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Rosetta
2020.50
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Rosetta
2020.50
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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>
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... | |
| 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... | |
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 |
| 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... | |
| 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) |
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.
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inline |
Referenced by clone().
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inlinestatic |
Referenced by core::fragment::FragFactory::FragFactory(), and type().
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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().
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inlineoverridevirtual |
type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc)
Reimplemented from core::fragment::Frame.
References _static_type_name().
1.8.7