protocols::toolbox::pose_metric_calculators::FragQualCalculator Class Reference

#include <FragQualCalculator.hh>

Public Types
typedef core::pose::metrics::StructureDependentCalculator	Super
typedef std::string	String
typedef core::Size	Size
typedef core::Real	Real
typedef core::pose::Pose	Pose
typedef core::pose::metrics::PoseMetricCalculatorOP	PoseMetricCalculatorOP
typedef basic::MetricValueBase	MetricValueBase
typedef core::fragment::FragSet	FragSet
typedef core::fragment::FragSetOP	FragSetOP
typedef utility::tag::TagCOP	TagCOP
typedef protocols::filters::Filters_map	Filters_map
typedef basic::datacache::DataMap	DataMap
typedef protocols::moves::Movers_map	Movers_map

Public Member Functions
	FragQualCalculator ()
	default constructor More...
	FragQualCalculator (FragSetOP const &frag, Real const rmsd=1.0, Real const ratio=30.0)
	default constructor More...
	FragQualCalculator (FragQualCalculator const &rval)
	copy constructor More...
virtual	~FragQualCalculator ()
	destructor More...
PoseMetricCalculatorOP	clone () const
	make clone More...
void	set_fragset (FragSetOP const &frags)
	set fragments More...
void	rmsd_cutoff (Real const &val)
	rmsd cutoff of good fragments More...
void	ratio_cutoff (Real const &val)
void	set_region (Size const val1, Size const val2)
void	begin (Size const begin)
void	end (Size const end)
void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &, Movers_map const &, Pose const &pose)
	parse xml More...
Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
	StructureDependentCalculator ()
void	notify_structure_change ()
void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose)
std::string	get (std::string const &key, Pose const &this_pose)

Protected Member Functions
virtual void	lookup (String const &key, MetricValueBase *valptr) const
virtual std::string	print (String const &key) const
virtual void	recompute (Pose const &this_pose)
	recomute ncontacts More...

Private Attributes
Real	rmsd_cutoff_goodfrag_
Real	ratio_cutoff_goodfrag_
Real	total_goodfrags_
Real	coverage_
utility::vector1< Size >	goodfrags_
FragSetOP	frag_
Size	begin_
Size	end_
bool	verbose_

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::toolbox::pose_metric_calculators::FragQualCalculator::DataMap

typedef protocols::filters::Filters_map protocols::toolbox::pose_metric_calculators::FragQualCalculator::Filters_map

typedef core::fragment::FragSet protocols::toolbox::pose_metric_calculators::FragQualCalculator::FragSet

typedef core::fragment::FragSetOP protocols::toolbox::pose_metric_calculators::FragQualCalculator::FragSetOP

typedef basic::MetricValueBase protocols::toolbox::pose_metric_calculators::FragQualCalculator::MetricValueBase

typedef protocols::moves::Movers_map protocols::toolbox::pose_metric_calculators::FragQualCalculator::Movers_map

typedef core::pose::Pose protocols::toolbox::pose_metric_calculators::FragQualCalculator::Pose

typedef core::pose::metrics::PoseMetricCalculatorOP protocols::toolbox::pose_metric_calculators::FragQualCalculator::PoseMetricCalculatorOP

typedef core::Real protocols::toolbox::pose_metric_calculators::FragQualCalculator::Real

typedef core::Size protocols::toolbox::pose_metric_calculators::FragQualCalculator::Size

typedef std::string protocols::toolbox::pose_metric_calculators::FragQualCalculator::String

typedef core::pose::metrics::StructureDependentCalculator protocols::toolbox::pose_metric_calculators::FragQualCalculator::Super

typedef utility::tag::TagCOP protocols::toolbox::pose_metric_calculators::FragQualCalculator::TagCOP

Constructor & Destructor Documentation

protocols::toolbox::pose_metric_calculators::FragQualCalculator::FragQualCalculator

(

)

default constructor

References goodfrags_.

Referenced by clone().

protocols::toolbox::pose_metric_calculators::FragQualCalculator::FragQualCalculator	(	FragSetOP const &	frag,
		Real const	rmsd = 1.0,
		Real const	ratio = 30.0
	)

default constructor

value constructor

References goodfrags_.

protocols::toolbox::pose_metric_calculators::FragQualCalculator::FragQualCalculator

(

FragQualCalculator const &

rval

)

copy constructor

protocols::toolbox::pose_metric_calculators::FragQualCalculator::~FragQualCalculator ( )

virtual

destructor

Member Function Documentation

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::begin ( Size const  begin )

inline

References begin(), and begin_.

