Description
mech2mod is a Perl program to convert a reaction network into a file suitable for use with the parest library of functions capable of integrating the system and performing parameter estimation on the system parameters.

Below are descriptions of the usage of mech2mod and the syntax for the reaction network. The reaction network section has two subsections, each discussing an individual part of the reaction network: the required reactions and the optional info sections.

Usage
The usage of mech2mod is as follows:

usage: mech2mod [options] [file ...]

available options:
-d --debug
Run mech2mod using the Perl debugger and -w flags
See the perldebug(1) manpage for instructions on how to use
the Perl debugger
-f --force
Do not prompt when files will be overwritten and ignore
less serious errors
-g FILE --gregfile FILE
Write GREG input to FILE rather than default, greg10.in
-h --help
Print this most helpful message
-i FILE --integfile FILE
Write integrator input to FILE rather than default, ddat.in
-l --log
Map macro parameters beginning with A using exp(k[i])
-n --noinput
Do not create any input files, only the compilable model
-o FILE --odefile FILE
Write output to FILE rather than to the default, model.c
-p FILE --paramfile FILE
Write parameter data to FILE rather than default, param.dat
-t --type
Put constant type flag, c, before each value in parameter file
to use with the libparest.a -t option

[file ...]
This file(s) contains the reaction network
If no file is given, read standard input for network
The syntax of the file is discussed below

As can be seen above, this program supports the traditional single character option flags as well as the GNU style extended option flags. The descriptions above for the most part self explanatory. More complete descriptions for some flags are given in the appropriate sections of this document.

mech2mod typically generates four output files (unless the -n option is used): model.c, greg10.in, ddat.in, and param.dat. If any of these files exist in the current working directory, the user is prompted before they are overwritten, unless -f or --force was specified on the command line. If any file but model.c is chosen to not be overwritten, the program continues and simply does not write the file. If model.c is chosen to not be overwritten, the program terminates. Any of the default file names may be avoided using the above flags. If the -n option is specified, only the model.c file (or its equivalent if -o is used) is written unless the user explicitly supplies a file name using the -g, -i, or -p flag, in which case all explicitly supplied files are output.