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Public Member Functions | Private Attributes | List of all members
core::sequence::PairScoringScheme Class Reference

#include <PairScoringScheme.hh>

Inheritance diagram for core::sequence::PairScoringScheme:
Inheritance graph

Public Member Functions

 PairScoringScheme ()
 PairScoringScheme (Real gap_open_in, Real gap_extend_in, utility::vector1< utility::vector1< core::Real > > pairs)
 ctor More...
ScoringSchemeOP clone () const override
 clone method. More...
< utility::vector1< core::Real > > 
pairs () const
void add_scored_pair (core::Size const res1, core::Size const res2, core::Real const score)
 ~PairScoringScheme () override=default
 dtor More...
void read_from_file (utility::file::FileName const &fn) override
 Initialize from a file. More...
Real score (SequenceOP seq1, SequenceOP seq2, core::Size pos1, core::Size pos2) override
- Public Member Functions inherited from core::sequence::ScoringScheme
 ScoringScheme ()
 ctor More...
 ~ScoringScheme () override
 dtor More...
virtual void read_data (utility::io::izstream &)
virtual Real gap_open () const
 Gets the gap opening penalty. More...
virtual Real gap_extend () const
 Gets the gap extension penalty. More...
void gap_open (Real const gap_open)
 Sets the gap opening penalty. More...
void gap_extend (Real const gap_extend)
 Sets the gap extension penalty. More...
std::string type () const
 getters for type, which is a unique string name for this object. More...
void type (std::string new_type)
 getters for type, which is a unique string name for this object. More...
virtual Real score (SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2)=0
void unimplemented_method_error (std::string const &method_name) const
 Utility method for producing useful error messages and exiting from program. Declared const which is funny, because exiting the program certainly changes the state of this object! This might be replaced with exception handling if we ever start using those. More...
bool is_good (Real const &num)

Private Attributes

< utility::vector1< core::Real > > 

Constructor & Destructor Documentation

core::sequence::PairScoringScheme::PairScoringScheme ( )
core::sequence::PairScoringScheme::PairScoringScheme ( Real  gap_open_in,
Real  gap_extend_in,
utility::vector1< utility::vector1< core::Real > >  pairs 
core::sequence::PairScoringScheme::~PairScoringScheme ( )


Member Function Documentation

void core::sequence::PairScoringScheme::add_scored_pair ( core::Size const  res1,
core::Size const  res2,
core::Real const  score 

References pairs_, and score().

ScoringSchemeOP core::sequence::PairScoringScheme::clone ( ) const
utility::vector1< utility::vector1< core::Real > > core::sequence::PairScoringScheme::pairs ( ) const

References pairs_.

Referenced by clone().

void core::sequence::PairScoringScheme::read_from_file ( utility::file::FileName const &  )

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

Real core::sequence::PairScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
core::Size  pos1,
core::Size  pos2 

References pairs_.

Referenced by add_scored_pair().

Member Data Documentation

utility::vector1< utility::vector1< core::Real > > core::sequence::PairScoringScheme::pairs_

Referenced by add_scored_pair(), pairs(), and score().

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