Rosetta 3.4
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core::fragment::FragSet Class Reference

The FragSet: (Interface Definition -- Virtual BaseClass ) More...

#include <FragSet.hh>

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List of all members.

Public Member Functions

 FragSet ()
virtual ~FragSet ()
virtual FragSetOP clone () const =0
 clone and copy the pointer of all Frames (Frames will not be copied)
virtual FragSetOP empty_clone () const =0
 create an empty clone
virtual FrameIterator begin () const =0
 iterate over contents
virtual FrameIterator end () const =0
virtual Size frames (core::Size pos, FrameList &frames) const
 appends frames at sequence position pos to frames, returns nr of frames added
virtual Size region_simple (core::Size start, core::Size end, FrameList &frames) const
 returns fragments that exactly span seq_pos start...end
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
virtual Size region (kinematics::MoveMap const &move_map, core::Size start, core::Size end, core::Size min_overlap, core::Size min_length, FrameList &frames) const =0
 the region thing has to be thought-over. How do we really want to sample fragments? for now, we ignore everything in this call and just return frags that have "start" as there specified start() entry.
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.
Size max_pos () const
 returns the maximal sequence position that can be affected by fragments in this set
Size min_pos () const
 returns the first sequence position that can be affected by fragments in this set
Size max_frag_length () const
 returns the longest fragment stored in this FragSet.
void add (FrameOP aFrame)
 add a single frame. if compatible frame is already in set the frames will be merged
void add (FrameList const &frames)
 add all Frames in list
void add (FragSet const &frames)
 add all Frames in FragSet
void add (FragID const &)
 add single fragment
void add (FragID_List &list)
void insert_fragID_list (FragID_List &list)
 add all fragments in FragID_List
Size size () const
 returns total size--> counts together all frags in each frame
Size nr_frames () const
 counts number of frames ( slow! - it really counts )
virtual bool empty () const =0

Protected Member Functions

void set_max_frag_length (Size setting)
 setter for max_frag_length_
void set_max_pos (Size pos)
void set_min_pos (Size pos)
virtual void add_ (FrameOP aFrame)=0
 storage classes have to overload this one to add frames to their container

Friends

std::ostream & operator<< (std::ostream &out, FragSet const &frags)

Detailed Description

The FragSet: (Interface Definition -- Virtual BaseClass )


Constructor & Destructor Documentation

core::fragment::FragSet::FragSet ( ) [inline]
virtual core::fragment::FragSet::~FragSet ( ) [inline, virtual]

Member Function Documentation

void core::fragment::FragSet::add ( FrameOP  aFrame)
void core::fragment::FragSet::add ( FragID const &  frag_id)
void core::fragment::FragSet::add ( FragID_List list) [inline]

References insert_fragID_list().

void core::fragment::FragSet::add ( FrameList const &  frames)

add all Frames in list

void core::fragment::FragSet::add ( FragSet const &  frames)

add all Frames in FragSet

References begin(), and end().

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

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

Implemented in core::fragment::ConstantLengthFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.

virtual FrameIterator core::fragment::FragSet::begin ( ) const [pure virtual]
virtual FragSetOP core::fragment::FragSet::clone ( ) const [pure virtual]

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

Implemented in core::fragment::ConstantLengthFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.

Referenced by core::fragment::merge_frags().

virtual bool core::fragment::FragSet::empty ( ) const [pure virtual]
virtual FragSetOP core::fragment::FragSet::empty_clone ( ) const [pure virtual]
virtual FrameIterator core::fragment::FragSet::end ( ) const [pure virtual]
virtual Size core::fragment::FragSet::frames ( core::Size  pos,
FrameList frames 
) const [inline, virtual]

appends frames at sequence position pos to frames, returns nr of frames added

Reimplemented in core::fragment::OrderedFragSet.

References region_simple().

Referenced by core::fragment::merge_frags(), and protocols::loops::select_loop_frags().

void core::fragment::FragSet::generate_insert_map ( kinematics::MoveMap const &  mm,
InsertMap insert_map,
InsertSize insert_size 
) const [virtual]

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.

References make_table_of_pilot_apps::begin, core::sequence::end, core::kinematics::MoveMap::get_bb(), and core::fragment::tr().

Referenced by protocols::loops::select_loop_frags().

void core::fragment::FragSet::insert_fragID_list ( FragID_List list)

add all fragments in FragID_List

References core::fragment::tr().

Referenced by add().

Size core::fragment::FragSet::max_frag_length ( ) const [inline]
Size core::fragment::FragSet::max_pos ( ) const [inline]

returns the maximal sequence position that can be affected by fragments in this set

Referenced by core::fragment::FragSetCollection::add_fragset(), core::fragment::chop_fragments(), core::fragment::compute_per_residue_coverage(), and core::fragment::merge_frags().

Size core::fragment::FragSet::min_pos ( ) const [inline]

returns the first sequence position that can be affected by fragments in this set

Referenced by core::fragment::FragSetCollection::add_fragset().

Size core::fragment::FragSet::nr_frames ( ) const

counts number of frames ( slow! - it really counts )

References make_table_of_pilot_apps::begin, and core::sequence::end.

virtual Size core::fragment::FragSet::region ( kinematics::MoveMap const &  move_map,
core::Size  start,
core::Size  end,
core::Size  min_overlap,
core::Size  min_length,
FrameList frames 
) const [pure virtual]

the region thing has to be thought-over. How do we really want to sample fragments? for now, we ignore everything in this call and just return frags that have "start" as there specified start() entry.

Implemented in core::fragment::ConstantLengthFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.

Size core::fragment::FragSet::region_all ( core::Size  start,
core::Size  end,
core::Size  min_overlap,
core::Size  min_length,
FrameList frames 
) const [virtual]

return a list of frames that all sample the specified region, assume all motions are allowed

References core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by region_simple().

virtual Size core::fragment::FragSet::region_simple ( core::Size  start,
core::Size  end,
FrameList frames 
) const [inline, virtual]

returns fragments that exactly span seq_pos start...end

References region_all().

Referenced by frames().

void core::fragment::FragSet::set_max_frag_length ( Size  setting) [inline, protected]
void core::fragment::FragSet::set_max_pos ( Size  pos) [inline, protected]
void core::fragment::FragSet::set_min_pos ( Size  pos) [inline, protected]
Size core::fragment::FragSet::size ( ) const

returns total size--> counts together all frags in each frame

References make_table_of_pilot_apps::begin, and core::sequence::end.


Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
FragSet const &  frags 
) [friend]

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