protocols::frag_picker::VallProvider Class Reference

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

VallProvider()

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

inline

References cached_pose_id_, cached_profile_id_, and largest_chunk_size_.

~VallProvider()

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

overridedefault

Member Function Documentation

at()

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

inline

returns a certain chunk (starts from 1)

References chunks_.

cache_pose()

core::pose::PoseOP protocols::frag_picker::VallProvider::cache_pose

(

VallChunkOP

source_chunk

)

cache a pose for a given chunk

References protocols::frag_picker::TR().

cache_profile()

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().

find_chunk()

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 protocols::frag_picker::TR().

get_largest_chunk_size()

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_.

get_self_ptr() [1/2]

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

inline

get_self_ptr() [2/2]

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

inline

get_self_weak_ptr() [1/2]

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

inline

get_self_weak_ptr() [2/2]

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

inline

get_vall_by_key()

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

inline

References vall_keys_.

get_vall_count()

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

inline

References vall_keys_.

get_vall_end_line_by_key()

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

inline

References vall_end_line_.

get_vall_last_residue_key_by_key()

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

inline

References vall_last_residue_key_.

get_vall_start_line_by_key()

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

inline

References vall_start_line_.

push_back()

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

inline

adds a new chunk to this provider

References chunks_.

size()

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

inline

says how many chunks do we have

References chunks_.

vallChunksFromLibraries()

core::Size protocols::frag_picker::VallProvider::vallChunksFromLibraries

(

utility::vector1< std::string > const &

fns

)

vallChunksFromLibrary()

core::Size protocols::frag_picker::VallProvider::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.

References protocols::abinitio::filename(), core::pose::make_pose_from_sequence(), protocols::hybridization::t, and protocols::frag_picker::TR().

vallNumLines()

core::Size protocols::frag_picker::VallProvider::vallNumLines

(

std::string const &

filename

)

Runs through the Vall and stores number of lines.

References protocols::abinitio::filename().

Member Data Documentation

cached_pose_

core::pose::PoseOP protocols::frag_picker::VallProvider::cached_pose_

private

cached_pose_id_

std::string protocols::frag_picker::VallProvider::cached_pose_id_

private

Referenced by VallProvider().

cached_profile_

core::sequence::SequenceProfileOP protocols::frag_picker::VallProvider::cached_profile_

private

cached_profile_id_

std::string protocols::frag_picker::VallProvider::cached_profile_id_

private

Referenced by VallProvider().

chunks_

utility::vector1<VallChunkOP> protocols::frag_picker::VallProvider::chunks_

private

Referenced by at(), push_back(), and size().

largest_chunk_size_

core::Size protocols::frag_picker::VallProvider::largest_chunk_size_

private

Referenced by get_largest_chunk_size(), and VallProvider().

poly_A_seq_

std::string protocols::frag_picker::VallProvider::poly_A_seq_

private

vall_end_line_

utility::vector1<core::Size> protocols::frag_picker::VallProvider::vall_end_line_

private

Referenced by get_vall_end_line_by_key().

vall_keys_

utility::vector1<std::string> protocols::frag_picker::VallProvider::vall_keys_

private

Referenced by get_vall_by_key(), and get_vall_count().

vall_last_residue_key_

utility::vector1<core::Size> protocols::frag_picker::VallProvider::vall_last_residue_key_

private

Referenced by get_vall_last_residue_key_by_key().

vall_start_line_

utility::vector1<core::Size> protocols::frag_picker::VallProvider::vall_start_line_

private

Referenced by get_vall_start_line_by_key().

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

• src/protocols/frag_picker/VallProvider.hh
• src/protocols/frag_picker/VallProvider.cc