Rosetta 3.4
Public Member Functions | Protected Member Functions
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>

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List of all members.

Public Member Functions

 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!
virtual bool moves_residue (core::Size pos) const
virtual bool is_continuous () const
 true if frame is continuous
void set_pos (Size intra_pos, Size setting)
 assign sequence position or jump_nr to internal position pos
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

Protected Member Functions

void show_pos (std::ostream &out) const
PosListpos ()
PosList const & pos () const

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


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) [virtual]

change frames residue numbers accoriding to map

change frames residue numbers according to map

Reimplemented from core::fragment::Frame.

virtual bool core::fragment::NonContinuousFrame::is_continuous ( ) const [inline, virtual]

true if frame is continuous

Reimplemented from core::fragment::Frame.

virtual bool core::fragment::NonContinuousFrame::moves_residue ( core::Size  pos) const [inline, virtual]

Reimplemented from core::fragment::Frame.

References pos().

PosList& core::fragment::NonContinuousFrame::pos ( ) [inline, protected]
PosList const& core::fragment::NonContinuousFrame::pos ( ) const [inline, protected]
void core::fragment::NonContinuousFrame::read ( std::istream &  in) [virtual]

Reimplemented from core::fragment::Frame.

virtual core::Size core::fragment::NonContinuousFrame::seqpos ( core::Size  intra_pos) const [inline, virtual]

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

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

Reimplemented from core::fragment::Frame.

References core::fragment::Frame::length().

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().

Referenced by protocols::jumping::JumpSample::generate_jump_frames().

void core::fragment::NonContinuousFrame::show ( std::ostream &  out) const [virtual]

Reimplemented from core::fragment::Frame.

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

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