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protocols::frag_picker::VallProvider Class Reference

a vector of vall chunks More...

#include <VallProvider.hh>

Inheritance diagram for protocols::frag_picker::VallProvider:
Inheritance graph
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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< VallChunkOPchunks_
 
utility::vector1< std::string > vall_keys_
 
utility::vector1< core::Sizevall_start_line_
 
utility::vector1< core::Sizevall_end_line_
 
utility::vector1< core::Sizevall_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
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
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 
)

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

core::Size protocols::frag_picker::VallProvider::vallNumLines ( std::string const &  filename)

Runs through the Vall and stores number of lines.

Member Data Documentation

core::pose::PoseOP protocols::frag_picker::VallProvider::cached_pose_
private
std::string protocols::frag_picker::VallProvider::cached_pose_id_
private

Referenced by VallProvider().

core::sequence::SequenceProfileOP protocols::frag_picker::VallProvider::cached_profile_
private
std::string protocols::frag_picker::VallProvider::cached_profile_id_
private

Referenced by VallProvider().

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

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

core::Size protocols::frag_picker::VallProvider::largest_chunk_size_
private
std::string protocols::frag_picker::VallProvider::poly_A_seq_
private
utility::vector1<core::Size> protocols::frag_picker::VallProvider::vall_end_line_
private
utility::vector1<std::string> protocols::frag_picker::VallProvider::vall_keys_
private

Referenced by get_vall_by_key(), and get_vall_count().

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

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