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core::fragment::picking_old::vall::VallLibrarian Class Reference

Librarian that picks fragments from the Vall. More...

#include <VallLibrarian.hh>

Inheritance diagram for core::fragment::picking_old::vall::VallLibrarian:
Inheritance graph
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Public Types

typedef core::Size Size
 
typedef core::fragment::FragDataOPs FragDataOPs
 
typedef core::fragment::FragData FragData
 
typedef core::fragment::FragDataOP FragDataOP
 
typedef eval::VallFragmentEval VallFragmentEval
 
typedef scores::VallFragmentScore VallFragmentScore
 
typedef Super::BookIterator BookIterator
 
typedef Super::BookConstIterator BookConstIterator
 
typedef Super::PageConstIterator PageConstIterator
 
typedef Super::PageIterator PageIterator
 
typedef Super::ExtentEvalOP ExtentEvalOP
 
typedef Super::ExtentEvalCOP ExtentEvalCOP
 
typedef Super::ExtentGenOP ExtentGenOP
 
typedef Super::ExtentGenCOP ExtentGenCOP
 
typedef Super::Bookmarks Bookmarks
 
typedef
Super::BookmarkConstIterator 
BookmarkConstIterator
 
typedef Super::BookmarkIterator BookmarkIterator
 
typedef Super::ExtentGenOPs ExtentGenOPs
 
typedef Super::ExtentEvalOPs ExtentEvalOPs
 
typedef ExtentEvalOP VallFragmentEvalOP
 
typedef ExtentEvalCOP VallFragmentEvalCOP
 
typedef ExtentGenOP VallFragmentGenOP
 
typedef ExtentGenCOP VallFragmentGenCOP
 
typedef Bookmarks Scores
 
typedef BookmarkConstIterator ScoreConstIterator
 
typedef BookmarkIterator ScoreIterator
 
- Public Types inherited from core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >
typedef core::Size Size
 
typedef VallLibrary::BookIterator BookIterator
 
typedef
VallLibrary::BookConstIterator 
BookConstIterator
 
typedef VallLibrary::Book Book
 
typedef Book::PageConstIterator PageConstIterator
 
typedef Book::PageIterator PageIterator
 
typedef Book::Page Page
 
typedef
gen::VallFragmentGen::Extent 
Extent
 
typedef
utility::pointer::shared_ptr
< eval::VallFragmentEval > 
ExtentEvalOP
 
typedef
utility::pointer::shared_ptr
< eval::VallFragmentEvalconst > 
ExtentEvalCOP
 
typedef
utility::pointer::shared_ptr
< gen::VallFragmentGen > 
ExtentGenOP
 
typedef
utility::pointer::shared_ptr
< gen::VallFragmentGenconst > 
ExtentGenCOP
 
typedef utility::vector1
< scores::VallFragmentScore > 
Bookmarks
 
typedef Bookmarks::const_iterator BookmarkConstIterator
 
typedef Bookmarks::iterator BookmarkIterator
 

Public Member Functions

 VallLibrarian ()
 default constructor More...
 
 ~VallLibrarian () override
 default destructor More...
 
bool preallocate () const
 preallocate scores container prior to catalog() to attempt speedup?, default true More...
 
void preallocate (bool const flag)
 set flag to preallocate scores container prior to catalog() to attempt speedup More...
 
void add_fragment_gen (VallFragmentGenCOP const &gen)
 add a fragment generator (aka extent generator) More...
 
void clear_fragment_gen ()
 clear list of generators More...
 
Size n_fragment_gen () const
 the number of currently defined fragment generators More...
 
void add_fragment_eval (VallFragmentEvalCOP eval)
 add a fragment evaluator (aka extent evaluator) More...
 
void clear_fragment_eval ()
 clear list of evaluators More...
 
Size n_fragment_eval () const
 the number of currently defined fragment evaluators More...
 
bool catalog (VallLibrary const &library)
 create sorted list corresponding to fragments in Library More...
 
template<typename LessThan >
bool catalog (VallLibrary const &library, LessThan const &lt)
 create sorted list corresponding to fragments in Library More...
 
