Rosetta: protocols::pose_metric_calculators::FragQualCalculator Class Reference

Rosetta

#include <FragQualCalculator.hh>

Inheritance diagram for protocols::pose_metric_calculators::FragQualCalculator:

Inheritance graph

[legend]

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 basic::datacache::DataMap	DataMap

Public Member Functions
	FragQualCalculator ()
	default constructor More...

	FragQualCalculator (FragSetOP frag, Real const rmsd=1.0, Real const ratio=30.0)
	default constructor More...

	FragQualCalculator (FragQualCalculator const &rval)
	copy constructor More...

	~FragQualCalculator () override
	destructor More...

PoseMetricCalculatorOP	clone () const override
	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 (core::Size const val1, core::Size const val2)

void	begin (core::Size const begin)

void	end (core::Size const end)

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	parse xml More...

Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
	StructureDependentCalculator ()

void	notify_structure_change () override

void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override

std::string	get (std::string const &key, Pose const &this_pose) override

Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()

virtual void	notify_energy_change ()

Protected Member Functions
void	lookup (String const &key, MetricValueBase *valptr) const override

std::string	print (String const &key) const override

void	recompute (Pose const &this_pose) override
	recomute ncontacts More...

Private Attributes
Real	rmsd_cutoff_goodfrag_

Real	ratio_cutoff_goodfrag_

Real	total_goodfrags_

Real	coverage_

utility::vector1< core::Size >	goodfrags_

FragSetOP	frag_

core::pose::ResidueIndexDescriptionCOP	begin_

core::pose::ResidueIndexDescriptionCOP	end_

bool	verbose_

Member Typedef Documentation

◆ DataMap

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

◆ FragSet

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

◆ FragSetOP

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

◆ MetricValueBase

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

◆ Pose

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

◆ PoseMetricCalculatorOP

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

◆ Real

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

◆ Size

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

◆ String

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

◆ Super

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

◆ TagCOP

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

Constructor & Destructor Documentation

◆ FragQualCalculator() [1/3]

protocols::pose_metric_calculators::FragQualCalculator::FragQualCalculator ( )

default constructor

References goodfrags_.

◆ FragQualCalculator() [2/3]

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

default constructor

value constructor

References goodfrags_.

◆ FragQualCalculator() [3/3]

protocols::pose_metric_calculators::FragQualCalculator::FragQualCalculator ( FragQualCalculator const & rval )

default

copy constructor

◆ ~FragQualCalculator()

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

overridedefault

destructor

Member Function Documentation

◆ begin()

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

References begin_, and core::pose::make_rid_posenum().

Referenced by recompute().

◆ clone()

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

inlineoverridevirtual

make clone

Implements core::pose::metrics::PoseMetricCalculator.

◆ end()

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

References end_, and core::pose::make_rid_posenum().

Referenced by recompute().

◆ lookup()

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

overrideprotectedvirtual

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

References coverage_, total_goodfrags_, and protocols::pose_metric_calculators::TR().

◆ parse_my_tag()

void protocols::pose_metric_calculators::FragQualCalculator::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

parse xml

References begin_, end_, frag_, core::pose::parse_resnum(), ratio_cutoff_goodfrag_, rmsd_cutoff_goodfrag_, and verbose_.

◆ print()

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

overrideprotectedvirtual

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

References coverage_, core::id::to_string(), and total_goodfrags_.

◆ ratio_cutoff()

void protocols::pose_metric_calculators::FragQualCalculator::ratio_cutoff ( Real const & val )

References ratio_cutoff_goodfrag_, and protocols::hybridization::val.

◆ recompute()

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

overrideprotectedvirtual

recomute ncontacts

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

References begin(), begin_, core::scoring::CA_rmsd(), core::chemical::CENTROID_t, coverage_, end(), end_, core::chemical::element::F, frag_, goodfrags_, ratio_cutoff_goodfrag_, rmsd_cutoff_goodfrag_, core::pose::Pose::size(), protocols::loops::start, core::util::switch_to_residue_type_set(), total_goodfrags_, protocols::pose_metric_calculators::TR(), and verbose_.

◆ rmsd_cutoff()

void protocols::pose_metric_calculators::FragQualCalculator::rmsd_cutoff ( Real const & val )

rmsd cutoff of good fragments

References rmsd_cutoff_goodfrag_, and protocols::hybridization::val.

◆ set_fragset()

void protocols::pose_metric_calculators::FragQualCalculator::set_fragset ( FragSetOP const & frags )

set fragments

References frag_.

◆ set_region()

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

References begin_, end_, and core::pose::make_rid_posenum().

Member Data Documentation

◆ begin_

core::pose::ResidueIndexDescriptionCOP protocols::pose_metric_calculators::FragQualCalculator::begin_

private

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

◆ coverage_

Real protocols::pose_metric_calculators::FragQualCalculator::coverage_

private

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

◆ end_

core::pose::ResidueIndexDescriptionCOP protocols::pose_metric_calculators::FragQualCalculator::end_

private

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

◆ frag_

FragSetOP protocols::pose_metric_calculators::FragQualCalculator::frag_

private

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

◆ goodfrags_

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

private

Referenced by FragQualCalculator(), and recompute().

◆ ratio_cutoff_goodfrag_

Real protocols::pose_metric_calculators::FragQualCalculator::ratio_cutoff_goodfrag_

private

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

◆ rmsd_cutoff_goodfrag_

Real protocols::pose_metric_calculators::FragQualCalculator::rmsd_cutoff_goodfrag_

private

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

◆ total_goodfrags_

Real protocols::pose_metric_calculators::FragQualCalculator::total_goodfrags_

private

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

◆ verbose_

bool protocols::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/pose_metric_calculators/FragQualCalculator.hh
src/protocols/pose_metric_calculators/FragQualCalculator.cc