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

#include <ConstantLengthFragSet.hh>

Inheritance diagram for core::fragment::ConstantLengthFragSet:

Public Member Functions
	ConstantLengthFragSet (Size frag_length)

	ConstantLengthFragSet (Size frag_length, std::string filename)

	ConstantLengthFragSet ()

	~ConstantLengthFragSet () override

	ConstantLengthFragSet (FragSet const &fragments)

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

FragSetOP	empty_clone () const override
	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 (std::string const &filename, std::string const &first_line, std::istream &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 override
	there is only one Frame per position, end / max_overlap are ignored More...

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 override
	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...

ConstFrameIterator	begin () const override
	iterate over contents More...

ConstFrameIterator	end () const override

FrameIterator	nonconst_begin () override
	iterate over contents More...

FrameIterator	nonconst_end () override

bool	empty () const override

Public Member Functions inherited from core::fragment::FragSet
	FragSet ()

	~FragSet () override=default

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 (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 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	add_ (FrameOP aframe) override
	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

typedef FragSet core::fragment::ConstantLengthFragSet::Parent

private

Constructor & Destructor Documentation

core::fragment::ConstantLengthFragSet::ConstantLengthFragSet ( Size frag_length )

inline

References core::fragment::FragSet::set_max_frag_length().

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

core::fragment::ConstantLengthFragSet::ConstantLengthFragSet ( )

inline

core::fragment::ConstantLengthFragSet::~ConstantLengthFragSet ( )

overridedefault

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

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

Member Function Documentation

void core::fragment::ConstantLengthFragSet::add_ ( FrameOP aFrame )

overrideprotectedvirtual

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

Implements core::fragment::FragSet.

ConstFrameIterator core::fragment::ConstantLengthFragSet::begin ( ) const

overridevirtual

iterate over contents

Implements core::fragment::FragSet.

FragSetOP core::fragment::ConstantLengthFragSet::clone ( ) const

inlineoverridevirtual

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

Implements core::fragment::FragSet.

bool core::fragment::ConstantLengthFragSet::empty ( ) const

inlineoverridevirtual

Implements core::fragment::FragSet.

References frames_.

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

inlineoverridevirtual

create an empty clone

Implements core::fragment::FragSet.

ConstFrameIterator core::fragment::ConstantLengthFragSet::end ( ) const

overridevirtual

Implements core::fragment::FragSet.

FrameIterator core::fragment::ConstantLengthFragSet::nonconst_begin ( )

overridevirtual

iterate over contents

Implements core::fragment::FragSet.

FrameIterator core::fragment::ConstantLengthFragSet::nonconst_end ( )

overridevirtual

Implements core::fragment::FragSet.

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

overridevirtual

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 from core::fragment::FragSet.

References protocols::mean_field::max(), and protocols::mean_field::min().

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

void core::fragment::ConstantLengthFragSet::read_fragment_stream	(	std::string const &	filename,
		std::string const &	first_line,
		std::istream &	data,
		Size	top25 = `0`,
		Size	ncopies = `1`,
		bool	bAnnotation = `false`
	)

References protocols::cluster::calibur::aa, protocols::mean_field::add(), core::conformation::membrane::in, protocols::mean_field::max(), core::scoring::omega, protocols::hybridization::score, and core::fragment::tr().

Size core::fragment::ConstantLengthFragSet::region	(	kinematics::MoveMap const &	mm,
		core::Size	start,
		core::Size	end,
		core::Size	,
		core::Size	,
		FrameList &	frames
	)		const

overridevirtual

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

Implements core::fragment::FragSet.

Member Data Documentation

FrameList core::fragment::ConstantLengthFragSet::frames_

private

Referenced by empty().

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

src/core/fragment/ConstantLengthFragSet.hh
src/core/fragment/ConstantLengthFragSet.cc

Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation