protocols::pose_metric_calculators::FragQualCalculator Class Reference

#include <FragQualCalculator.hh>

Inheritance diagram for protocols::pose_metric_calculators::FragQualCalculator:

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

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

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

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

protocols::pose_metric_calculators::FragQualCalculator::FragQualCalculator

(

)

default constructor

References goodfrags_.

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

default constructor

value constructor

References goodfrags_.

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

default

copy constructor

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

overridedefault

destructor

Member Function Documentation

void protocols::pose_metric_calculators::FragQualCalculator::begin

(

core::Size const

begin

)

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

Referenced by recompute().

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

inlineoverridevirtual

make clone

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

void protocols::pose_metric_calculators::FragQualCalculator::end

(

core::Size const

end

)

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

Referenced by recompute().

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().

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_.

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_.

void protocols::pose_metric_calculators::FragQualCalculator::ratio_cutoff

(

Real const &

val

)

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

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_.

void protocols::pose_metric_calculators::FragQualCalculator::rmsd_cutoff

(

Real const &

val

)

rmsd cutoff of good fragments

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

void protocols::pose_metric_calculators::FragQualCalculator::set_fragset

(

FragSetOP const &

frags

)

set fragments

References frag_.

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

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

private

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

Real protocols::pose_metric_calculators::FragQualCalculator::coverage_

private

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

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

private

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

FragSetOP protocols::pose_metric_calculators::FragQualCalculator::frag_

private

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

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

private

Referenced by FragQualCalculator(), and recompute().

Real protocols::pose_metric_calculators::FragQualCalculator::ratio_cutoff_goodfrag_

private

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

Real protocols::pose_metric_calculators::FragQualCalculator::rmsd_cutoff_goodfrag_

private

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

Real protocols::pose_metric_calculators::FragQualCalculator::total_goodfrags_

private

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

bool protocols::pose_metric_calculators::FragQualCalculator::verbose_

private

Referenced by parse_my_tag(), and recompute().

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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