readme

ViennaRNA-1.6.1

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Folding Modes:

(1) default mode:
    start structure is open chain
    stop structure is minimum free enegy structure
    example: hairpin.log, traj
     ../Kinfold --log hpin --num 10 <./hpin.in>& traj

(2) multi-stop mode:
    start structure is open chain
    stop structure(s) are 2nd and following lines in hpin.in
    example: hairpin.e.log, traj.e
     ../Kinfold --stop --log hpin.e --num 10 <./hpin.in>& traj.e

(3) refolding mode:
    start structure is 2nd line in hpin.in
    stop structure(s) are 3rd and following lines in hpin.in
    example: hairpin.ae.log, traj.ae
     ../Kinfold --start --stop --log hpin.ae --num 10 <./hpin.in>& traj.ae

if you don't want to log the trajectories use option --silent
(trajectory files can get petty huge)

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Output:

(A) log files (on each line you find):
    randon seed
    stop-structure-label or O ( for didn't reach stop-structure(s) )
    first passage time
    stop-structure if stop-structure-label equals O

(B) trajectory files (on each line you find):
    structure
    energy
    time
    number of neighbours of structure (only with --verbose)
    code for the move                 (only with --verbose)
     (i=base pair insert move,
      d=base pair delete move,
      s,S=base pair shift move,
      I=base pair double insert move (only with --noLP)
      D=base pair double delete move (only with --noLP)
     )
    code for type of structure        (only with --verbose)
     (1=strict local minimum,
      2=degenerate local minimum,
      0=anything else
     )
    stop-structure-label or O ( for didn't reach stop-structure(s) )

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canonical example: hpin.nolp, traj.nolp
 ../Kinfold --verbose --noLP --num 10 --log hpin.nolp < ./hpin.in > traj.nolp