Referenced by begin().

PoseMetricCalculatorOP protocols::toolbox::pose_metric_calculators::FragQualCalculator::clone ( ) const

inline

make clone

References FragQualCalculator().

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::end ( Size const  end )

inline

References end(), and end_.

Referenced by end().

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::lookup ( String const &  key, MetricValueBase *  valptr  ) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References basic::check_cast(), coverage_, total_goodfrags_, protocols::toolbox::pose_metric_calculators::TR, and utility_exit.

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	,
		Movers_map const &	,
		Pose const &	pose
	)

parse xml

References begin_, end_, frag_, basic::datacache::DataMap::get(), basic::datacache::DataMap::has(), ratio_cutoff_goodfrag_, rmsd_cutoff_goodfrag_, runtime_assert, core::pose::Pose::total_residue(), and verbose_.

std::string protocols::toolbox::pose_metric_calculators::FragQualCalculator::print ( String const &  key ) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References coverage_, basic::Error(), utility::to_string(), and total_goodfrags_.

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::ratio_cutoff

(

Real const &

val

)

References ratio_cutoff_goodfrag_.

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute ( Pose const &  this_pose )

protectedvirtual

recomute ncontacts

Implements core::pose::metrics::StructureDependentCalculator.

References core::fragment::FragSet::begin(), begin_, core::scoring::CA_rmsd(), CA_rmsd(), core::chemical::CENTROID, coverage_, core::fragment::FragSet::end(), end_, F, frag_, frame(), goodfrags_, ratio_cutoff_goodfrag_, rmsd, rmsd_cutoff_goodfrag_, runtime_assert, protocols::loops::start, core::util::switch_to_residue_type_set(), total_goodfrags_, core::pose::Pose::total_residue(), protocols::toolbox::pose_metric_calculators::TR, and verbose_.

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::rmsd_cutoff

(

Real const &

val

)

rmsd cutoff of good fragments

References rmsd_cutoff_goodfrag_.

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::set_fragset

(

FragSetOP const &

frags

)

set fragments

References frag_.

void protocols::toolbox::pose_metric_calculators::FragQualCalculator::set_region	(	Size const	val1,
		Size const	val2
	)

References begin_, and end_.

Member Data Documentation

Size protocols::toolbox::pose_metric_calculators::FragQualCalculator::begin_

private

Referenced by begin(), parse_my_tag(), recompute(), and set_region().

Real protocols::toolbox::pose_metric_calculators::FragQualCalculator::coverage_

private

Referenced by lookup(), print(), and recompute().

Size protocols::toolbox::pose_metric_calculators::FragQualCalculator::end_

private

Referenced by end(), parse_my_tag(), recompute(), and set_region().

FragSetOP protocols::toolbox::pose_metric_calculators::FragQualCalculator::frag_

private

Referenced by parse_my_tag(), recompute(), and set_fragset().

utility::vector1< Size > protocols::toolbox::pose_metric_calculators::FragQualCalculator::goodfrags_

private

Referenced by FragQualCalculator(), and recompute().

Real protocols::toolbox::pose_metric_calculators::FragQualCalculator::ratio_cutoff_goodfrag_

private

Referenced by parse_my_tag(), ratio_cutoff(), and recompute().

Real protocols::toolbox::pose_metric_calculators::FragQualCalculator::rmsd_cutoff_goodfrag_

private

Referenced by parse_my_tag(), recompute(), and rmsd_cutoff().

Real protocols::toolbox::pose_metric_calculators::FragQualCalculator::total_goodfrags_

private

Referenced by lookup(), print(), and recompute().

bool protocols::toolbox::pose_metric_calculators::FragQualCalculator::verbose_

private

Referenced by parse_my_tag(), and recompute().

---

The documentation for this class was generated from the following files:

• src/protocols/toolbox/pose_metric_calculators/FragQualCalculator.hh
• src/protocols/toolbox/pose_metric_calculators/FragQualCalculator.cc