Size n_scores () const
 number of scores currently filed More...
 
FragDataOPs top_fragments (Size const n, BBTorsionSRFD const &srfd_type=BBTorsionSRFD()) const
 get top 'N' fragments from prior catalog() More...
 
FragDataOPs fragments (Size from, Size to, BBTorsionSRFD const &srfd_type=BBTorsionSRFD()) const
 get fragments from prior catalog() [from, to] More...
 
Scores const & scores () const
 return scores container More...
 
Scoresscores ()
 return scores container More...
 
- Public Member Functions inherited from core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >
 Librarian ()
 default constructor More...
 
virtual ~Librarian ()
 default destructor More...
 
bool catalog (VallLibraryconst &library)
 create sorted list corresponding to fragments in Library More...
 
bool catalog (VallLibraryconst &library, LessThan const &lt)
 create sorted list corresponding to fragments in Library More...
 
void add_extent_gen (ExtentGenCOP const &gen)
 add an extent generator More...
 
void clear_extent_gen ()
 clear list of generators More...
 
void add_extent_eval (ExtentEvalCOP val)
 add extent evaluator More...
 
void clear_extent_eval ()
 clear list of evaluators More...
 

Protected Types

typedef BookConstIterator VallSectionConstIterator
 
typedef BookIterator VallSectionIterator
 
typedef PageConstIterator VallResidueConstIterator
 
typedef PageIterator VallResidueIterator
 
typedef ExtentGenOPs VallFragmentGenOPs
 
typedef ExtentEvalOPs VallFragmentEvalOPs
 
- Protected Types inherited from core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >
typedef utility::vector1
< ExtentGenOP
ExtentGenOPs
 
typedef utility::vector1
< ExtentEvalOP
ExtentEvalOPs
 

Private Types

typedef
core::fragment::picking_old::concepts::Librarian
< scores::VallFragmentScore,
eval::VallFragmentEval,
gen::VallFragmentGen,
VallLibrary
Super
 

Private Member Functions

 VallLibrarian (VallLibrarian const &rval)
 disallow copy constructor More...
 
VallLibrarianoperator= (VallLibrarian const &rval)
 disallow copy assignment More...
 
void pre_catalog_ops (VallLibrary const &library)
 this function runs before main routine in catalog() starts More...
 
void post_catalog_ops (VallLibrary const &library)
 this function runs after main routine catalog() finishes More...
 

Private Attributes

bool preallocate_
 flag controls preallocation of score container, default true More...
 

Additional Inherited Members

- Protected Member Functions inherited from core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >
bool evaluate_extent (Extent const &extent, scores::VallFragmentScore &mark)
 evaluate a fragment starting from Page at iterator More...
 
Bookmarks const & bookmarks () const
 get the current bookmark heap More...
 
Bookmarksbookmarks ()
 get the current bookmark heap More...
 
ExtentGenOPs const & extent_gen () const
 the list of extent generators More...
 
ExtentGenOPsextent_gen ()
 the list of extent generators More...
 
ExtentEvalOPs const & extent_eval () const
 the list of extent evaluators More...
 
ExtentEvalOPsextent_eval ()
 the list of extent evaluators More...
 

Detailed Description

Librarian that picks fragments from the Vall.

Member Typedef Documentation

Constructor & Destructor Documentation

core::fragment::picking_old::vall::VallLibrarian::VallLibrarian ( )

default constructor

core::fragment::picking_old::vall::VallLibrarian::~VallLibrarian ( )
overridedefault

default destructor

core::fragment::picking_old::vall::VallLibrarian::VallLibrarian ( VallLibrarian const &  rval)
private

disallow copy constructor

Member Function Documentation

void core::fragment::picking_old::vall::VallLibrarian::add_fragment_eval ( VallFragmentEvalCOP  eval)
inline
void core::fragment::picking_old::vall::VallLibrarian::add_fragment_gen ( VallFragmentGenCOP const &  gen)
inline
bool core::fragment::picking_old::vall::VallLibrarian::catalog ( VallLibrary const &  library)
inline

create sorted list corresponding to fragments in Library

uses Score's '<' for evaluation

Returns
true if creation successful, false otherwise (e.g. no VallFragmentEval or VallFragmentGen found)

