Rosetta Core  2014.35
Namespaces
ProfSimScoringScheme.cc File Reference

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

#include <core/types.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/SequenceProfile.fwd.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/ProfSimScoringScheme.hh>
#include <utility/exit.hh>
#include <core/chemical/AA.hh>
#include <string>
#include <utility/vector1.hh>
#include <complex>
#include <map>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::sequence
 

Detailed Description

class definition for a given scoring scheme for an alignment.

Detailed: Simply based on comparing single profiles 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