protocols::frags::TorsionFragment Class Reference

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

#include <TorsionFragment.hh>

Inheritance diagram for protocols::frags::TorsionFragment:

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 (core::Size const size_in, core::Size const nbb_in)
void	set_size_and_nbb (core::Size const size, core::Size const nbb)
	~TorsionFragment () override
core::Size	size () const
	fragment size, 3mer or 9mer? More...
core::Size	nbb () const
	number of backbone torsions. More...
void	insert (core::pose::Pose &pose, core::Size const begin) const
	insert this piece of fragment to a pose at position "begin" More...
void	set_torsion (core::Size const pos, core::Size const tor, Real const setting)
	set value for specific torsion in this piece of fragment. More...
void	set_secstruct (core::Size const pos, char const setting)
	set secstruct for this position More...
char	get_secstruct (core::Size const pos) const
void	set_sequence (core::Size const pos, char const setting)
	set seq for this position More...
char	get_sequence (core::Size const pos) const
Real	get_torsion (core::Size const pos, core::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

Real

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

Size

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

Constructor & Destructor Documentation

TorsionFragment() [1/3]

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

inline

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

TorsionFragment() [2/3]

protocols::frags::TorsionFragment::TorsionFragment

(

TorsionFragment const &

src

)

TorsionFragment() [3/3]

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

inline

References set_size_and_nbb().

~TorsionFragment()

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

overridedefault

Member Function Documentation

clone()

TorsionFragmentOP protocols::frags::TorsionFragment::clone

(

)

const

get_secstruct()

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

inline

References secstruct_.

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

get_sequence()

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

inline

References sequence_.

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

get_torsion()

Real protocols::frags::TorsionFragment::get_torsion ( core::Size const  pos, core::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<<().

insert()

void protocols::frags::TorsionFragment::insert	(	core::pose::Pose &	pose,
		core::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::conformation::Residue::atom_index(), core::id::BB, core::pose::Pose::conformation(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), secstruct_, core::pose::Pose::set_secstruct(), core::pose::Pose::set_torsion(), core::conformation::Conformation::set_torsion_angle(), size(), and torsions_.

nbb()

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

inline

number of backbone torsions.

References torsions_.

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

set_secstruct()

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

inline

set secstruct for this position

References secstruct_.

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

set_sequence()

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

inline

set seq for this position

References sequence_.

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

set_size_and_nbb()

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

inline

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

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

set_torsion()

void protocols::frags::TorsionFragment::set_torsion ( core::Size const  pos, core::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()

core::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

secstruct_

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().

sequence_

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().

torsions_

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().

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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