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:

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...
Scores &	scores ()
	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...
VallLibrarian &	operator= (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...
Bookmarks &	bookmarks ()
	get the current bookmark heap More...
ExtentGenOPs const &	extent_gen () const
	the list of extent generators More...
ExtentGenOPs &	extent_gen ()
	the list of extent generators More...
ExtentEvalOPs const &	extent_eval () const
	the list of extent evaluators More...
ExtentEvalOPs &	extent_eval ()
	the list of extent evaluators More...

Detailed Description

Librarian that picks fragments from the Vall.

Member Typedef Documentation

typedef Super::BookConstIterator core::fragment::picking_old::vall::VallLibrarian::BookConstIterator

typedef Super::BookIterator core::fragment::picking_old::vall::VallLibrarian::BookIterator

typedef Super::BookmarkConstIterator core::fragment::picking_old::vall::VallLibrarian::BookmarkConstIterator

typedef Super::BookmarkIterator core::fragment::picking_old::vall::VallLibrarian::BookmarkIterator

typedef Super::Bookmarks core::fragment::picking_old::vall::VallLibrarian::Bookmarks

typedef Super::ExtentEvalCOP core::fragment::picking_old::vall::VallLibrarian::ExtentEvalCOP

typedef Super::ExtentEvalOP core::fragment::picking_old::vall::VallLibrarian::ExtentEvalOP

typedef Super::ExtentEvalOPs core::fragment::picking_old::vall::VallLibrarian::ExtentEvalOPs

typedef Super::ExtentGenCOP core::fragment::picking_old::vall::VallLibrarian::ExtentGenCOP

typedef Super::ExtentGenOP core::fragment::picking_old::vall::VallLibrarian::ExtentGenOP

typedef Super::ExtentGenOPs core::fragment::picking_old::vall::VallLibrarian::ExtentGenOPs

typedef core::fragment::FragData core::fragment::picking_old::vall::VallLibrarian::FragData

typedef core::fragment::FragDataOP core::fragment::picking_old::vall::VallLibrarian::FragDataOP

typedef core::fragment::FragDataOPs core::fragment::picking_old::vall::VallLibrarian::FragDataOPs

typedef Super::PageConstIterator core::fragment::picking_old::vall::VallLibrarian::PageConstIterator

typedef Super::PageIterator core::fragment::picking_old::vall::VallLibrarian::PageIterator

typedef BookmarkConstIterator core::fragment::picking_old::vall::VallLibrarian::ScoreConstIterator

typedef BookmarkIterator core::fragment::picking_old::vall::VallLibrarian::ScoreIterator

typedef Bookmarks core::fragment::picking_old::vall::VallLibrarian::Scores

typedef core::Size core::fragment::picking_old::vall::VallLibrarian::Size

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

private

typedef eval::VallFragmentEval core::fragment::picking_old::vall::VallLibrarian::VallFragmentEval

typedef ExtentEvalCOP core::fragment::picking_old::vall::VallLibrarian::VallFragmentEvalCOP

typedef ExtentEvalOP core::fragment::picking_old::vall::VallLibrarian::VallFragmentEvalOP

typedef ExtentEvalOPs core::fragment::picking_old::vall::VallLibrarian::VallFragmentEvalOPs

protected

typedef ExtentGenCOP core::fragment::picking_old::vall::VallLibrarian::VallFragmentGenCOP

typedef ExtentGenOP core::fragment::picking_old::vall::VallLibrarian::VallFragmentGenOP

typedef ExtentGenOPs core::fragment::picking_old::vall::VallLibrarian::VallFragmentGenOPs

protected

typedef scores::VallFragmentScore core::fragment::picking_old::vall::VallLibrarian::VallFragmentScore

typedef PageConstIterator core::fragment::picking_old::vall::VallLibrarian::VallResidueConstIterator

protected

typedef PageIterator core::fragment::picking_old::vall::VallLibrarian::VallResidueIterator

protected

typedef BookConstIterator core::fragment::picking_old::vall::VallLibrarian::VallSectionConstIterator

protected

typedef BookIterator core::fragment::picking_old::vall::VallLibrarian::VallSectionIterator

protected

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

add a fragment evaluator (aka extent evaluator)

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::add_extent_eval().

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().

void core::fragment::picking_old::vall::VallLibrarian::add_fragment_gen ( VallFragmentGenCOP const &  gen )

inline

add a fragment generator (aka extent generator)

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::add_extent_gen().

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().

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

LessThan

predicate 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

clear list of evaluators

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::clear_extent_eval().

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

inline

clear list of generators

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::clear_extent_gen().

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

from	index of the first fragment in the list, indexing starts from '1'
to	index of the last fragment in the list (inclusive)
srfd_type	The BBTorsionSRFD type to use.

Returns

filled FragDataOPs if sort() was called successfully, otherwise empty FragDataOPs

Parameters

from	index of the first fragment in the list, indexing starts from '1'
to	index 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

the number of currently defined fragment evaluators

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::extent_eval().

Size core::fragment::picking_old::vall::VallLibrarian::n_fragment_gen ( ) const

inline

the number of currently defined fragment generators

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::extent_gen().

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

this function runs after main routine catalog() finishes

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::extent_eval().

Referenced by catalog().

void core::fragment::picking_old::vall::VallLibrarian::pre_catalog_ops ( VallLibrary const &  library )

private

this function runs before main routine in catalog() starts

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::extent_eval(), preallocate_, scores(), and core::fragment::picking_old::concepts::Library< Books >::size().

Referenced by catalog().

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

return scores container

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::bookmarks().

Referenced by catalog(), fragments(), n_scores(), and pre_catalog_ops().

Scores& core::fragment::picking_old::vall::VallLibrarian::scores ( )

inline

return scores container

References core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary >::bookmarks().

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

n	The number of fragments to get.
srfd_type	The 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:

• src/core/fragment/picking_old/vall/VallLibrarian.hh
• src/core/fragment/picking_old/vall/VallLibrarian.cc