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protocols::frags::TorsionFragment Class Reference

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

#include <TorsionFragment.hh>

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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
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().


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