Rosetta 3.4
Public Member Functions | Protected Member Functions
core::fragment::ConstantLengthFragSet Class Reference

A set of fragments that contains fragments of a constant length read in from a fragment file. More...

#include <ConstantLengthFragSet.hh>

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List of all members.

Public Member Functions

 ConstantLengthFragSet (Size frag_length)
 ConstantLengthFragSet (Size frag_length, std::string filename)
 ConstantLengthFragSet ()
 ~ConstantLengthFragSet ()
 ConstantLengthFragSet (FragSet const &fragments)
virtual FragSetOP clone () const
 clone and copy the pointer of all Frames (Frames will not be copied)
virtual FragSetOP empty_clone () const
 create an empty clone
void read_fragment_file (std::string filename, Size top25=0, Size ncopies=1, bool bAnnotation=false)
 Loads the contents of <filename> into the ConstantLengthFragSet.
void read_fragment_stream (utility::io::izstream &data, Size top25=0, Size ncopies=1, bool bAnnotation=false)
Size region (kinematics::MoveMap const &mm, core::Size start, core::Size end, core::Size, core::Size, FrameList &frames) const
 there is only one Frame per position, end / max_overlap are ignored
FrameIterator begin () const
 iterate over contents
FrameIterator end () const
virtual bool empty () const

Protected Member Functions

virtual void add_ (FrameOP aframe)
 storage classes have to overload this one to add frames to their container

Detailed Description

A set of fragments that contains fragments of a constant length read in from a fragment file.

Note:
this object is a simple implementation of the FragSet
for custom fragments, check out https://robetta.bakerlab.org/fragmentsubmit.jsp

example: ninemers = ConstantLengthFragSet(9) ninemers.read_fragment_file("test9_fragments") See also: Pose ClassicFragmentMover


Constructor & Destructor Documentation

core::fragment::ConstantLengthFragSet::ConstantLengthFragSet ( Size  frag_length) [inline]
core::fragment::ConstantLengthFragSet::ConstantLengthFragSet ( Size  frag_length,
std::string  filename 
)
core::fragment::ConstantLengthFragSet::ConstantLengthFragSet ( ) [inline]

Referenced by clone(), and empty_clone().

core::fragment::ConstantLengthFragSet::~ConstantLengthFragSet ( )
core::fragment::ConstantLengthFragSet::ConstantLengthFragSet ( FragSet const &  fragments)

Member Function Documentation

void core::fragment::ConstantLengthFragSet::add_ ( FrameOP  aFrame) [protected, virtual]

storage classes have to overload this one to add frames to their container

Implements core::fragment::FragSet.

FrameIterator core::fragment::ConstantLengthFragSet::begin ( ) const [virtual]

iterate over contents

Implements core::fragment::FragSet.

virtual FragSetOP core::fragment::ConstantLengthFragSet::clone ( ) const [inline, virtual]

clone and copy the pointer of all Frames (Frames will not be copied)

Implements core::fragment::FragSet.

References ConstantLengthFragSet().

virtual bool core::fragment::ConstantLengthFragSet::empty ( ) const [inline, virtual]
virtual FragSetOP core::fragment::ConstantLengthFragSet::empty_clone ( ) const [inline, virtual]

create an empty clone

Implements core::fragment::FragSet.

References ConstantLengthFragSet().

FrameIterator core::fragment::ConstantLengthFragSet::end ( ) const [virtual]
void core::fragment::ConstantLengthFragSet::read_fragment_file ( std::string  filename,
Size  top25 = 0,
Size  ncopies = 1,
bool  bAnnotation = false 
)

Loads the contents of <filename> into the ConstantLengthFragSet.

example: ninemers.read_fragment_file("test9_fragments") See also: ConstantLengthFragSet Pose Pose.omega Pose.phi Pose.psi ClassicFragmentMover

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio().

void core::fragment::ConstantLengthFragSet::read_fragment_stream ( utility::io::izstream &  data,
Size  top25 = 0,
Size  ncopies = 1,
bool  bAnnotation = false 
)
Size core::fragment::ConstantLengthFragSet::region ( kinematics::MoveMap const &  mm,
core::Size  start,
core::Size  end,
core::Size  ,
core::Size  ,
FrameList frames 
) const [virtual]

there is only one Frame per position, end / max_overlap are ignored

Implements core::fragment::FragSet.

References core::sequence::end.


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