# Name of your program
package "RNA2Dfold" # don't use package if you're using automake
purpose "Compute MFE structure, partition function and representative sample structures of k,l neighborhoods"

# Version of your program
#version "0.9"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNA2Dfold_cmdl --include-getopt --default-optional --func-name=RNA2Dfold_cmdline_parser --arg-struct-name=RNA2Dfold_args_info"

description "The program partitions the secondary structure space into (basepair)distance classes according to\
 two fixed reference structures. It expects a sequence and two secondary structures in dot-bracket notation as\
 its inputs. For each distance class, the MFE representative, Boltzmann probabilities and Gibbs free energy is\
 computed. Additionally, a stochastic backtracking routine allows to produce samples of representative suboptimal\
 secondary structures from each partition\n\n"


# Options
section "General Options"
sectiondesc="Below are command line options which alter the general behavior of this program\n\n"

option  "noconv"  -
"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
flag
off

option  "numThreads"  j
"Set the number of threads used for calculations (only available when compiled with OpenMP support)\n\n"
int
optional

section "Algorithms"

option  "partfunc"  p
"calculate partition function and thus, Boltzmann probabilities and Gibbs free energy\n\n"
flag
off


option  "stochBT" -
"backtrack a certain number of Boltzmann samples from the appropriate k,l neighborhood(s)\n\n"
int
optional

option  "neighborhood"  -
"backtrack structures from certain k,l-neighborhood only, can be specified multiple times (<k>:<l>,<m>:<n>,...)\n\n"
string
typestr="<k>:<l>"
multiple
dependon="stochBT"

option  "pfScale" S
"scaling factor for pf to avoid overflows\n\n"
double
optional

option  "noBT"  -
"do not backtrack structures, calculate energy contributions only\n\n"
flag
off

option  "circ"  c
"Assume a circular (instead of linear) RNA molecule.\n\n"
flag
off

section "Model Details"

option  "temp"  T
"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
double
optional

option  "maxDist1"  K
"maximum distance to first reference structure"
details="If this value is set all structures that exhibit a basepair distance greater than maxDist1 will\
 be thrown into a distance class denoted by K=L=-1\n\n"
int
optional

option  "maxDist2"  L
"maximum distance to second reference structure"
details="If this value is set all structures that exhibit a basepair distance greater than maxDist1 will\
 be thrown into a distance class denoted by K=L=-1\n\n"
int 

option  "noTetra" 4
"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
flag
off

option  "parameterFile" P
"Read energy parameters from paramfile, instead of using the default parameter set.\n"
details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
 documentation for details on the file format.\n\n"
string
typestr="paramfile"

option  "dangles" d
"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
details="\nWith -d2 dangling energies will be added for the bases adjacent to a helix on both sides
 in any case.\nThe option -d0 ignores dangling ends altogether (mostly for debugging).\n\n"
int
default="2" 
values="0","2"

option  "noGU"  -
"Do not allow GU pairs\n\n"
flag
off

option  "noClosingGU" -
"Do not allow GU pairs at the end of helices\n\n"
flag
off

text    "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
 rna@tbi.univie.ac.at.\n\n"