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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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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) More...
 
virtual FragSetOP empty_clone () const
 create an empty clone More...
 
void read_fragment_file (std::string filename, Size top25=0, Size ncopies=1, bool bAnnotation=false)
 Loads the contents of <filename> into the ConstantLengthFragSet. More...
 
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 More...
 
FrameIterator begin () const
 iterate over contents More...
 
FrameIterator end () const
 
virtual bool empty () const
 
- Public Member Functions inherited from core::fragment::FragSet
 FragSet ()
 
virtual ~FragSet ()
 
virtual Size frames (core::Size pos, FrameList &frames) const
 appends frames at sequence position pos to frames, returns nr of frames added More...
 
virtual Size region_simple (core::Size start, core::Size end, FrameList &frames) const
 returns fragments that exactly span seq_pos start...end More...
 
virtual Size region_all (core::Size start, core::Size end, core::Size min_overlap, core::Size min_length, FrameList &frames) const
 return a list of frames that all sample the specified region, assume all motions are allowed More...
 
virtual void generate_insert_map (kinematics::MoveMap const &mm, InsertMap &insert_map, InsertSize &insert_size) const
 InsertMap and InsertSize gives quick overview which residues can be affected by fragments. insert_map — list of start-positions, insert_size corresponding list of longest fragment at position x. More...
 
Size max_pos () const
 returns the maximal sequence position that can be affected by fragments in this set More...
 
Size min_pos () const
 returns the first sequence position that can be affected by fragments in this set More...
 
Size max_frag_length () const
 returns the longest fragment stored in this FragSet. More...
 
void add (FrameOP aFrame)
 add a single frame. if compatible frame is already in set the frames will be merged More...
 
void add (FrameList const &frames)
 add all Frames in list More...
 
void add (FragSet const &frames)
 add all Frames in FragSet More...
 
void add (FragID const &)
 add single fragment More...
 
void add (FragID_List &list)
 
void insert_fragID_list (FragID_List &list)
 add all fragments in FragID_List More...
 
Size size () const
 returns total size–> counts together all frags in each frame More...
 
Size nr_frames () const
 counts number of frames ( slow! - it really counts ) More...
 

Protected Member Functions

virtual void add_ (FrameOP aframe)
 storage classes have to overload this one to add frames to their container More...
 
- Protected Member Functions inherited from core::fragment::FragSet
void set_max_frag_length (Size setting)
 setter for max_frag_length_ More...
 
void set_max_pos (Size pos)
 
void set_min_pos (Size pos)
 

Private Types

typedef FragSet Parent
 

Private Attributes

FrameList frames_
 

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

Member Typedef Documentation

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)
protectedvirtual

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
inlinevirtual

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
inlinevirtual

Implements core::fragment::FragSet.

References frames_.

virtual FragSetOP core::fragment::ConstantLengthFragSet::empty_clone ( ) const
inlinevirtual

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.

Member Data Documentation

FrameList core::fragment::ConstantLengthFragSet::frames_
private

Referenced by empty().


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