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MatrixScoringScheme.hh File Reference

class definition for a given scoring scheme for an alignment. More...

#include <core/types.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/chemical/AA.hh>
#include <utility/io/izstream.fwd.hh>
#include <utility/file/FileName.fwd.hh>
#include <utility/vector1_bool.hh>

Classes

class  core::sequence::MatrixScoringScheme
 

Namespaces

 core
 A class for defining atom parameters, known as atom_types.
 
 core::sequence
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::sequence
 

Detailed Description

class definition for a given scoring scheme for an alignment.

Detailed: Simply based on comparing single characters from two protein
sequences, along with affine gap penalties of the form penalty = A + Bk, where A represents the penalty for starting a gap, and B represents the penalty for extending a previously opened gap by k characters.
Author
James Thompson