Rosetta 3.4
Public Member Functions
protocols::frag_picker::VallProvider Class Reference

a vector of vall chunks More...

#include <VallProvider.hh>

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List of all members.

Public Member Functions

 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.
Size vallChunksFromLibraries (utility::vector1< std::string > const &fns)
Size vallNumLines (std::string const &filename)
 Runs through the Vall and stores number of lines.
Size size ()
 says how many chunks do we have
VallChunkOP at (Size index)
 returns a certain chunk (starts from 1)
void push_back (VallChunkOP what)
 adds a new chunk to this provider
Size get_largest_chunk_size ()
 says what is the length of the largest chunk known to this provider
VallChunkOP find_chunk (std::string, char, Size)
 tries to find a chunk defined by PDB id, chain id and a residue sequence id
core::sequence::SequenceProfileOP cache_profile (VallChunkOP source_chunk)
 cache a sequence profile for a given chunk
core::pose::PoseOP cache_pose (VallChunkOP source_chunk)
 cache a pose for a given chunk

Detailed Description

a vector of vall chunks


Constructor & Destructor Documentation

protocols::frag_picker::VallProvider::VallProvider ( ) [inline]

Member Function Documentation

VallChunkOP protocols::frag_picker::VallProvider::at ( Size  index) [inline]

returns a certain chunk (starts from 1)

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,
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.

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

void protocols::frag_picker::VallProvider::push_back ( VallChunkOP  what) [inline]

adds a new chunk to this provider

Size protocols::frag_picker::VallProvider::size ( ) [inline]

says how many chunks do we have

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

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.

References core::chemical::ChemicalManager::get_instance(), core::pose::make_pose_from_sequence(), 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.


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