protocols::frags::TorsionFragment Class Reference

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

#include <TorsionFragment.hh>

Inheritance diagram for protocols::frags::TorsionFragment:

Collaboration diagram for protocols::frags::TorsionFragment:

Public Member Functions
	TorsionFragment (Size const size_in, Size const nbb_in)
	constructor, fragment_size (3mer or 9mer) and number of backbone torsions(3 for protein) More...
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...
Real	get_torsion (Size const pos, Size const tor) const
	get value for specific torsion in this piece of fragment More...
char	get_secstruct (Size const pos) const

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...

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]

Constructor & Destructor Documentation

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

inline

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

References torsions_.

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

virtual

Member Function Documentation

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

inline

References secstruct_.

Referenced by protocols::frags::TorsionFragmentLibrary::derive_from_src_lib().

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().

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::set_secstruct(), core::pose::Pose::set_torsion(), and core::io::serialization::size().

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

inline

number of backbone torsions.

References torsions_.

Referenced by protocols::frags::TorsionFragmentLibrary::derive_from_src_lib().

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

inline

set secstruct for this position

References secstruct_.

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_.

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

inline

fragment size, 3mer or 9mer?

References torsions_.

Member Data Documentation

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

private

secstruct, dimensioned as fragment size

Referenced by get_secstruct(), and set_secstruct().

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(), nbb(), set_torsion(), size(), and TorsionFragment().

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

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