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core::fragment::picking_old::vall::eval::ABEGOEval Class Reference

scores a fragment based on sum of secondary structure identity and sequence identity More...

#include <ABEGOEval.hh>

Inheritance diagram for core::fragment::picking_old::vall::eval::ABEGOEval:
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Public Types

typedef Super::VallFragmentScore VallFragmentScore
 
typedef std::string String
 
typedef core::Real Real
 
typedef
core::sequence::ABEGOManager 
ABEGOManager
 
typedef
core::sequence::ABEGOManagerOP 
ABEGOManagerOP
 
typedef Super::PageConstIterator PageConstIterator
 typedef for ExtentEvaluator concept More...
 
typedef Super::Extent Extent
 typedef for ExtentEvaluator concept More...
 
typedef PageConstIterator VallResidueConstIterator
 
- Public Types inherited from core::fragment::picking_old::vall::eval::VallFragmentEval
typedef
core::fragment::picking_old::vall::scores::VallFragmentScore 
VallFragmentScore
 
typedef
VallFragmentScore::PageConstIterator 
PageConstIterator
 typedef for ExtentEvaluator concept More...
 
typedef
core::fragment::picking_old::concepts::Extent
< VallSection::PageConstIterator
Extent
 typedef for ExtentEvaluator concept More...
 
typedef PageConstIterator VallResidueConstIterator
 

Public Member Functions

 ABEGOEval ()
 default constructor More...
 
 ABEGOEval (utility::vector1< String > const &input, Real const penalty=1.0, bool const randomize=true)
 full values constructor More...
 
 ABEGOEval (ABEGOEval const &rval)
 default copy constructor More...
 
 ~ABEGOEval () override
 default destructor More...
 
ABEGOEvaloperator= (ABEGOEval const &rval)
 copy assignment More...
 
VallFragmentEvalOP clone () const override
 clone this object More...
 
bool eval_impl (Extent const &extent, VallFragmentScore &fs) override
 for a fragment extent, evaluate and store results in a VallFragmentScore More...
 
utility::vector1< String > const & abego_str () const
 get secondary structure string More...
 
void abego_str (utility::vector1< String > const &abego)
 set abego vector of string More...
 
Real penalty () const
 get secondary structure penalty More...
 
bool randomize () const
 adding random noise to score? More...
 
void pre_catalog_op (VallLibrary const &) override
 operation to be perform before catalog() starts More...
 
- Public Member Functions inherited from core::fragment::picking_old::vall::eval::VallFragmentEval
 VallFragmentEval ()
 default constructor More...
 
 VallFragmentEval (VallFragmentEval const &rval)
 default copy constructor More...
 
 ~VallFragmentEval () override
 default destructor More...
 
VallFragmentEvaloperator= (VallFragmentEval const &rval)
 copy assignment More...
 
bool operator() (Extent const &extent, VallFragmentScore &fs)
 called by VallLibrarian: for a fragment extent, evaluate and store results in a VallFragmentScore More...
 
virtual void post_catalog_op (VallLibrary const &)
 operation to be performed after catalog() finished More...
 

Private Types

typedef VallFragmentEval Super
 

Private Attributes

utility::vector1< Stringabego_
 abego string to match against More...
 
Real penalty_
 abego penalty if non-matching More...
 
bool randomize_
 flag to add random noise between [0, 0.001) into score More...
 
ABEGOManagerOP am_
 

Detailed Description

scores a fragment based on sum of secondary structure identity and sequence identity

Member Typedef Documentation

typedef for ExtentEvaluator concept

typedef for ExtentEvaluator concept

Constructor & Destructor Documentation

core::fragment::picking_old::vall::eval::ABEGOEval::ABEGOEval ( )

default constructor

References abego_, and am_.

core::fragment::picking_old::vall::eval::ABEGOEval::ABEGOEval ( utility::vector1< String > const &  abego,
Real const  penalty = 1.0,
bool const  randomize = true 
)

full values constructor

Parameters
sssecondary structure string to match against
aaamino acid structure string to match against
abegoabego string to match against

References am_.

core::fragment::picking_old::vall::eval::ABEGOEval::ABEGOEval ( ABEGOEval const &  rval)
default

default copy constructor

core::fragment::picking_old::vall::eval::ABEGOEval::~ABEGOEval ( )
overridedefault

default destructor

Member Function Documentation

utility::vector1< String > const& core::fragment::picking_old::vall::eval::ABEGOEval::abego_str ( ) const
inline

get secondary structure string

References abego_.

void core::fragment::picking_old::vall::eval::ABEGOEval::abego_str ( utility::vector1< String > const &  abego)
inline

set abego vector of string

References core::scoring::abego, and abego_.

VallFragmentEvalOP core::fragment::picking_old::vall::eval::ABEGOEval::clone ( ) const
overridevirtual
bool core::fragment::picking_old::vall::eval::ABEGOEval::eval_impl ( Extent const &  extent,
VallFragmentScore fs 
)
overridevirtual
ABEGOEval & core::fragment::picking_old::vall::eval::ABEGOEval::operator= ( ABEGOEval const &  rval)
Real core::fragment::picking_old::vall::eval::ABEGOEval::penalty ( ) const
inline

get secondary structure penalty

References penalty_.

void core::fragment::picking_old::vall::eval::ABEGOEval::pre_catalog_op ( VallLibrary const &  )
overridevirtual

operation to be perform before catalog() starts

Reimplemented from core::fragment::picking_old::vall::eval::VallFragmentEval.

References core::scoring::abego, and abego_.

bool core::fragment::picking_old::vall::eval::ABEGOEval::randomize ( ) const
inline

adding random noise to score?

References randomize_.

Member Data Documentation

utility::vector1< String > core::fragment::picking_old::vall::eval::ABEGOEval::abego_
private

abego string to match against

Referenced by abego_str(), ABEGOEval(), eval_impl(), operator=(), and pre_catalog_op().

ABEGOManagerOP core::fragment::picking_old::vall::eval::ABEGOEval::am_
private

Referenced by ABEGOEval(), eval_impl(), and operator=().

Real core::fragment::picking_old::vall::eval::ABEGOEval::penalty_
private

abego penalty if non-matching

Referenced by eval_impl(), operator=(), and penalty().

bool core::fragment::picking_old::vall::eval::ABEGOEval::randomize_
private

flag to add random noise between [0, 0.001) into score

Referenced by eval_impl(), operator=(), and randomize().


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