Rosetta 3.5: core::sequence::PairScoringScheme Class Reference

#include <PairScoringScheme.hh>

Inheritance diagram for core::sequence::PairScoringScheme:

Inheritance graph

Collaboration diagram for core::sequence::PairScoringScheme:

Collaboration 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
	clone method. More...

utility::vector1 < utility::vector1< core::Real > >	pairs () const

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

virtual	~PairScoringScheme ()
	dtor More...

virtual void	read_from_file (utility::file::FileName const &fn)
	Initialize from a file. More...

virtual Real	score (SequenceOP seq1, SequenceOP seq2, core::Size pos1, core::Size pos2)

Public Member Functions inherited from core::sequence::ScoringScheme
	ScoringScheme ()
	ctor More...

virtual	~ScoringScheme ()
	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 < utility::vector1< core::Real > >	pairs_

Detailed Description

Definition at line 32 of file PairScoringScheme.hh.

Constructor & Destructor Documentation

core::sequence::PairScoringScheme::PairScoringScheme ( )

inline

Definition at line 35 of file PairScoringScheme.hh.

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

Referenced by clone().

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

inline

ctor

Definition at line 42 of file PairScoringScheme.hh.

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

virtual core::sequence::PairScoringScheme::~PairScoringScheme ( )

inlinevirtual

dtor

Definition at line 85 of file PairScoringScheme.hh.

Member Function Documentation

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

inline

Definition at line 68 of file PairScoringScheme.hh.

References pairs_, score(), and core::io::serialization::size().

ScoringSchemeOP core::sequence::PairScoringScheme::clone ( ) const

inlinevirtual

clone method.

Implements core::sequence::ScoringScheme.

Definition at line 54 of file PairScoringScheme.hh.

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

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

inline

Definition at line 64 of file PairScoringScheme.hh.

References pairs_.

Referenced by clone().

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

virtual

Initialize from a file.

Reimplemented from core::sequence::ScoringScheme.

Definition at line 29 of file PairScoringScheme.cc.

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

virtual

Definition at line 35 of file PairScoringScheme.cc.

References pairs_.

Referenced by add_scored_pair().

Member Data Documentation

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

private

Definition at line 97 of file PairScoringScheme.hh.

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

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

src/core/sequence/PairScoringScheme.hh
src/core/sequence/PairScoringScheme.cc