find_existing_residues	(	core::pose::PoseCOP	pose,
		std::string const &	tag,
		core::scoring::ResidueSelection &	selection
	)

References tr().

Referenced by protocols::simple_filters::RmsdTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::ChiWellRmsdEvaluator::ChiWellRmsdEvaluator(), protocols::simple_filters::SelectGdtEvaluator::SelectGdtEvaluator(), protocols::simple_filters::SelectMaxsubEvaluator::SelectMaxsubEvaluator(), protocols::simple_filters::SelectRDC_Evaluator::SelectRDC_Evaluator(), and protocols::simple_filters::SelectRmsdEvaluator::SelectRmsdEvaluator().

invert_include_residues()

void protocols::evaluation::invert_include_residues	(	core::Size	nres,
		core::scoring::ResidueSelectionVector const &	include_list,
		core::scoring::ResidueSelectionVector &	exclude_list
	)

Referenced by protocols::simple_filters::TruncatedScoreEvaluator::apply(), and protocols::simple_filters::TruncatedScoreEvaluator::TruncatedScoreEvaluator().

register_options()

void protocols::evaluation::register_options

(

)

register cmd-line options relevant for evaluators...

References options_registered_, and core::scoring::rdc.

Referenced by protocols::abinitio::AbrelaxApplication::register_options(), protocols::abinitio::IterativeAbrelax::register_options(), protocols::abinitio::IterativeBase::register_options(), protocols::abinitio::IterativeFullatom::register_options(), protocols::abinitio::Templates::register_options(), protocols::canonical_sampling::SimulatedTempering::register_options(), protocols::jd2::register_options(), and protocols::loops::loop_closure::ccd::CCDLoopClosureMover::register_options().

ROTATE()

template<class T >

void protocols::evaluation::ROTATE	(	T &	a,
		int	i,
		int	j,
		int	k,
		int	l,
		core::Real	s,
		core::Real	tau
	)

References core::pose::motif::a().

Referenced by protocols::evaluation::PCA::jacobi().

tr() [1/2]

static basic::Tracer protocols::evaluation::tr ( "protocols.evaluation.PCA"  , basic::t_info    )

static

tr() [2/2]

static basic::Tracer protocols::evaluation::tr ( "protocols.evaluator.EvaluatorFactory"  )

static

Referenced by protocols::evaluation::EvaluatorFactory::add_evaluators(), protocols::evaluation::PCA::calc_fit_R(), protocols::evaluation::PCA::eval(), find_existing_residues(), protocols::evaluation::AlignEvaluator::get_alignment(), and protocols::evaluation::PCA::read_structure().

Variable Documentation

DIM6

constexpr int protocols::evaluation::DIM6 = 6

constexpr

Referenced by protocols::evaluation::PCA::calc_fit_R(), and protocols::evaluation::PCA::jacobi().

options_registered_

bool protocols::evaluation::options_registered_ =false

static

Referenced by protocols::jd2::archive::NormalizedEvaluatedArchive::NormalizedEvaluatedArchive(), protocols::abinitio::IterativeAbrelax::register_options(), protocols::abinitio::IterativeBase::register_options(), protocols::abinitio::IterativeFullatom::register_options(), protocols::canonical_sampling::CanonicalSamplingMover::register_options(), protocols::canonical_sampling::SilentTrajectoryRecorder::register_options(), protocols::canonical_sampling::SimulatedTempering::register_options(), protocols::canonical_sampling::TemperingBase::register_options(), register_options(), protocols::jd2::archive::ArchiveBase::register_options(), protocols::jd2::archive::ArchiveManager::register_options(), protocols::jd2::archive::EvaluatedArchive::register_options(), protocols::jd2::archive::NormalizedEvaluatedArchive::register_options(), protocols::sparta::Sparta::register_options(), and protocols::canonical_sampling::SilentTrajectoryRecorder::SilentTrajectoryRecorder().

XX

constexpr int protocols::evaluation::XX = 0

constexpr

Referenced by protocols::evaluation::PCA::oprod().

YY

constexpr int protocols::evaluation::YY = 1

constexpr

Referenced by protocols::evaluation::PCA::oprod().

ZZ

constexpr int protocols::evaluation::ZZ = 2

constexpr

Referenced by protocols::evaluation::PCA::oprod().