protocols::frag_picker::VallProvider Class Reference

a vector of vall chunks More...

#include <VallProvider.hh>

Inheritance diagram for protocols::frag_picker::VallProvider:

Collaboration diagram for protocols::frag_picker::VallProvider:

Public Member Functions
	VallProvider ()
virtual	~VallProvider ()
Size	vallChunksFromLibrary (std::string const &filename, Size startline=1, 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...
Size	vallChunksFromLibraries (utility::vector1< std::string > const &fns)
Size	vallNumLines (std::string const &filename)
	Runs through the Vall and stores number of lines. More...
Size	size ()
	says how many chunks do we have More...
VallChunkOP	at (Size index)
	returns a certain chunk (starts from 1) More...
void	push_back (VallChunkOP what)
	adds a new chunk to this provider More...
Size	get_largest_chunk_size ()
	says what is the length of the largest chunk known to this provider More...
VallChunkOP	find_chunk (std::string, char, 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_
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

Definition at line 38 of file VallProvider.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 42 of file VallProvider.hh.

References cached_pose_id_, cached_profile_id_, and largest_chunk_size_.

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

virtual

Definition at line 57 of file VallProvider.cc.

Member Function Documentation

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

inline

returns a certain chunk (starts from 1)

Definition at line 64 of file VallProvider.hh.

References chunks_.

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

(

VallChunkOP

source_chunk)

cache a pose for a given chunk

Definition at line 80 of file VallProvider.cc.

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

Definition at line 107 of file VallProvider.cc.

References protocols::frag_picker::TR().

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

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

Detailed: If this VallProvider does not contain a desired

chunk, 0 is returned.

Definition at line 59 of file VallProvider.cc.

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

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

inline

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

Definition at line 75 of file VallProvider.hh.

References largest_chunk_size_.

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

inline

adds a new chunk to this provider

Definition at line 69 of file VallProvider.hh.

References chunks_.

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

inline

says how many chunks do we have

Definition at line 59 of file VallProvider.hh.

References chunks_.

Size protocols::frag_picker::VallProvider::vallChunksFromLibraries

(

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

fns)

Definition at line 135 of file VallProvider.cc.

References core::sequence::end.

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.

Definition at line 164 of file VallProvider.cc.

References core::chemical::ChemicalManager::get_instance(), core::pose::make_pose_from_sequence(), core::io::serialization::size(), core::scoring::hbonds::t(), and protocols::frag_picker::TR().

Size protocols::frag_picker::VallProvider::vallNumLines

(

std::string const &

filename)

Runs through the Vall and stores number of lines.

Definition at line 147 of file VallProvider.cc.

Member Data Documentation

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

private

Definition at line 95 of file VallProvider.hh.

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

private

Definition at line 96 of file VallProvider.hh.

Referenced by VallProvider().

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

private

Definition at line 94 of file VallProvider.hh.

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

private

Definition at line 93 of file VallProvider.hh.

Referenced by VallProvider().

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

private

Definition at line 91 of file VallProvider.hh.

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

Size protocols::frag_picker::VallProvider::largest_chunk_size_

private

Definition at line 92 of file VallProvider.hh.

Referenced by get_largest_chunk_size(), and VallProvider().

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

private

Definition at line 97 of file VallProvider.hh.

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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