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:

Collaboration diagram for core::fragment::ConstantLengthFragSet:

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

Definition at line 68 of file ConstantLengthFragSet.hh.

Member Typedef Documentation

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

private

Definition at line 69 of file ConstantLengthFragSet.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 73 of file ConstantLengthFragSet.hh.

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

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

Definition at line 64 of file ConstantLengthFragSet.cc.

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

inline

Definition at line 79 of file ConstantLengthFragSet.hh.

Referenced by clone(), and empty_clone().

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

Definition at line 62 of file ConstantLengthFragSet.cc.

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

Definition at line 70 of file ConstantLengthFragSet.cc.

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

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.

Definition at line 99 of file ConstantLengthFragSet.cc.

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

virtual

iterate over contents

Implements core::fragment::FragSet.

Definition at line 246 of file ConstantLengthFragSet.cc.

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.

Definition at line 85 of file ConstantLengthFragSet.hh.

References ConstantLengthFragSet().

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

inlinevirtual

Implements core::fragment::FragSet.

Definition at line 132 of file ConstantLengthFragSet.hh.

References frames_.

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

inlinevirtual

create an empty clone

Implements core::fragment::FragSet.

Definition at line 90 of file ConstantLengthFragSet.hh.

References ConstantLengthFragSet().

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

virtual

Implements core::fragment::FragSet.

Definition at line 250 of file ConstantLengthFragSet.cc.

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

Definition at line 109 of file ConstantLengthFragSet.cc.

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`
	)

Definition at line 122 of file ConstantLengthFragSet.cc.

References core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), and core::chemical::tr().

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