The primary mode of MEASURE calculates the phenomenological rate coefficients for a reaction network specified in an input file. To do so, run Python on the main measure.py file, passing the input file as a parameter on the command line, e.g.
$ python measure.py FILE
When MEASURE execution is complete, it will save an output file in the same directory as the input file but with the name output.py. If you wish to change the location of the output, use, the -o/--output flag, e.g.
$ python measure.py INPUTFILE -o OUTPUTFILE
MEASURE contains functionality for automatically generating an image of the potential energy surface for a reaction network. To do so, run Python on the main measure.py file, passing the input file as a parameter on the command line, and also add the -d/--draw flag along with the output image, e.g.
$ python measure.py INPUTFILE -d OUTPUTIMAGE
The potential energy surface can be generated in PNG, SVG, PDF, and PS formats. The format is automatically chosen based on the output image file extension. If your input file contains structure information (e.g. SMILES or InChI strings), then the generated image will use structures to depict the species; otherwise it will use the string labels.
You can manipulate the amount of information logged to the console window using the -q/--quiet flag (for quiet mode) or the -v/--verbose flag (for verbose mode). The former causes the amount of logging information shown to decrease; the latter causes it to increase.
To view help information and all available options, use the -h/--help flag, e.g.
$ python measure.py -h