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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
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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

Constructor & Destructor Documentation

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

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

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

References set_size_and_nbb().

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

Member Function Documentation

TorsionFragmentOP protocols::frags::TorsionFragment::clone ( ) const
char protocols::frags::TorsionFragment::get_secstruct ( core::Size const  pos) const
inline
char protocols::frags::TorsionFragment::get_sequence ( core::Size const  pos) const
inline
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<<().

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::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_.

core::Size protocols::frags::TorsionFragment::nbb ( ) const
inline
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>>().

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>>().

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

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

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: