# Name of your program
package "RNAdos" # don't use package if you're using automake

purpose "Calculate the density of states for each energy band of an RNA"

usage "RNAdos [OPTIONS]"

#version "1.0"   # don't use version if you're using automake

# command line options passed to gengetopt
args "--file-name=RNAdos_cmdl --include-getopt --default-optional --unamed-opts --func-name=RNAdos_cmdline_parser --arg-struct-name=RNAdos_args_info"


description "The program reads an RNA sequence and computes the density of states for each energy band.\n\n"

# Options

option  "verbose" v
"Be verbose.\n\n"
flag
off


section "I/O Options"
sectiondesc="Command line options for input and output (pre-)processing\n\n"

option  "sequence" s
"The RNA sequence (ACGU).\n"
string
optional

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


section "Algorithms"
sectiondesc="Select additional algorithms which should be included in the calculations.\nThe Minimum free energy\
 (MFE) and a structure representative are calculated in any case.\n\n"

option  "max-energy"  e
"Structures are only counted until this threshold is reached. Default is 0 kcal/mol.\n"
int
default="0"
optional

option  "hashtable-bits"  b
"Set the size of the hash table for each cell in the dp-matrices.\n\n"
int
default="20"
optional
hidden


section "Energy Parameters"
sectiondesc="Energy parameter sets can be adapted or loaded from user-provided input files\n\n"

option  "temp"  T
"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
double
default="37.0"
optional

option  "paramFile" P
"Read energy parameters from paramfile, instead of using the default parameter set.\n"
details="Different sets of energy parameters for RNA and DNA should accompany your distribution.\nSee the\
 RNAlib documentation for details on the file format. The placeholder file name 'DNA' can be used\
 to load DNA parameters without the need to actually specify any input file.\n\n"
string
typestr="paramfile"
optional

option  "salt" -
"Set salt concentration in molar (M). Default is 1.021M.\n\n"
double
optional


section "Model Details"
sectiondesc="Tweak the energy model and pairing rules additionally using the following parameters\n\n"

option  "dangles" d
"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops.\n"
details="\nWith -d1 only unpaired bases can participate in at most one dangling end. With -d2 this\
 check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in\
 any case; this is the default for mfe and partition function folding (-p).\nThe option -d0 ignores\
 dangling ends altogether (mostly for debugging).\nWith -d3 mfe folding will allow coaxial stacking\
 of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking\
 of the two interior pairs in a loop of degree 3 and works only for mfe folding.\n\nNote that with\
 -d1 and -d3 only the MFE computations will be using this setting while partition function uses\
 -d2 setting, i.e. dangling ends will be treated differently.\n\n"
int
default="2"
optional

option  "helical-rise"  -
"Set the helical rise of the helix in units of Angstrom.\n"
details="Use with caution! This value will be re-set automatically to 3.4 in case DNA\
 parameters are loaded via -P DNA and no further value is provided.\n\n"
float
optional
default="2.8"
hidden

option  "backbone-length"  -
"Set the average backbone length for looped regions in units of Angstrom.\n"
details="Use with caution! This value will be re-set automatically to 6.76 in case DNA\
 parameters are loaded via -P DNA and no further value is provided.\n\n"
float
optional
default="6.0"
hidden


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