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Old version of cobra (like the one used in padmet: 0.10.1) cannot be installed in Python 3.7 (opencobra/cobrapy#734).

Need to use a newer version of cobra and at least version 0.13.4:

https://github.com/opencobra/cobrapy/blob/0.13.4/release-notes/0.13.4.md

Some reactions like RXN-2103 contain the same compounds multiple times as products or reactants:

1-4-alpha-D-galacturonosyl + WATER -> 1-4-alpha-D-galacturonosyl + 1-4-alpha-D-galacturonosyl

But by using padmet_to_padmet, this will be converted into:

1-4-alpha-D-galacturonosyl + WATER -> 1-4-alpha-D-galacturonosyl

This is due to the use of the _addRelation function of 'padmet/classes/padmetSpec.py' which does not allow to have the same relations multiple times.

There should be a way to add the same multiple relations of 'consumes' or 'produces' between a reaction and its compounds without adding all the other relations multiple times.

Issue found in 6767816.

Hello,

I installed padmet in a virtual enviroment, but I couldn't install docopt 0.6.2 because is available for python3.3 and below. Also, it seems docopt is not under maintenance, and a derivative project is here https://github.com/jazzband/docopt-ng

Best!

There is big issue with how the sbml IDs are handled and converted in sbmlPlugin.

There should not be the compartment in the SBML ID, this lead to a lot of issue especially when trying to parse sbml ID from multiple databases.