WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / Kinfold / kinfold.ggo

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