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

#include <FragSet.hh>

Inheritance diagram for core::fragment::FragSet:

Public Member Functions
	FragSet ()

	~FragSet () override=default

virtual FragSetOP	clone () const =0
	clone and copy the pointer of all Frames (Frames will not be copied) More...

virtual FragSetOP	empty_clone () const =0
	create an empty clone More...

virtual ConstFrameIterator	begin () const =0
	iterate over contents More...

virtual ConstFrameIterator	end () const =0

virtual FrameIterator	nonconst_begin ()=0
	iterate over contents More...

virtual FrameIterator	nonconst_end ()=0

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 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. More...

virtual Size	overlapping_with_region (kinematics::MoveMap const &mm, core::Size start, core::Size end, core::Size min_overlap, core::Size min_length, FrameList &frames) const
	returns the number and list of all fragment alignment frames that somehow overlap with the given region (also allows those frames that start before the region and reach into it) 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 (FrameCOP 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...

virtual bool	empty () const =0

virtual void	shift_by (int offset)
	shift all frames in FragSet by offset More...

int	global_offset () const

void	global_offset (int)
	resets global_offset of FragSet and shifts FragSet if necessary by calling shift_to More...

FragSetOP	clone_shifted (int) const

Protected Member Functions
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)

virtual void	add_ (FrameOP aFrame)=0
	storage classes have to overload this one to add frames to their container More...

Private Attributes
Size	min_pos_

Size	max_pos_

Size	max_frag_length_

int	global_offset_
	global offset of current Fragmentset. Default = 0 More...

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

core::fragment::FragSet::~FragSet ( )

overridedefault

Member Function Documentation

void core::fragment::FragSet::add ( FrameCOP aFrame )

add a single frame. if compatible frame is already in set the frames will be merged

References core::sequence::end, protocols::loops::start, and core::fragment::tr().

Referenced by core::fragment::chop_fragments(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::jumping::DisulfPairingLibrary::generate_jump_frags(), protocols::jumping::PairingLibrary::generate_jump_frags(), protocols::loops::select_loop_frags(), core::fragment::steal_constant_length_frag_set_from_pose(), and core::fragment::steal_frag_set_from_pose().

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

add all Frames in list

References protocols::mean_field::add().

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

add all Frames in FragSet

References protocols::mean_field::add(), begin(), and end().

void core::fragment::FragSet::add ( FragID const & frag_id )

add single fragment

References core::sequence::end, core::fragment::FragID::fragment_ptr(), core::fragment::FragID::frame(), core::fragment::FragID::id(), protocols::denovo_design::movers::new_id(), protocols::loops::start, and core::fragment::tr().

void core::fragment::FragSet::add ( FragID_List & list )

inline

References insert_fragID_list().

virtual void core::fragment::FragSet::add_ ( FrameOP aFrame )

protectedpure virtual

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

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

virtual ConstFrameIterator core::fragment::FragSet::begin ( ) const

pure virtual

iterate over contents

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

Referenced by add(), core::fragment::chop_fragments(), core::fragment::SecondaryStructure::compute_fractions(), core::fragment::compute_per_residue_coverage(), core::fragment::operator<<(), and core::fragment::FragmentIO::write_data().

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::MinimalFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.

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

FragSetOP core::fragment::FragSet::clone_shifted ( int offset ) const

References core::sequence::end.

virtual bool core::fragment::FragSet::empty ( ) const

pure virtual

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

virtual FragSetOP core::fragment::FragSet::empty_clone ( ) const

pure virtual

create an empty clone

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

virtual ConstFrameIterator core::fragment::FragSet::end ( ) const

pure virtual

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

Referenced by add(), core::fragment::chop_fragments(), core::fragment::SecondaryStructure::compute_fractions(), core::fragment::compute_per_residue_coverage(), core::fragment::operator<<(), and core::fragment::FragmentIO::write_data().

virtual Size core::fragment::FragSet::frames	(	core::Size	pos,
		FrameList &	frames
	)		const

inlinevirtual

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

Reimplemented in core::fragment::MinimalFragSet, and 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 core::sequence::end, core::kinematics::MoveMap::get_bb(), and core::fragment::tr().

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

int core::fragment::FragSet::global_offset ( ) const

inline

References global_offset_.

Referenced by core::fragment::SecondaryStructure::compute_fractions().

void core::fragment::FragSet::global_offset ( int offset )

resets global_offset of FragSet and shifts FragSet if necessary by calling shift_to

References core::fragment::tr().

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

add all fragments in FragID_List

References protocols::mean_field::add(), and core::fragment::tr().

Referenced by add().

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

inline

returns the longest fragment stored in this FragSet.

References max_frag_length_.

Referenced by core::fragment::chop_fragments(), protocols::medal::MedalMover::compute_per_residue_probabilities(), core::fragment::ConstantLengthFragSet::ConstantLengthFragSet(), and core::fragment::steal_constant_length_frag_set_from_pose().

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

inline

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

References max_pos_.

Referenced by core::fragment::chop_fragments(), core::fragment::SecondaryStructure::compute_fractions(), 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

References min_pos_.

virtual FrameIterator core::fragment::FragSet::nonconst_begin ( )

pure virtual

iterate over contents

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

virtual FrameIterator core::fragment::FragSet::nonconst_end ( )

pure virtual

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

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

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

References core::sequence::end.

Size core::fragment::FragSet::overlapping_with_region	(	kinematics::MoveMap const &	mm,
		core::Size	start,
		core::Size	end,
		core::Size	min_overlap,
		core::Size	min_length,
		FrameList &	frames
	)		const

virtual

returns the number and list of all fragment alignment frames that somehow overlap with the given region (also allows those frames that start before the region and reach into it)

Reimplemented in core::fragment::ConstantLengthFragSet.

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::MinimalFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.