1
$\begingroup$

I am trying to collect the ec-code (and gene) of a reaction. I have tried the following:

import pythoncyc
pgdb = pythoncyc.PGDB("sco")
r = "RXN1A0-6128"
gene = "SCP1.233B"
enzyme = pgdb.enzymes_of_reaction(r)
enzyme = pgdb.enzymes_of_gene(gene)
pgdb.full_enzyme_name(enzyme)

However, I only get an enzyme id, and not the ec-code, which is visible on biocyc.

$\endgroup$
  • 1
    $\begingroup$ Have you looked at the documentation for pythoncyc? I have not used that library before but it seems like the .full_enzyme_name() function would only return that. Is there another function to get the ec-code? $\endgroup$ – Bioathlete Nov 6 '17 at 4:28
  • $\begingroup$ It seems that ec_number is a key in the dictionary you get when you call PFrame() with getFrameData=True. $\endgroup$ – BioGeek Nov 6 '17 at 12:21
1
$\begingroup$

BioGeek is correct, however I will post a full answer.

import pythoncyc
# To get ec-code
db = pythoncyc.select_organism('sco')
reaction = db["RXN1A0-6128"]
ec_code = reaction["ec_number"]

# To get genes
pgdb = pythoncyc.PGDB("sco")
genes = pgdb.genes_of_reaction("RXN1A0-6128")
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.