a vector of vall chunks More...

#include <VallProvider.hh>

Inheritance diagram for protocols::frag_picker::VallProvider:

Public Member Functions
	VallProvider ()

	~VallProvider () override

VallProviderCOP	get_self_ptr () const

VallProviderOP	get_self_ptr ()

VallProviderCAP	get_self_weak_ptr () const

VallProviderAP	get_self_weak_ptr ()

core::Size	vallChunksFromLibrary (std::string const &filename, core::Size startline=1, core::Size endline=0)
	Vall reader THe defaults should ensure that the file is fully read if startline and endline ar not specified. endline = 0 means read to the end. More...

core::Size	vallChunksFromLibraries (utility::vector1< std::string > const &fns)

core::Size	vallNumLines (std::string const &filename)
	Runs through the Vall and stores number of lines. More...

core::Size	size ()
	says how many chunks do we have More...

VallChunkOP	at (core::Size index)
	returns a certain chunk (starts from 1) More...

void	push_back (VallChunkOP what)
	adds a new chunk to this provider More...

core::Size	get_largest_chunk_size ()
	says what is the length of the largest chunk known to this provider More...

core::Size	get_vall_count ()

std::string	get_vall_by_key (core::Size index)

core::Size	get_vall_start_line_by_key (core::Size index)

core::Size	get_vall_end_line_by_key (core::Size index)

core::Size	get_vall_last_residue_key_by_key (core::Size index)

VallChunkOP	find_chunk (std::string, char, core::Size)
	tries to find a chunk defined by PDB id, chain id and a residue sequence id More...

core::sequence::SequenceProfileOP	cache_profile (VallChunkOP source_chunk)
	cache a sequence profile for a given chunk More...

core::pose::PoseOP	cache_pose (VallChunkOP source_chunk)
	cache a pose for a given chunk More...

Private Attributes
utility::vector1< VallChunkOP >	chunks_

utility::vector1< std::string >	vall_keys_

utility::vector1< core::Size >	vall_start_line_

utility::vector1< core::Size >	vall_end_line_

utility::vector1< core::Size >	vall_last_residue_key_

core::Size	largest_chunk_size_

std::string	cached_profile_id_

core::sequence::SequenceProfileOP	cached_profile_

core::pose::PoseOP	cached_pose_

std::string	cached_pose_id_

std::string	poly_A_seq_

Detailed Description

a vector of vall chunks

Constructor & Destructor Documentation

protocols::frag_picker::VallProvider::VallProvider ( )

inline

References cached_pose_id_, cached_profile_id_, and largest_chunk_size_.

protocols::frag_picker::VallProvider::~VallProvider ( )

overridedefault

Member Function Documentation

VallChunkOP protocols::frag_picker::VallProvider::at ( core::Size index )

inline

returns a certain chunk (starts from 1)

References chunks_.

core::pose::PoseOP protocols::frag_picker::VallProvider::cache_pose ( VallChunkOP source_chunk )

cache a pose for a given chunk

References protocols::frag_picker::TR().

core::sequence::SequenceProfileOP protocols::frag_picker::VallProvider::cache_profile ( VallChunkOP source_chunk )

cache a sequence profile for a given chunk

References protocols::frag_picker::TR().

VallChunkOP protocols::frag_picker::VallProvider::find_chunk	(	std::string	pdb_id,
		char	chain_id,
		core::Size	residue_id
	)

tries to find a chunk defined by PDB id, chain id and a residue sequence id

If this VallProvider does not contain a desired chunk, 0 is returned.

References core::pack::dunbrack::c, and protocols::frag_picker::TR().

core::Size protocols::frag_picker::VallProvider::get_largest_chunk_size ( )

inline

says what is the length of the largest chunk known to this provider

References largest_chunk_size_.

VallProviderCOP protocols::frag_picker::VallProvider::get_self_ptr ( ) const

inline

VallProviderOP protocols::frag_picker::VallProvider::get_self_ptr ( )

inline

VallProviderCAP protocols::frag_picker::VallProvider::get_self_weak_ptr ( ) const

inline

VallProviderAP protocols::frag_picker::VallProvider::get_self_weak_ptr ( )

inline

std::string protocols::frag_picker::VallProvider::get_vall_by_key ( core::Size index )

inline

References vall_keys_.

core::Size protocols::frag_picker::VallProvider::get_vall_count ( )

inline

References vall_keys_.

core::Size protocols::frag_picker::VallProvider::get_vall_end_line_by_key ( core::Size index )

inline

References vall_end_line_.

core::Size protocols::frag_picker::VallProvider::get_vall_last_residue_key_by_key ( core::Size index )

inline

References vall_last_residue_key_.

core::Size protocols::frag_picker::VallProvider::get_vall_start_line_by_key ( core::Size index )

inline

References vall_start_line_.

void protocols::frag_picker::VallProvider::push_back ( VallChunkOP what )

inline

adds a new chunk to this provider

References chunks_.

core::Size protocols::frag_picker::VallProvider::size ( )

inline

says how many chunks do we have

References chunks_.

core::Size protocols::frag_picker::VallProvider::vallChunksFromLibraries ( utility::vector1< std::string > const & fns )

core::Size protocols::frag_picker::VallProvider::vallChunksFromLibrary	(	std::string const &	filename,
		core::Size	startline = `1`,
		core::Size	endline = `0`
	)