Referenced by core::fragment::picking_old::vall::pick_fragments(), core::fragment::picking_old::vall::pick_fragments_by_ss(), and core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa().

template<typename LessThan >
bool core::fragment::picking_old::vall::VallLibrarian::catalog ( VallLibrary const &  library,
LessThan const &  lt 
)
inline

create sorted list corresponding to fragments in Library

Template Parameters
LessThanpredicate Pr( left, right ) evaluating left < right for Scores (aka Bookmarks)
Returns
true if creation successful, false otherwise (e.g. no VallFragmentEval or VallFragmentGen found)

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::catalog(), post_catalog_ops(), pre_catalog_ops(), scores(), core::fragment::picking_old::concepts::Library< Books >::size(), and core::fragment::picking_old::vall::TR().

void core::fragment::picking_old::vall::VallLibrarian::clear_fragment_eval ( )
inline
void core::fragment::picking_old::vall::VallLibrarian::clear_fragment_gen ( )
inline
VallLibrarian::FragDataOPs core::fragment::picking_old::vall::VallLibrarian::fragments ( Size  from,
Size  to,
BBTorsionSRFD const &  srfd_type = BBTorsionSRFD() 
) const

get fragments from prior catalog() [from, to]

Parameters
fromindex of the first fragment in the list, indexing starts from '1'
toindex of the last fragment in the list (inclusive)
srfd_typeThe BBTorsionSRFD type to use.
Returns
filled FragDataOPs if sort() was called successfully, otherwise empty FragDataOPs
Parameters
fromindex of the first fragment in the list, indexing starts from '1'
toindex of the last fragment in the list (inclusive)
Returns
filled FragDataOPs if sort() was called successfully, otherwise empty FragDataOPs

References core::sequence::end, core::fragment::picking_old::vall::extent_to_fragdata(), scores(), and core::fragment::picking_old::vall::TR().

Referenced by top_fragments().

Size core::fragment::picking_old::vall::VallLibrarian::n_fragment_eval ( ) const
inline
Size core::fragment::picking_old::vall::VallLibrarian::n_fragment_gen ( ) const
inline
Size core::fragment::picking_old::vall::VallLibrarian::n_scores ( ) const
inline

number of scores currently filed

References scores().

VallLibrarian& core::fragment::picking_old::vall::VallLibrarian::operator= ( VallLibrarian const &  rval)
private

disallow copy assignment

void core::fragment::picking_old::vall::VallLibrarian::post_catalog_ops ( VallLibrary const &  library)
private
void core::fragment::picking_old::vall::VallLibrarian::pre_catalog_ops ( VallLibrary const &  library)
private
bool core::fragment::picking_old::vall::VallLibrarian::preallocate ( ) const
inline

preallocate scores container prior to catalog() to attempt speedup?, default true

References preallocate_.

void core::fragment::picking_old::vall::VallLibrarian::preallocate ( bool const  flag)
inline

set flag to preallocate scores container prior to catalog() to attempt speedup

References preallocate_.

Scores const& core::fragment::picking_old::vall::VallLibrarian::scores ( ) const
inline
Scores& core::fragment::picking_old::vall::VallLibrarian::scores ( )
inline
VallLibrarian::FragDataOPs core::fragment::picking_old::vall::VallLibrarian::top_fragments ( Size const  n,
BBTorsionSRFD const &  srfd_type = BBTorsionSRFD() 
) const

get top 'N' fragments from prior catalog()

Parameters
nThe number of fragments to get.
srfd_typeThe BBTorsionSRFD type to use.

References fragments().

Referenced by core::fragment::picking_old::vall::pick_fragments(), core::fragment::picking_old::vall::pick_fragments_by_ss(), and core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa().

Member Data Documentation

bool core::fragment::picking_old::vall::VallLibrarian::preallocate_
private

flag controls preallocation of score container, default true

Referenced by pre_catalog_ops(), and preallocate().


The documentation for this class was generated from the following files: