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core::fragment::NonContinuousFrame Class Reference

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>

Inheritance diagram for core::fragment::NonContinuousFrame:
Inheritance graph
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Public Member Functions

 NonContinuousFrame (Size start, Size end, Size length)
 
FrameOP clone () const override
 clone method, new frame with same alignment position, fragments are not copied! More...
 
core::Size seqpos (core::Size intra_pos) const override
 translate intra-frame position into sequence position. (trivial for base-class) More...
 
bool moves_residue (core::Size pos) const override
 
bool is_continuous () const override
 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...
 
void shift_to (core::Size setting) override
 shift to new start position ( change end accordingly ) More...
 
void shift_by (int offset) override
 shift frame by offset relative to current start position ( change end accordingly ) More...
 
void show (std::ostream &) const override
 
void read (std::istream &) override
 
bool align (core::id::SequenceMapping const &map) override
 change frames residue numbers accoriding to map More...
 
- Public Member Functions inherited from core::fragment::Frame
 ~Frame () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. 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...
 
BaseCacheUnitcache (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
 
PosListpos ()
 
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...
 
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< SizePosList
 
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

Member Typedef Documentation

typedef utility::vector1< Size > core::fragment::NonContinuousFrame::PosList
private

Constructor & Destructor Documentation

core::fragment::NonContinuousFrame::NonContinuousFrame ( Size  start,
Size  end,
Size  length 
)
inline

Member Function Documentation

bool core::fragment::NonContinuousFrame::align ( core::id::SequenceMapping const &  map)
overridevirtual

change frames residue numbers accoriding to map

change frames residue numbers according to map

Reimplemented from core::fragment::Frame.

FrameOP core::fragment::NonContinuousFrame::clone ( ) const
overridevirtual

clone method, new frame with same alignment position, fragments are not copied!

Reimplemented from core::fragment::Frame.

Reimplemented in core::fragment::JumpingFrame.

References core::sequence::end, and protocols::loops::start.

bool core::fragment::NonContinuousFrame::is_continuous ( ) const
inlineoverridevirtual

true if frame is continuous

Reimplemented from core::fragment::Frame.

bool core::fragment::NonContinuousFrame::moves_residue ( core::Size  pos) const
inlineoverridevirtual

Reimplemented from core::fragment::Frame.

References pos(), and pos_.

PosList& core::fragment::NonContinuousFrame::pos ( )
inlineprotected
PosList const& core::fragment::NonContinuousFrame::pos ( ) const
inlineprotected
void core::fragment::NonContinuousFrame::read ( std::istream &  in)
overridevirtual

Reimplemented from core::fragment::Frame.

core::Size core::fragment::NonContinuousFrame::seqpos ( core::Size  intra_pos) const
inlineoverridevirtual

translate intra-frame position into sequence position. (trivial for base-class)

Reimplemented from core::fragment::Frame.

References core::fragment::Frame::length(), and pos_.

void core::fragment::NonContinuousFrame::set_pos ( Size  intra_pos,
Size  setting 
)
inline

assign sequence position or jump_nr to internal position pos

References core::fragment::Frame::length(), and pos_.

void core::fragment::NonContinuousFrame::shift_by ( int  offset)
overridevirtual

shift frame by offset relative to current start position ( change end accordingly )

Reimplemented from core::fragment::Frame.

void core::fragment::NonContinuousFrame::shift_to ( core::Size  setting)
overridevirtual

shift to new start position ( change end accordingly )

Reimplemented from core::fragment::Frame.

void core::fragment::NonContinuousFrame::show ( std::ostream &  out) const
overridevirtual

Reimplemented from core::fragment::Frame.

void core::fragment::NonContinuousFrame::show_pos ( std::ostream &  out) const
protected

Member Data Documentation

PosList core::fragment::NonContinuousFrame::pos_
private

stores the residue number's or jump_nr's associated with the SRFDs in FragData

Referenced by moves_residue(), pos(), seqpos(), and set_pos().


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