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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.hh>
#include <protocols/frag_picker/scores/CachingScoringMethod.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <utility/vector1.hh>

Classes

class  protocols::frag_picker::scores::SecondarySimilarity
 scores a fragment by secondary structure similarity 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)