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L1ScoringScheme.hh File Reference

class definition for a profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance. More...

#include <core/types.hh>
#include <core/sequence/ScoringScheme.hh>

Classes

class  core::sequence::L1ScoringScheme
 

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 profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance.

Detailed: Simply based on comparing single profiles from two protein
sequences by computing the sum of P(A) - P(B) for all matching probabilities in the profiles A and B. Also includes 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