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Rosetta 3.5
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Rosetta 3.5
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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) | |
| 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... | |
| FragData & | fragment (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... | |
| 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) |
| 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 |
| PosList & | pos () |
| PosList const & | pos () const |
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.
Definition at line 115 of file JumpingFrame.hh.
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inline |
Definition at line 118 of file JumpingFrame.hh.
Referenced by clone().
Definition at line 121 of file JumpingFrame.hh.
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inlinestatic |
Definition at line 134 of file JumpingFrame.hh.
Referenced by core::fragment::FragFactory::FragFactory(), and type().
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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.
Definition at line 128 of file JumpingFrame.hh.
References core::fragment::Frame::end(), JumpingFrame(), core::fragment::Frame::length(), core::fragment::NonContinuousFrame::pos(), and core::fragment::Frame::start().
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inlinevirtual |
type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc)
Reimplemented from core::fragment::Frame.
Definition at line 138 of file JumpingFrame.hh.
References _static_type_name().
1.8.4