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

Typedef Documentation

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

Definition at line 24 of file AlignEvaluator.fwd.hh.

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

Definition at line 22 of file AlignEvaluator.fwd.hh.

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

Definition at line 28 of file EvaluatorCreator.fwd.hh.

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

Definition at line 25 of file EvaluatorCreator.fwd.hh.

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

Definition at line 40 of file PoseEvaluator.fwd.hh.

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

Definition at line 38 of file PoseEvaluator.fwd.hh.

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

Definition at line 41 of file PCA.fwd.hh.

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

Definition at line 36 of file PoseEvaluator.fwd.hh.

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

Definition at line 33 of file PoseEvaluator.fwd.hh.

typedef MetaPoseEvaluator protocols::evaluation::PoseEvaluators

Definition at line 29 of file PoseEvaluator.fwd.hh.

typedef MetaPoseEvaluatorCOP protocols::evaluation::PoseEvaluatorsCOP

Definition at line 41 of file PoseEvaluator.fwd.hh.

typedef MetaPoseEvaluatorOP protocols::evaluation::PoseEvaluatorsOP

Definition at line 39 of file PoseEvaluator.fwd.hh.

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

Definition at line 31 of file TimeEvaluator.fwd.hh.

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

Definition at line 28 of file TimeEvaluator.fwd.hh.

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.

Definition at line 57 of file PCA.cc.

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.

Definition at line 60 of file PCA.cc.

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

Definition at line 143 of file util.cc.

References protocols::evaluation::PoseEvaluator::apply(), 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
	)

Definition at line 120 of file util.cc.

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().

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

Definition at line 100 of file util.cc.

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...

Definition at line 87 of file util.cc.

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

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(), protocols::canonical_sampling::SimulatedTempering::register_options(), and protocols::abinitio::IterativeBase::register_options().

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

static

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

static

Referenced by 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

bool protocols::evaluation::options_registered_ =false

static

Definition at line 85 of file util.cc.

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