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

#include <FragQualCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::FragQualCalculator:

Collaboration diagram for protocols::toolbox::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::TagPtr	TagPtr
typedef protocols::filters::Filters_map	Filters_map
typedef protocols::moves::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 (TagPtr const tag, 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)
Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()
virtual void	notify_energy_change ()

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_

Detailed Description

Definition at line 40 of file FragQualCalculator.hh.

Member Typedef Documentation

typedef protocols::moves::DataMap protocols::toolbox::pose_metric_calculators::FragQualCalculator::DataMap

Definition at line 56 of file FragQualCalculator.hh.

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

Definition at line 55 of file FragQualCalculator.hh.

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

Definition at line 51 of file FragQualCalculator.hh.

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

Definition at line 52 of file FragQualCalculator.hh.

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

Definition at line 50 of file FragQualCalculator.hh.

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

Definition at line 57 of file FragQualCalculator.hh.

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

Definition at line 48 of file FragQualCalculator.hh.

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

Definition at line 49 of file FragQualCalculator.hh.

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

Definition at line 47 of file FragQualCalculator.hh.

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

Definition at line 46 of file FragQualCalculator.hh.

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

Definition at line 45 of file FragQualCalculator.hh.

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

Definition at line 44 of file FragQualCalculator.hh.

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

Definition at line 54 of file FragQualCalculator.hh.

Constructor & Destructor Documentation

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

(

)

default constructor

Definition at line 62 of file FragQualCalculator.cc.

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

Definition at line 76 of file FragQualCalculator.cc.

References goodfrags_.

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

(

FragQualCalculator const &

rval)

copy constructor

Definition at line 93 of file FragQualCalculator.cc.

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

virtual

destructor

Definition at line 107 of file FragQualCalculator.cc.

Member Function Documentation

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

inline

Definition at line 99 of file FragQualCalculator.hh.

References begin(), and begin_.

Referenced by begin().

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

inlinevirtual

make clone

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

Definition at line 80 of file FragQualCalculator.hh.

References FragQualCalculator().

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

inline

Definition at line 102 of file FragQualCalculator.hh.

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.

Definition at line 141 of file FragQualCalculator.cc.

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

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

parse xml

Definition at line 249 of file FragQualCalculator.cc.

References begin_, end_, frag_, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), ratio_cutoff_goodfrag_, rmsd_cutoff_goodfrag_, 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.

Definition at line 163 of file FragQualCalculator.cc.

References coverage_, and total_goodfrags_.

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

(

Real const &

val)

Definition at line 126 of file FragQualCalculator.cc.

References ratio_cutoff_goodfrag_.

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

protectedvirtual

recomute ncontacts

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

Definition at line 179 of file FragQualCalculator.cc.

References begin_, core::scoring::CA_rmsd(), core::chemical::CENTROID, coverage_, end_, frag_, goodfrags_, ratio_cutoff_goodfrag_, rmsd_cutoff_goodfrag_, 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

Definition at line 119 of file FragQualCalculator.cc.

References rmsd_cutoff_goodfrag_.

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

(

FragSetOP const &

frags)

set fragments

Definition at line 112 of file FragQualCalculator.cc.

References frag_.

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

Definition at line 133 of file FragQualCalculator.cc.

References begin_, and end_.

Member Data Documentation

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

private

Definition at line 143 of file FragQualCalculator.hh.

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

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

private

Definition at line 134 of file FragQualCalculator.hh.

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

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

private

Definition at line 146 of file FragQualCalculator.hh.

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

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

private

Definition at line 140 of file FragQualCalculator.hh.

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

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

private

Definition at line 137 of file FragQualCalculator.hh.

Referenced by FragQualCalculator(), and recompute().

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

private

Definition at line 129 of file FragQualCalculator.hh.

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

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

private

Definition at line 126 of file FragQualCalculator.hh.

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

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

private

Definition at line 132 of file FragQualCalculator.hh.

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

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

private

Definition at line 149 of file FragQualCalculator.hh.

Referenced by parse_my_tag(), and recompute().

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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