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protocols::frags::TorsionFragmentLibrary Class Reference

a class for classic Rosetta fragment library More...

#include <TorsionFragment.hh>

Inheritance diagram for protocols::frags::TorsionFragmentLibrary:
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Public Types

typedef core::Real Real
 
typedef core::Size Size
 

Public Member Functions

 TorsionFragmentLibrary ()
 default constructor More...
 
 ~TorsionFragmentLibrary () override
 
 TorsionFragmentLibrary (core::Size const size_in)
 constructor with size (number of residue positions) More...
 
core::Size size () const
 number of residues More...
 
SingleResidueTorsionFragmentLibraryoperator[] (core::Size const pos)
 overloaded [] operator to get framgnet pieces for a certain residue position More...
 
SingleResidueTorsionFragmentLibrary
const & 
operator[] (core::Size const pos) const
 overloaded [] operator to get framgnet pieces for a certain residue position (access only) More...
 
void resize (core::Size const new_size)
 change the size of fragment library More...
 
void delete_residue (core::Size const seqpos)
 
void shift (int const current2desired_offset)
 
void copy_fragments (TorsionFragmentLibrary const &src)
 
bool read_file (std::string const &name, core::Size const frag_size, core::Size const nbb)
 initialize fragment data from a classic Rosetta fragment library More...
 
bool derive_from_src_lib (core::Size const my_size, core::Size const src_size, TorsionFragmentLibraryCOP src_lib_op)
 
bool derive_from_src_lib (core::Size const my_size, core::Size const src_size, TorsionFragmentLibrary const &src_lib)
 extract a fragment library with smaller fragment size from the one with larger lize More...
 
void print (std::ostream &os) const
 Show some info – right now just for debugging, ie not a full dump of the library. More...
 
void clear ()
 

Private Attributes

utility::vector1
< SingleResidueTorsionFragmentLibraryOP
fragments_
 a collection of SingleResidueTorsionFragmentLibrary owning pointers More...
 

Detailed Description

a class for classic Rosetta fragment library

essentially a collection of SingleResidueTorsionFragmentLibrary (indexed by residue position)

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::frags::TorsionFragmentLibrary::TorsionFragmentLibrary ( )
inline

default constructor


Code duplication alert: TorsionFragment is going to be phased out Please avoid writing any new code using these classes: look in core/fragment/ instead look in /protocols/abinitio/FragmentMover for usage examples


protocols::frags::TorsionFragmentLibrary::~TorsionFragmentLibrary ( )
overridedefault
protocols::frags::TorsionFragmentLibrary::TorsionFragmentLibrary ( core::Size const  size_in)
inline

constructor with size (number of residue positions)

References resize().

Member Function Documentation

void protocols::frags::TorsionFragmentLibrary::clear ( )
inline

References fragments_.

Referenced by protocols::frags::operator>>().

void protocols::frags::TorsionFragmentLibrary::copy_fragments ( TorsionFragmentLibrary const &  src)
void protocols::frags::TorsionFragmentLibrary::delete_residue ( core::Size const  seqpos)
bool protocols::frags::TorsionFragmentLibrary::derive_from_src_lib ( core::Size const  my_size,
core::Size const  src_size,
TorsionFragmentLibraryCOP  src_lib_op 
)
bool protocols::frags::TorsionFragmentLibrary::derive_from_src_lib ( core::Size const  my_size,
core::Size const  src_size,
TorsionFragmentLibrary const &  src_lib 
)

extract a fragment library with smaller fragment size from the one with larger lize

for example, 1-mer library can ben extracted from 3-mer library. This function is set up in a general way that both sizes of smaller fragment and larger fragment can be flexibly specified by my_size and src_size. Also, the source library does not have to contain fragment data for every residue position. For example, for loop modeling, we only need fragment for loop segment and after this function is called, smaller library is created only for regions in which there is data in the larger library. Lastly, smaller fragment is aligned in the center of larger fragment to have data extracted.

References fragments_, protocols::frags::TorsionFragment::get_secstruct(), protocols::frags::TorsionFragment::get_sequence(), protocols::frags::TorsionFragment::get_torsion(), protocols::frags::TorsionFragment::nbb(), resize(), protocols::frags::SingleResidueTorsionFragmentLibrary::size(), and size().

SingleResidueTorsionFragmentLibrary& protocols::frags::TorsionFragmentLibrary::operator[] ( core::Size const  pos)
inline

overloaded [] operator to get framgnet pieces for a certain residue position

References fragments_.

SingleResidueTorsionFragmentLibrary const& protocols::frags::TorsionFragmentLibrary::operator[] ( core::Size const  pos) const
inline

overloaded [] operator to get framgnet pieces for a certain residue position (access only)

References fragments_.

void protocols::frags::TorsionFragmentLibrary::print ( std::ostream &  os) const

Show some info – right now just for debugging, ie not a full dump of the library.

Show size info about library

References fragments_, and size().

bool protocols::frags::TorsionFragmentLibrary::read_file ( std::string const &  filename,
core::Size const  frag_size,
core::Size const  nbb 
)

initialize fragment data from a classic Rosetta fragment library

frag_size is the size of fragment in the library and nbb is the number of backbone torision angles stored in each fragment, for protein, this will be 3. Return false if there is a reading error and all the data which have been stored will be erased.

References protocols::cluster::calibur::aa, protocols::frags::SingleResidueTorsionFragmentLibrary::append_fragment(), resize(), and protocols::frags::TR().

void protocols::frags::TorsionFragmentLibrary::resize ( core::Size const  new_size)
inline
void protocols::frags::TorsionFragmentLibrary::shift ( int const  current2desired_offset)

after calling, the size will be the oldsize + current2desired_offset

References fragments_.

core::Size protocols::frags::TorsionFragmentLibrary::size ( ) const
inline

Member Data Documentation

utility::vector1< SingleResidueTorsionFragmentLibraryOP > protocols::frags::TorsionFragmentLibrary::fragments_
private

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