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	MetaPoseEvaluator
class	PCA
class	PoseEvaluator
class	SingleValuePoseEvaluator
class	TimeEvaluator

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

Functions
template<class T >
void	dump_matrix (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 (Size nr, T const &a, basic::Tracer &tr)
	A function (not a macro) that will print a square matrix to tr.Debug. More...
void	register_options ()
	register cmd-line options relevant for evaluators... More...
void	invert_include_residues (Size nres, core::scoring::ResidueSelectionVector const &include_list, core::scoring::ResidueSelectionVector &exclude_list)
void	find_existing_residues (core::pose::PoseCOP pose, std::string tag, core::scoring::ResidueSelection &selection)
void	evaluate_pose (core::pose::Pose &pose, PoseEvaluator &eval, std::ostream &os)

Variables
static basic::Tracer	tr ("protocols.evaluator.EvaluatorFactory")
static basic::Tracer	tr ("protocols.evaluation.PCA", basic::t_info)
static bool	options_registered_ =false

Typedef Documentation

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

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

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

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

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

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

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

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

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

typedef MetaPoseEvaluator protocols::evaluation::PoseEvaluators

typedef MetaPoseEvaluatorCOP protocols::evaluation::PoseEvaluatorsCOP

typedef MetaPoseEvaluatorOP protocols::evaluation::PoseEvaluatorsOP

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

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

Function Documentation

template<class T >

void protocols::evaluation::dump_matrix	(	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().

template<class T >

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

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

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

References protocols::evaluation::PoseEvaluator::apply(), core::io::silent::SilentStruct::fill_struct(), core::io::silent::SilentStructFactory::get_instance(), and core::io::silent::SilentStructFactory::get_silent_struct_out().

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

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

References j, length, and 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().

void protocols::evaluation::invert_include_residues	(	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().

void protocols::evaluation::register_options

(

)

register cmd-line options relevant for evaluators...

References evaluation::chemical_shifts, evaluation::constraints, evaluation::gdtmm, in::file::native, OPT, options_registered_, evaluation::pool, evaluation::rdc, and evaluation::rmsd.

Referenced by OPT_1GRP_KEY(), protocols::abinitio::IterativeFullatom::register_options(), protocols::noesy_assign::NoesyModule::register_options(), protocols::jd2::register_options(), protocols::abinitio::Templates::register_options(), protocols::abinitio::IterativeAbrelax::register_options(), protocols::abinitio::AbrelaxApplication::register_options(), and protocols::abinitio::IterativeBase::register_options().

Variable Documentation

bool protocols::evaluation::options_registered_ =false

static

Referenced by protocols::jd2::archive::NormalizedEvaluatedArchive::NormalizedEvaluatedArchive(), OPT_1GRP_KEY(), protocols::noesy_assign::PeakFileFormat::PeakFileFormat(), protocols::sparta::Sparta::register_options(), protocols::canonical_sampling::TrajectoryRecorder::register_options(), protocols::canonical_sampling::SilentTrajectoryRecorder::register_options(), protocols::abinitio::IterativeFullatom::register_options(), protocols::noesy_assign::NoesyModule::register_options(), protocols::jd2::archive::EvaluatedArchive::register_options(), protocols::jd2::archive::NormalizedEvaluatedArchive::register_options(), protocols::abinitio::IterativeAbrelax::register_options(), register_options(), protocols::canonical_sampling::TemperatureController::register_options(), protocols::toolbox::DecoySetEvaluation::register_options(), protocols::canonical_sampling::SimulatedTempering::register_options(), protocols::jd2::archive::ArchiveBase::register_options(), protocols::canonical_sampling::MpiHamiltonianExchange::register_options(), protocols::noesy_assign::PeakFileFormat::register_options(), protocols::jd2::archive::ArchiveManager::register_options(), protocols::abinitio::IterativeBase::register_options(), and protocols::canonical_sampling::SilentTrajectoryRecorder::SilentTrajectoryRecorder().

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

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().