JumpingFrame is a discontinuous frame i.e, the SRFDs stored in the FragData objects can be applied to residues anywhere a 5 7 9 Frame of a FragData containing three BBTorsionSRFDs would change torsions of 5 7 9 a 5 32 2 Frame of a FragData containing two BBTorsionSRFD and on JumpSRFD would change torsions of 5 and 32 and the RT of jump_nr 2 note that in the latter case the 2 is not coding for a residue number! More...

#include <JumpingFrame.hh>

Public Member Functions
	NonContinuousFrame (Size start, Size end, Size length)

virtual FrameOP	clone () const
	clone method, new frame with same alignment position, fragments are not copied! More...

virtual core::Size	seqpos (core::Size intra_pos) const
	translate intra-frame position into sequence position. (trivial for base-class) More...

virtual bool	moves_residue (core::Size pos) const

virtual bool	is_continuous () const
	true if frame is continuous More...

void	set_pos (Size intra_pos, Size setting)
	assign sequence position or jump_nr to internal position pos More...

virtual void	shift_to (core::Size setting)
	shift to new start position ( change end accordingly ) More...

virtual void	shift_by (int offset)
	shift frame by offset relative to current start position ( change end accordingly ) More...

virtual void	show (std::ostream &) const

virtual void	read (std::istream &)

virtual bool	align (core::id::SequenceMapping const &map)
	change frames residue numbers accoriding to map More...

Public Member Functions inherited from core::fragment::Frame
virtual	~Frame ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	Frame ()

	Frame (core::Size begin, core::Size end, core::Size nr_res)

	Frame (core::Size start, core::Size length)

	Frame (core::Size start)

	Frame (core::Size start, FragDataCOP const &frag1)

	Frame (core::Size start, core::Size length, SingleResidueFragDataOP srfd)

virtual FrameOP	clone_with_frags () const
	clone method, new frame with same alignment position, fragments are not copied! More...

virtual FrameOP	clone_with_template ()
	clone method, new frame with same alignment position, one fragments is copied as template ( valid() == false ) More...

virtual std::string	type () const
	type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc) More...

core::Size	add_fragment (FragDataCOP new_frag)
	add a fragment .. return new frag_nr More...

bool	add_fragment (FragDataCOPs new_frags)
	add all fragments in list More...

FragData const &	fragment (core::Size frag_num) const
	delete a fragment: Attention: all data in the FragCache is invalidated ( and deleted ) it would be complicated to change this behaviour. Thus, it is desirable to avoid using delete_fragment() altogether. Faster: Make a new Frame and add all fragments you are interested in. More...

FragDataCOP	fragment_ptr (core::Size frag_num) const
	accessor for underlying FragData More...

bool	is_valid () const
	accessor for underlying FragData as owning ptr More...

core::Size	apply (kinematics::MoveMap const &, core::Size frag_num, pose::Pose &pose) const
	insert fragment frag_num into pose More...

core::Size	apply (core::Size frag_num, pose::Pose &pose) const
	insert fragment frag_num into pose — ignore movemap More...

core::Size	apply_ss (kinematics::MoveMap const &, core::Size frag_num, std::string &ss) const
	change ss-string according to sec-struct info in fragments More...

bool	steal (pose::Pose const &pose)
	obtain fragment from pose at frame position More...

core::Size	is_applicable (kinematics::MoveMap const &) const
	is the Frame applicable to the pose with the given movemap? More...

core::Size	frag_id (core::Size frag_num) const
	a unique id for every fragment in the list. his is silly, but would enable later on to avoid cache_clearence on deletion of FragData entries in this case, we would require that the ID of a certain fragment never changes, even if the position in FragList changes More...

void	fragment_as_pose (core::Size frag_num, pose::Pose &pose, chemical::ResidueTypeSetCAP restype_set) const
	returns a (small) pose with fragment ( continous from seqpos 1 ... nr_res_affected() ) More...

core::Size	nr_frags () const
	number of fragments attached to this frame More...

void	clear ()
	remove all valid fragments, a template fragment will be left over More...

bool	contains_seqpos (core::Size seqpos) const
	whether this fragment contains a certain position More...

core::Size	start () const
	first seqpos of this frame More...

core::Size	end () const
	last sequence position affected by this frame More...

core::Size	stop () const
	/// More...

core::Size	nr_res_affected (kinematics::MoveMap const &mm) const
	number of residues affected by this frame More...

core::Size	length () const
	number of residues in this frame ( for continuous frames it is the same as end()-start() + 1 ) More...

BaseCacheUnit &	cache (std::string tag, BaseCacheUnitOP const &new_cache) const
	return handle to cached data stored under "tag" shouldn't be called directly More...

void	clone_cache_data (Frame const &source, core::Size sid, core::Size nid)
	copies all entries in the Frame-Cache for fragment "sid" of Frame "source" to fragment "nid" of "this" frame More...

virtual void	show_classic (std::ostream &out) const

virtual void	show_header (std::ostream &out) const

bool	is_mergeable (Frame const &other) const

bool	merge (Frame const &other)

FrameOP	generate_sub_frame (Size length, Size start=1) const
	generate_sub_frame of length from start ( internal numbers ) More...

Protected Member Functions
void	show_pos (std::ostream &out) const

PosList &	pos ()

PosList const &	pos () const

Protected Member Functions inherited from core::fragment::Frame
virtual void	show_fragments (std::ostream &out) const
	NOT IMPLEMENTED YET: generate_sub_frame according to mapping ( residue numbers ) returns NULL if mapping invalid. More...

virtual bool	is_compatible (FragDataCOP new_frag) const
	is a FragData object compatible with the already stored ones ? you can only add instances of FragData to the same Frame that are compatible, i.e., that contain the same class of FragData, e.g., based on BBTorsionSRFD, if you want to have different fragment for other dof's at the same sequence position create a new Frame. Users of the fragment-core are aware that multiple Frames for the same sequence position may exist. More...

void	init_length (core::Size start, core::Size end, core::Size length)

Private Types
typedef utility::vector1< Size >	PosList

typedef Frame	Parent

Private Attributes
PosList	pos_
	stores the residue number's or jump_nr's associated with the SRFDs in FragData More...

Additional Inherited Members
Static Public Member Functions inherited from core::fragment::Frame
static std::string	_static_type_name ()

Detailed Description

JumpingFrame is a discontinuous frame i.e, the SRFDs stored in the FragData objects can be applied to residues anywhere a 5 7 9 Frame of a FragData containing three BBTorsionSRFDs would change torsions of 5 7 9 a 5 32 2 Frame of a FragData containing two BBTorsionSRFD and on JumpSRFD would change torsions of 5 and 32 and the RT of jump_nr 2 note that in the latter case the 2 is not coding for a residue number!

what is meaning of start() and end() ? If some of the positions are actually jump_nr should we ignore them for the start() / end() question ? or should we store which positions are jumps and translate into residue numbers from jump_nr ? could a MixedFrame contain Frames MixedFrame – > non-cont-Frame, JumpFrame