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core::fragment::JumpingFrame Class Reference

JumpingFrame, so far there is nothing special about JumpingFrames. but I think we might want to have additionally information like the start and end residues that belong to a certain jump_nr.! okay: right now I require that the creator of a JumpingFrame sets start to the start-residue of the jump. More...

#include <JumpingFrame.hh>

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Public Member Functions

 JumpingFrame ()
 
 JumpingFrame (Size start, Size end, Size length)
 
virtual FrameOP clone () const
 convience — generate a matching FragData object dofs are unitialized! More...
 
virtual std::string type () const
 type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc) More...
 
- Public Member Functions inherited from core::fragment::NonContinuousFrame
 NonContinuousFrame (Size start, Size end, Size length)
 
virtual core::Size seqpos (core::Size intra_pos) const
 clone method, new frame with same alignment position, fragments are not copied! 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 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, FragDataOP frag1)
 
 Frame (core::Size start, core::Size length, SingleResidueFragDataOP srfd)
 
virtual FrameOP clone_with_frags ()
 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...
 
core::Size add_fragment (FragDataOP new_frag)
 add a fragment .. return new frag_nr More...
 
bool add_fragment (FragDataList 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...
 
FragDatafragment (core::Size frag_num)
 accessor for underlying FragData More...
 
FragDataCOP fragment_ptr (core::Size frag_num) const
 accessor for underlying FragData as owning ptr More...
 
FragDataOP fragment_ptr (core::Size frag_num)
 accessor for underlying FragData as owning ptr More...
 
bool is_valid () const
 a frame is considered valid if at least one fragment is contained and this fragment is also valid (not an empty template fragment) 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...
 
void shift_to (core::Size setting)
 set start position 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)
 generate_sub_frame of length from start ( internal numbers ) More...
 

Static Public Member Functions

static std::string _static_type_name ()
 

Additional Inherited Members

- Protected Member Functions inherited from core::fragment::NonContinuousFrame
void show_pos (std::ostream &out) const
 
PosListpos ()
 
PosList const & pos () const
 

Detailed Description

JumpingFrame, so far there is nothing special about JumpingFrames. but I think we might want to have additionally information like the start and end residues that belong to a certain jump_nr.! okay: right now I require that the creator of a JumpingFrame sets start to the start-residue of the jump.

Constructor & Destructor Documentation

core::fragment::JumpingFrame::JumpingFrame ( )
inline

Referenced by clone().

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

Member Function Documentation

static std::string core::fragment::JumpingFrame::_static_type_name ( )
inlinestatic
virtual FrameOP core::fragment::JumpingFrame::clone ( ) const
inlinevirtual

convience — generate a matching FragData object dofs are unitialized!

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

Reimplemented from core::fragment::Frame.

References core::fragment::Frame::end(), JumpingFrame(), core::fragment::Frame::length(), core::fragment::NonContinuousFrame::pos(), and core::fragment::Frame::start().

virtual std::string core::fragment::JumpingFrame::type ( ) const
inlinevirtual

type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc)

Reimplemented from core::fragment::Frame.

References _static_type_name().


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