SecondarySimilarity.hh File Reference

scores a fragment by secondary structure similarity More...

#include <core/types.hh>
#include <protocols/frag_picker/FragmentPicker.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.fwd.hh>
#include <protocols/frag_picker/scores/CachingScoringMethod.hh>
#include <core/fragment/SecondaryStructure.fwd.hh>
#include <utility/vector1.hh>
#include <protocols/frag_picker/VallProvider.hh>

Classes
class	protocols::frag_picker::scores::SecondarySimilarity
	scores a fragment by secondary structure similarity @detail The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster. More...
class	protocols::frag_picker::scores::MakeSecondarySimilarity
	Maker class that produces a new SecondarySimilarity object. More...

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::frag_picker
	protocols::frag_picker::scores

Typedefs
typedef utility::pointer::shared_ptr< SecondarySimilarity >	protocols::frag_picker::scores::SecondarySimilarityOP
typedef utility::pointer::shared_ptr< SecondarySimilarity const >	protocols::frag_picker::scores::SecondarySimilarityCOP

Detailed Description

scores a fragment by secondary structure similarity

Author

Dominik Gront (dgron.nosp@m.t@ch.nosp@m.em.uw.nosp@m..edu.nosp@m..pl)