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

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

#include <IdentityEval.hh>

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

typedef Super::VallFragmentScore VallFragmentScore
 
typedef std::string String
 
typedef core::Real Real
 
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

 IdentityEval ()
 default constructor More...
 
 IdentityEval (String const &ss, String const &aa, Real const ss_penalty=1.0, Real const aa_penalty=1.0, bool const randomize=true)
 full values constructor More...
 
 IdentityEval (String const &ss, Real const ss_penalty=1.0, bool const randomize=true)
 secondary structure constructor More...
 
 IdentityEval (IdentityEval const &rval)
 default copy constructor More...
 
 ~IdentityEval () override
 default destructor More...
 
IdentityEvaloperator= (IdentityEval 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...
 
String const & ss_str () const
 get secondary structure string More...
 
void ss_str (String const &ss)
 set secondary structure string More...
 
String const & aa_str () const
 get amino acid string More...
 
void aa_str (String const &aa)
 set amino acid string More...
 
Real ss_penalty () const
 get secondary structure penalty More...
 
void ss_penalty (Real const penalty)
 set secondary structure penalty More...
 
Real aa_penalty () const
 get amino acid penalty More...
 
void aa_penalty (Real const penalty)
 set amino acid penalty More...
 
bool randomize () const
 adding random noise to score? More...
 
void randomize (bool const flag)
 set flag to add random noise between [0, 0.001) 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

String ss_
 secondary structure string to match against More...
 
String aa_
 amino acid string to match against More...
 
Real ss_penalty_
 secondary structure penalty if non-matching More...
 
Real aa_penalty_
 amino acid penalty if non-matching More...
 
bool randomize_
 flag to add random noise between [0, 0.001) into score More...
 

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::IdentityEval::IdentityEval ( )

default constructor

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval ( String const &  ss,
String const &  aa,
Real const  ss_penalty = 1.0,
Real const  aa_penalty = 1.0,
bool const  randomize = true 
)

full values constructor

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

References aa_, and ss_.

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval ( String const &  ss,
Real const  ss_penalty = 1.0,
bool const  randomize = true 
)

secondary structure constructor

References aa_, and ss_.

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

default copy constructor

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

default destructor

Member Function Documentation

Real core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty ( ) const
inline

get amino acid penalty

References aa_penalty_.

void core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty ( Real const  penalty)
inline

set amino acid penalty

References aa_penalty_.

String const& core::fragment::picking_old::vall::eval::IdentityEval::aa_str ( ) const
inline

get amino acid string

References aa_.

void core::fragment::picking_old::vall::eval::IdentityEval::aa_str ( String const &  aa)
inline

set amino acid string

References protocols::cluster::calibur::aa, and aa_.

VallFragmentEvalOP core::fragment::picking_old::vall::eval::IdentityEval::clone ( ) const
overridevirtual
bool core::fragment::picking_old::vall::eval::IdentityEval::eval_impl ( Extent const &  extent,
VallFragmentScore fs 
)
overridevirtual
IdentityEval & core::fragment::picking_old::vall::eval::IdentityEval::operator= ( IdentityEval const &  rval)
void core::fragment::picking_old::vall::eval::IdentityEval::pre_catalog_op ( VallLibrary const &  )
overridevirtual

operation to be perform before catalog() starts

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

References aa_, ss_, and core::fragment::picking_old::vall::eval::TR().

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

adding random noise to score?

References randomize_.

void core::fragment::picking_old::vall::eval::IdentityEval::randomize ( bool const  flag)
inline

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

References randomize_.

Real core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty ( ) const
inline

get secondary structure penalty

References ss_penalty_.

void core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty ( Real const  penalty)
inline

set secondary structure penalty

References ss_penalty_.

String const& core::fragment::picking_old::vall::eval::IdentityEval::ss_str ( ) const
inline

get secondary structure string

References ss_.

void core::fragment::picking_old::vall::eval::IdentityEval::ss_str ( String const &  ss)
inline

set secondary structure string

References ss_.

Member Data Documentation

String core::fragment::picking_old::vall::eval::IdentityEval::aa_
private

amino acid string to match against

Referenced by aa_str(), eval_impl(), IdentityEval(), operator=(), and pre_catalog_op().

Real core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty_
private

amino acid penalty if non-matching

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

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

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

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

String core::fragment::picking_old::vall::eval::IdentityEval::ss_
private

secondary structure string to match against

Referenced by eval_impl(), IdentityEval(), operator=(), pre_catalog_op(), and ss_str().

Real core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty_
private

secondary structure penalty if non-matching

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


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