Cobrapy

test_writeModelinJSON[source]

test writing out a model in SBML with COBRA Toolbox, then reading it in with COBRApy, then writing it out in JSON with COBRApy.

writeModelinJSON(model, COBRApyPath)[source]

write out a model in JSON format using COBRApy

INPUT model

OPTIONAL INPUT dGPredictorPath path to the folder containg a git clone of https://github.com/maranasgroup/dGPredictor

path must be the full absolute path without ~/

cacheName fileName of cache to load (if it exists) or save to (if it does not exist)

OUTPUT success = 1,0

EXTERNAL DEPENDENCIES Python, see: [pyEnvironment,pySearchPath]=initPythonEnvironment(environmentName,reset)

rdkit, e.g., installed in an Anaconda environment https://www.rdkit.org https://www.rdkit.org/docs/Install.html#introduction-to-anaconda

COBRApy https://github.com/opencobra/cobrapy Install COBRApy using this command in a terminal: conda install -c bioconda cobra