Execution
There are two options for launching atomizer. You can either use the python script inside the SBMLparser folder using
python sbmlTranslator.py -i /path/to/sbml/file [-a] [-o output.bngl]However the preferred solution is to use the binary version of the script. See the installation section for a description on how to get this binary
./sbmlTranslator -i /path/to/sbml/file [-a] [-o output.bngl]Command line arguments
- [-a] activates the atomizer. Otherwise only a flat translation will be provided (no molecular structure)
- [-p] activates pathway commons querying. An internet connection is required
- [-b ] Enables post atomization analysis.
- See [-h] for a full list of arguments