Rosetta  2020.37
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core::sequence::MatrixScoringScheme Class Reference

#include <MatrixScoringScheme.hh>

Inheritance diagram for core::sequence::MatrixScoringScheme:
Inheritance graph
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Public Member Functions

 MatrixScoringScheme ()
 
 MatrixScoringScheme (Real open, Real extend, utility::file::FileName const &fn)
 ctor More...
 
 MatrixScoringScheme (Real open, Real extend, utility::vector1< utility::vector1< core::Real > > matrix)
 
ScoringSchemeOP clone () const override
 returns owning pointer to a new object with a deep copy of this object's values. More...
 
 ~MatrixScoringScheme () override=default
 dtor More...
 
void read_from_database (std::string name="BLOSUM62")
 Read an alignment matrix from the given database filename using the NCBI BLOSUM format for matrices. More...
 
void read_from_file (utility::file::FileName const &fn) override
 Read an alignment matrix from the given filename using the NCBI BLOSUM format for matrices. More...
 
void read_data (utility::io::izstream &input) override
 
utility::vector1< Realvalues_for_aa (char aa)
 Get the values for amino acid aa, in Rosetta aa order. More...
 
utility::vector1< Realvalues_for_aa (core::chemical::AA aa)
 Get the values for amino acid aa, in Rosetta aa order. More...
 
utility::vector1
< utility::vector1< Real > > 
scoring_matrix () const
 
Real score (SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2) override
 
- Public Member Functions inherited from core::sequence::ScoringScheme
 ScoringScheme ()
 ctor More...
 
 ~ScoringScheme () override
 dtor More...
 
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...
 
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 Member Functions

void init_type ()
 

Private Attributes

utility::vector1
< utility::vector1< Real > > 
scoring_matrix_
 

Constructor & Destructor Documentation

core::sequence::MatrixScoringScheme::MatrixScoringScheme ( )
inline
core::sequence::MatrixScoringScheme::MatrixScoringScheme ( Real  open,
Real  extend,
utility::file::FileName const &  fn 
)
inline
core::sequence::MatrixScoringScheme::MatrixScoringScheme ( Real  open,
Real  extend,
utility::vector1< utility::vector1< core::Real > >  matrix 
)
inline
core::sequence::MatrixScoringScheme::~MatrixScoringScheme ( )
overridedefault

dtor

Member Function Documentation

ScoringSchemeOP core::sequence::MatrixScoringScheme::clone ( ) const
inlineoverridevirtual

returns owning pointer to a new object with a deep copy of this object's values.

Implements core::sequence::ScoringScheme.

References core::sequence::ScoringScheme::gap_extend(), core::sequence::ScoringScheme::gap_open(), and scoring_matrix().

void core::sequence::MatrixScoringScheme::init_type ( )
inlineprivate
void core::sequence::MatrixScoringScheme::read_data ( utility::io::izstream &  input)
overridevirtual
void core::sequence::MatrixScoringScheme::read_from_database ( std::string  name = "BLOSUM62")

Read an alignment matrix from the given database filename using the NCBI BLOSUM format for matrices.

References read_from_file().

Referenced by core::sequence::SequenceProfile::generate_from_sequence().

void core::sequence::MatrixScoringScheme::read_from_file ( utility::file::FileName const &  fn)
overridevirtual
Real core::sequence::MatrixScoringScheme::score ( SequenceOP  seq1,
SequenceOP  seq2,
Size  pos1,
Size  pos2 
)
overridevirtual
utility::vector1< utility::vector1< Real > > core::sequence::MatrixScoringScheme::scoring_matrix ( ) const
utility::vector1< Real > core::sequence::MatrixScoringScheme::values_for_aa ( char  aa)
utility::vector1< Real > core::sequence::MatrixScoringScheme::values_for_aa ( core::chemical::AA  aa)

Get the values for amino acid aa, in Rosetta aa order.

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

Member Data Documentation

utility::vector1< utility::vector1< Real > > core::sequence::MatrixScoringScheme::scoring_matrix_
private

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