Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | List of all members
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>

Inheritance diagram for core::fragment::JumpingFrame:
Inheritance graph
[legend]

Public Member Functions

 JumpingFrame ()
 
 JumpingFrame (Size start, Size end, Size length)
 
FrameOP clone () const override
 convience — generate a matching FragData object dofs are unitialized! More...
 
std::string type () const override
 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)
 
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...
 
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...
 

Static Public Member Functions

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

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
FrameOP core::fragment::JumpingFrame::clone ( ) const
inlineoverridevirtual

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::NonContinuousFrame.

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

std::string core::fragment::JumpingFrame::type ( ) const
inlineoverridevirtual

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: