1 # Last changed Time-stamp: <2010-06-24 13:37:42 ivo>
2 # $Id kinfold.ggo,v 1.1 2008/07/02 15:42:20 ivo Exp $
4 purpose "Kinetic Folding Program for Nucleic Acids"
5 args "--default-optional --include-getopt"
8 option "dangle" d "<0|1|2> set dangling end model to (none|normal|double)" values="0","1","2" int default="2"
9 option "Temp" T "simulation temperature" float default="37"
10 option "Par" P "read energy-parameter-file" string typestr="filename"
11 option "logML" - "use logarithmic multiloop energies instead of linear" flag on
13 option "noShift" - "turn off shift-moves" flag off
14 option "noLP" - "forbid structures with isolated base-pairs" flag off
16 option "seed" - "set random number seed specify 3 integers as int=int=int" string default="clock"
17 option "time" - "set maxtime of simulation" float default="500"
18 option "num" - "set number of trajectories" int default="1"
19 option "start" - "read start structure from stdin (otherwise use open chain)" flag off
20 option "stop" - "read stop structure(s) from stdin (optherwise use MFE)" flag off
21 option "met" - "use Metropolis rule for rates (not Kawasaki rule)" flag off
22 option "fpt" - "compute first passage time (stop when a stop-structure is reached)" flag on
23 option "grow" - "grow chain every <float> time units" float default="0"
24 option "glen" - "initial size of growing chain" int default="15"
25 option "phi" - "set phi value" double hidden
26 option "pbounds" - "specify 3 floats for phi_min, phi_inc, phi_max in the form <d1=d2=d3>" string hidden
28 option "log" - "set basename of log-file" string typestr="filename" default="kinout"
29 option "silent" q "no output to stdout" flag off
30 option "verbose" v "more information to stdout" flag off
31 option "lmin" - "output only local minima to stdout" flag off
32 option "cut" - "output structures with E <= <float> to stdout" float default="20"
33 section "Input File Format"
34 text "1st line sequence"
35 text "2nd line start structure (if option --start is used)"
36 text "following lines stop structures"