Rosetta: protocols::frags::TorsionFragment Class Reference

a class for single piece of torsion fragment More...

#include <TorsionFragment.hh>

Inheritance diagram for protocols::frags::TorsionFragment:

Inheritance graph

Public Types
typedef core::Real	Real

typedef core::Size	Size

Public Member Functions
	TorsionFragment ()
	constructor, fragment_size (3mer or 9mer) and number of backbone torsions(3 for protein) More...

	TorsionFragment (TorsionFragment const &src)

TorsionFragmentOP	clone () const

	TorsionFragment (Size const size_in, Size const nbb_in)

void	set_size_and_nbb (Size const size, Size const nbb)

virtual	~TorsionFragment ()

Size	size () const
	fragment size, 3mer or 9mer? More...

Size	nbb () const
	number of backbone torsions. More...

void	insert (core::pose::Pose &pose, Size const begin) const
	insert this piece of fragment to a pose at position "begin" More...

void	set_torsion (Size const pos, Size const tor, Real const setting)
	set value for specific torsion in this piece of fragment. More...

void	set_secstruct (Size const pos, char const setting)
	set secstruct for this position More...

char	get_secstruct (Size const pos) const

void	set_sequence (Size const pos, char const setting)
	set seq for this position More...

char	get_sequence (Size const pos) const

Real	get_torsion (Size const pos, Size const tor) const
	get value for specific torsion in this piece of fragment More...

Private Attributes
utility::vector1 < utility::vector1< Real > >	torsions_
	torsion angles, the first dimension is fragment size, the second dimension is number of backbone torsions. More...

utility::vector1< char >	secstruct_
	secstruct, dimensioned as fragment size More...

utility::vector1< char >	sequence_
	original fragment sequence, dimensioned as fragment size More...

Detailed Description

a class for single piece of torsion fragment

It stores torsion angles and secondary structure. Torsions are stored as vector of vector, such as TorsionFragment[frag_size][n_bb_torsion]; SS are stored as vector, such as TorsionFragment[frag_length]

Member Typedef Documentation

typedef core::Real protocols::frags::TorsionFragment::Real

typedef core::Size protocols::frags::TorsionFragment::Size

Constructor & Destructor Documentation

protocols::frags::TorsionFragment::TorsionFragment ( )

inline

constructor, fragment_size (3mer or 9mer) and number of backbone torsions(3 for protein)

Referenced by clone().

protocols::frags::TorsionFragment::TorsionFragment ( TorsionFragment const & src )

protocols::frags::TorsionFragment::TorsionFragment	(	Size const	size_in,
		Size const	nbb_in
	)

inline

References set_size_and_nbb().

protocols::frags::TorsionFragment::~TorsionFragment ( )

virtual

Member Function Documentation

TorsionFragmentOP protocols::frags::TorsionFragment::clone ( ) const

References TorsionFragment().

char protocols::frags::TorsionFragment::get_secstruct ( Size const pos ) const

inline

References secstruct_.

Referenced by protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(), and protocols::frags::operator<<().

char protocols::frags::TorsionFragment::get_sequence ( Size const pos ) const

inline

References sequence_.

Referenced by protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(), and protocols::frags::operator<<().

Real protocols::frags::TorsionFragment::get_torsion	(	Size const	pos,
		Size const	tor
	)		const

inline

get value for specific torsion in this piece of fragment

References torsions_.

Referenced by protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(), and protocols::frags::operator<<().

void protocols::frags::TorsionFragment::insert	(	core::pose::Pose &	pose,
		Size const	begin
	)		const

insert this piece of fragment to a pose at position "begin"

call pose.set_torsion which maps TorsionID to DOF_ID, so it is safe to use even if the folding direction is not standard as N to C.

References core::id::BB, core::pose::Pose::conformation(), core::pose::Pose::residue(), secstruct_, core::pose::Pose::set_secstruct(), core::pose::Pose::set_torsion(), core::conformation::Conformation::set_torsion_angle(), size(), and torsions_.

Size protocols::frags::TorsionFragment::nbb ( ) const

inline

number of backbone torsions.

References torsions_.

Referenced by protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(), and protocols::frags::operator<<().

void protocols::frags::TorsionFragment::set_secstruct	(	Size const	pos,
		char const	setting
	)

inline

set secstruct for this position

References secstruct_.

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

void protocols::frags::TorsionFragment::set_sequence	(	Size const	pos,
		char const	setting
	)

inline

set seq for this position

References sequence_.

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

void protocols::frags::TorsionFragment::set_size_and_nbb	(	Size const	size,
		Size const	nbb
	)

inline

References secstruct_, sequence_, size(), and torsions_.

Referenced by protocols::frags::operator>>(), and TorsionFragment().

void protocols::frags::TorsionFragment::set_torsion	(	Size const	pos,
		Size const	tor,
		Real const	setting
	)

inline

set value for specific torsion in this piece of fragment.

References torsions_.

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

Size protocols::frags::TorsionFragment::size ( ) const

inline

fragment size, 3mer or 9mer?

References torsions_.

Referenced by insert(), protocols::frags::operator<<(), and set_size_and_nbb().

Member Data Documentation

utility::vector1< char > protocols::frags::TorsionFragment::secstruct_

private

secstruct, dimensioned as fragment size

Referenced by get_secstruct(), insert(), set_secstruct(), and set_size_and_nbb().

utility::vector1< char > protocols::frags::TorsionFragment::sequence_

private

original fragment sequence, dimensioned as fragment size

Referenced by get_sequence(), set_sequence(), and set_size_and_nbb().

utility::vector1< utility::vector1< Real > > protocols::frags::TorsionFragment::torsions_

private

torsion angles, the first dimension is fragment size, the second dimension is number of backbone torsions.

Referenced by get_torsion(), insert(), nbb(), set_size_and_nbb(), set_torsion(), and size().

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

src/protocols/frags/TorsionFragment.hh
src/protocols/frags/TorsionFragment.cc