search

ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
Other
19 stars 10 forks source link

Transport indicator in REACTION_MODEL table #130

Open samseaver opened 12 years ago

samseaver commented 12 years ago

Currently, the only way to know if a reaction is a transport reaction is to retrieve the equation from the reaction table, and to use the FIGMODELreaction::substrates_from_equation function to find it it has different compartments (or a regex if you'd like to code it yourself). This is a little awkward code-wise and as such I'd like to recommend that a binary TRANSPORT column gets added to the REACTION_MODEL table, and is populated upon model import.

Well, now that I think about it, the "compartment" of a transport reaction is defaulted to "c", as the actual compartments are found in the equation itself, so either a binary TRANSPORT column gets added, or the COMPARTMENT column gets extended to allow the definition of multiple compartments.

Thoughts?

devoid commented 12 years ago

I will implement a function isTransport() on both the reaction and the reaction_model ( the latter will just call the former ).