a class for classic Rosetta fragment library More...

#include <TorsionFragment.hh>

Public Types
typedef core::Real	Real

typedef core::Size	Size

Public Member Functions
	TorsionFragmentLibrary ()
	default constructor More...

virtual	~TorsionFragmentLibrary ()

	TorsionFragmentLibrary (Size const size_in)
	constructor with size (number of residue positions) More...

Size	size () const
	number of residues More...

SingleResidueTorsionFragmentLibrary &	operator[] (Size const pos)
	overloaded [] operator to get framgnet pieces for a certain residue position More...

SingleResidueTorsionFragmentLibrary const &	operator[] (Size const pos) const
	overloaded [] operator to get framgnet pieces for a certain residue position (access only) More...

void	resize (Size const new_size)
	change the size of fragment library More...

void	delete_residue (Size const seqpos)

void	shift (int const current2desired_offset)

void	copy_fragments (TorsionFragmentLibrary const &src)

bool	read_file (std::string const name, Size const frag_size, Size const nbb)
	initialize fragment data from a classic Rosetta fragment library More...

bool	derive_from_src_lib (Size const my_size, Size const src_size, TorsionFragmentLibraryCOP src_lib_op)

bool	derive_from_src_lib (Size const my_size, 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

typedef core::Real protocols::frags::TorsionFragmentLibrary::Real

typedef core::Size protocols::frags::TorsionFragmentLibrary::Size

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 ( )

virtual

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

References fragments_, resize(), and size().

Referenced by protocols::frags::FragLib::copy_fragments().

void protocols::frags::TorsionFragmentLibrary::delete_residue ( Size const seqpos )

References fragments_, size(), and protocols::frags::TR.

bool protocols::frags::TorsionFragmentLibrary::derive_from_src_lib	(	Size const	my_size,
		Size const	src_size,
		TorsionFragmentLibraryCOP	src_lib_op
	)

bool protocols::frags::TorsionFragmentLibrary::derive_from_src_lib	(	Size const	my_size,
		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(), runtime_assert, protocols::frags::SingleResidueTorsionFragmentLibrary::size(), and size().

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

inline

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

References fragments_.

SingleResidueTorsionFragmentLibrary const& protocols::frags::TorsionFragmentLibrary::operator[] ( 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,
		Size const	frag_size,
		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::frags::SingleResidueTorsionFragmentLibrary::append_fragment(), chain, getline(), neighbors, pdb, resize(), secstruct, torsion(), and protocols::frags::TR.