Vall fragment library. More...

#include <VallLibrary.hh>

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

Public Types
typedef Super::Size	Size

typedef Super::BookConstIterator	BookConstIterator
	typedef for Library concept More...

typedef Super::BookIterator	BookIterator
	typedef for Library concept More...

typedef BookConstIterator	VallSectionConstIterator

typedef BookIterator	VallSectionIterator

Public Types inherited from core::fragment::picking_old::concepts::Library< VallSections >
typedef core::Size	Size

typedef Books::Book	Book

typedef Books::const_iterator	BookConstIterator

typedef Books::iterator	BookIterator

Public Member Functions
VallSection const &	operator[] (Size idx) const
	access a specific VallSection within this section, 1-based indexing More...

void	add_section (VallSection const &section)
	brief add a section to the end of this library More...

VallSection const &	last_section () const
	access the last section in thie library More...

VallSection &	last_section ()
	access the last section in thie library More...

Size	n_residues () const
	total number of residues in the library More...

void	reindex_sections ()
	re-index VallSections within this library so they number 1 .. n More...

void	reserve (Size n)
	ensure storage currently allocated for VallSections is at least the given size More...

void	tighten_memory (bool const sections_only=true)
	tighten memory usage More...

Public Member Functions inherited from core::fragment::picking_old::concepts::Library< VallSections >
	Library ()
	default constructor More...

	Library (VallSections const &books)
	Books constructor. More...

	~Library ()
	default destructor More...

BookConstIterator	begin () const
	return an iterator that points to the first Book in this library More...

BookIterator	begin ()
	return an iterator that points to the first Book in this library More...

BookConstIterator	end () const
	return an iterator that points beyond the last Book in this library More...

BookIterator	end ()
	return an iterator that points beyond the last Book in this library More...

Size	size () const
	number of books in the library More...

void	clear ()
	clear the library More...

Private Types
typedef core::fragment::picking_old::concepts::Library< VallSections >	Super

Private Member Functions
VallSections const &	sections () const
	return sections container More...

VallSections &	sections ()
	return sections container More...

Additional Inherited Members
Protected Member Functions inherited from core::fragment::picking_old::concepts::Library< VallSections >
VallSections const &	books () const
	return the books in this library More...

VallSections &	books ()
	return the books in this library More...

Detailed Description

Vall fragment library.

Member Typedef Documentation

◆ BookConstIterator

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

typedef for Library concept

◆ BookIterator

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

typedef for Library concept

◆ Size

typedef Super::Size core::fragment::picking_old::vall::VallLibrary::Size

◆ Super

typedef core::fragment::picking_old::concepts::Library< VallSections > core::fragment::picking_old::vall::VallLibrary::Super

private

◆ VallSectionConstIterator

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

◆ VallSectionIterator

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

Member Function Documentation

◆ add_section()

void core::fragment::picking_old::vall::VallLibrary::add_section ( VallSection const & section )

inline

brief add a section to the end of this library

References protocols::sparta::section(), sections(), and core::fragment::picking_old::concepts::Library< VallSections >::size().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

◆ last_section() [1/2]

VallSection& core::fragment::picking_old::vall::VallLibrary::last_section ( )

inline

access the last section in thie library

References sections().

◆ last_section() [2/2]

VallSection const& core::fragment::picking_old::vall::VallLibrary::last_section ( ) const

inline

access the last section in thie library

References sections().

◆ n_residues()

Size core::fragment::picking_old::vall::VallLibrary::n_residues ( ) const

inline

total number of residues in the library

References core::fragment::picking_old::concepts::Library< VallSections >::begin(), and core::fragment::picking_old::concepts::Library< VallSections >::end().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

◆ operator[]()

VallSection const& core::fragment::picking_old::vall::VallLibrary::operator[] ( Size idx ) const

inline

access a specific VallSection within this section, 1-based indexing

References sections().

◆ reindex_sections()

void core::fragment::picking_old::vall::VallLibrary::reindex_sections ( )

inline

re-index VallSections within this library so they number 1 .. n

References core::fragment::picking_old::concepts::Library< VallSections >::begin(), and core::fragment::picking_old::concepts::Library< VallSections >::end().

◆ reserve()

void core::fragment::picking_old::vall::VallLibrary::reserve ( Size n )

inline

ensure storage currently allocated for VallSections is at least the given size

References sections().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

◆ sections() [1/2]

VallSections& core::fragment::picking_old::vall::VallLibrary::sections ( )

inlineprivate

return sections container

References core::fragment::picking_old::concepts::Library< VallSections >::books().

◆ sections() [2/2]

VallSections const& core::fragment::picking_old::vall::VallLibrary::sections ( ) const

inlineprivate

return sections container

References core::fragment::picking_old::concepts::Library< VallSections >::books().

Referenced by add_section(), last_section(), operator[](), reserve(), and tighten_memory().

◆ tighten_memory()

void core::fragment::picking_old::vall::VallLibrary::tighten_memory ( bool const sections_only = true )

inline

tighten memory usage

Parameters

sections_only if true, only tightens memory per-section and skips the operation for the whole library

Shrinks the capacity of the library by calling VallSection::tighten_memory() for each section. If 'sections_only' is false, will additionally perform a swap of the library, effectively requiring a similar amount of memory as the current library object.

Warning: The Vall libraries can be very large, so set 'sections_only' false only if you won't be running on a constrained memory platform.

References core::fragment::picking_old::concepts::Library< VallSections >::begin(), core::fragment::picking_old::concepts::Library< VallSections >::end(), and sections().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

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

src/core/fragment/picking_old/vall/VallLibrary.hh

Public Types

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ BookConstIterator

◆ BookIterator

◆ Size

◆ Super

◆ VallSectionConstIterator

◆ VallSectionIterator

Member Function Documentation

◆ add_section()

◆ last_section() [1/2]

◆ last_section() [2/2]

◆ n_residues()

◆ operator[]()

◆ reindex_sections()

◆ reserve()

◆ sections() [1/2]

◆ sections() [2/2]

◆ tighten_memory()