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

#include <VallLibrarian.hh>

Inheritance diagram for core::fragment::picking_old::vall::VallLibrarian:

Collaboration diagram for core::fragment::picking_old::vall::VallLibrarian:

Public Types
typedef core::Size	Size

typedef core::fragment::FragDataList	FragDataList

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::owning_ptr < eval::VallFragmentEval >	ExtentEvalOP

typedef utility::pointer::owning_ptr < eval::VallFragmentEvalconst >	ExtentEvalCOP

typedef utility::pointer::owning_ptr < gen::VallFragmentGen >	ExtentGenOP

typedef utility::pointer::owning_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...

virtual	~VallLibrarian ()
	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...

FragDataList	top_fragments (Size const n, BBTorsionSRFD const &srfd_type=BBTorsionSRFD()) const
	get top 'N' fragments from prior catalog() More...

FragDataList	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...

Static Private Attributes
static basic::Tracer	TR_
	static Tracer instance for this class 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.

Definition at line 59 of file VallLibrarian.hh.

Member Typedef Documentation

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

Definition at line 85 of file VallLibrarian.hh.

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

Definition at line 84 of file VallLibrarian.hh.

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

Definition at line 93 of file VallLibrarian.hh.

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

Definition at line 94 of file VallLibrarian.hh.

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

Definition at line 92 of file VallLibrarian.hh.

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

Definition at line 89 of file VallLibrarian.hh.

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

Definition at line 88 of file VallLibrarian.hh.

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

Definition at line 97 of file VallLibrarian.hh.

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

Definition at line 91 of file VallLibrarian.hh.

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

Definition at line 90 of file VallLibrarian.hh.

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

Definition at line 96 of file VallLibrarian.hh.

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

Definition at line 74 of file VallLibrarian.hh.

typedef core::fragment::FragDataList core::fragment::picking_old::vall::VallLibrarian::FragDataList

Definition at line 73 of file VallLibrarian.hh.

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

Definition at line 75 of file VallLibrarian.hh.

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

Definition at line 86 of file VallLibrarian.hh.

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

Definition at line 87 of file VallLibrarian.hh.

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

Definition at line 108 of file VallLibrarian.hh.

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

Definition at line 109 of file VallLibrarian.hh.

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

Definition at line 107 of file VallLibrarian.hh.

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

Definition at line 71 of file VallLibrarian.hh.

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

private

Definition at line 65 of file VallLibrarian.hh.

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

Definition at line 77 of file VallLibrarian.hh.

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

Definition at line 104 of file VallLibrarian.hh.

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

Definition at line 103 of file VallLibrarian.hh.

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

protected

Definition at line 120 of file VallLibrarian.hh.

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

Definition at line 106 of file VallLibrarian.hh.

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

Definition at line 105 of file VallLibrarian.hh.

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

protected

Definition at line 119 of file VallLibrarian.hh.

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

Definition at line 78 of file VallLibrarian.hh.

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

protected

Definition at line 117 of file VallLibrarian.hh.

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

protected

Definition at line 118 of file VallLibrarian.hh.

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

protected

Definition at line 115 of file VallLibrarian.hh.

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

protected

Definition at line 116 of file VallLibrarian.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 37 of file VallLibrarian.cc.

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

virtual

default destructor

Definition at line 44 of file VallLibrarian.cc.

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)

Definition at line 199 of file VallLibrarian.hh.

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)

Definition at line 175 of file VallLibrarian.hh.

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)

Definition at line 224 of file VallLibrarian.hh.

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)

Definition at line 233 of file VallLibrarian.hh.

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 TR_.

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

inline

clear list of evaluators

Definition at line 206 of file VallLibrarian.hh.

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

Definition at line 182 of file VallLibrarian.hh.

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

VallLibrarian::FragDataList 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 FragDataList if sort() was called successfully, otherwise empty FragDataList

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 FragDataList if sort() was called successfully, otherwise empty FragDataList

Definition at line 61 of file VallLibrarian.cc.

References core::sequence::end, core::fragment::picking_old::vall::extent_to_fragdata(), scores(), core::io::serialization::size(), and TR_.

Referenced by top_fragments().

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

inline

the number of currently defined fragment evaluators

Definition at line 213 of file VallLibrarian.hh.

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

Definition at line 189 of file VallLibrarian.hh.

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

Definition at line 252 of file VallLibrarian.hh.

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

Definition at line 131 of file VallLibrarian.cc.

References core::sequence::end, and 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

Definition at line 117 of file VallLibrarian.cc.

References core::sequence::end, 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

Definition at line 154 of file VallLibrarian.hh.

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

Definition at line 165 of file VallLibrarian.hh.

References preallocate_.

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

inline

return scores container

Definition at line 286 of file VallLibrarian.hh.

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

Definition at line 293 of file VallLibrarian.hh.

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

VallLibrarian::FragDataList 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.

Definition at line 49 of file VallLibrarian.cc.

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

Definition at line 313 of file VallLibrarian.hh.

Referenced by pre_catalog_ops(), and preallocate().

basic::Tracer core::fragment::picking_old::vall::VallLibrarian::TR_

staticprivate

static Tracer instance for this class

Definition at line 317 of file VallLibrarian.hh.

Referenced by catalog(), and fragments().

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

Public Types

Public Member Functions

Protected Types

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation