problematic reaction string
Hi Elad, The reaction below for phosphoadenylyl-sulfate reductase seems to have some unusual issues. For the most part, the common names returned by equilibrator_api 0.4.0 are not recognized when they are instead used as input. (The line that is commented out uses the common names; the uncommented rxn_str line works fine, but uses Kegg compound numbers.
code: from equilibrator_api import ComponentContribution, Q_ cc = ComponentContribution()
#rxn_str = "3'-Phosphoadenylylsulfate + reduced thioredoxin = adenosine 3',5'-bisphosphate + Sulfite + oxidized Thioredoxin" rxn_str = "3'-Phosphoadenylylsulfate + C00342 = C00054 + C00094 + C00343" rxn = cc.parse_reaction_formula(rxn_str) if not rxn.is_balanced(): print('%s is not balanced' % rxn)
for item in rxn.items(protons=False): print(item[0].get_common_name())
output = str(cc.dg_prime(rxn)) print(output,'\n') dG0_prime,dG0_uncertainty = output.strip('kilojoule / mole').replace('(','').replace(')','').split("+/-")
Output: 3'-Phosphoadenylyl sulfate Reduced thioredoxin Adenosine 3',5'-bisphosphate Sulfite Oxidized thioredoxin (-43 +/- 6) kilojoule / mole