search

latendre / PythonCyc

MIT License
22 stars 6 forks source link

Stoichiometry #3

Open asaldivar93 opened 4 years ago

asaldivar93 commented 4 years ago

is there any way to get the stoichiometric coefficients for a reaction? thanks

glucksfall commented 4 years ago

Hello @asaldivar93,

I'm a user of pythoncyc and a few years ago I tested all functions from the python suite. The stoichiometry of the reaction is not the only property that pythoncyc couldn't retrieve from pathwaytools. From the ptools documentation, when retrieving data for a reaction, when the 'left' or 'right' slots have a stoichiometric coefficient different of one, it also retrieves the coefficients as a list.

I tested with the YEAST database and the ACETYL-COA-ACETYLTRANSFER-RXN, reaction which uses two molecules of ACETYL-COA. Sadly, the coefficient is not retrieved (See https://biocyc.org/YEAST/NEW-IMAGE?type=REACTION&object=ACETYL-COA-ACETYLTRANSFER-RXN)

I believe there is a function in ptools not implemented in pythoncyc that retrieves the coefficients as a side-effect of retrieving data for the reaction.

I will investigate further if I found a solution. I'm also interested in having that data for reactions.

glucksfall commented 4 years ago

Hi @asaldivar93,

I found the function rxn-stoich-multipliers in the code of pathwaytools. Sadly, the function won't work from the pythoncyc because an error I don't understand: :error, The function 'RXN-STOICH-MULTIPLIERS' is not allowed to be called in restricted mode.. Also, it seems isn't the function we need to retrieve the data. I tested in the LISP interpreter of ptools and returns 1: ((ACETYL-COA-ACETYLTRANSFER-ENZRXN . 1))

I hope to find something useful for both.

Best regards.