Utils

Parsers

Contains a parser for reaction strings and another of lists as strings.

class app.utils.parsers.ReactionParser

ReactionParser class, whose goal is to parse a reaction string in the format: A_c + B_c <-> P_c

parse_coefficients(expression, sense)

Parses the stoichiometric coefficients from expression. Expression has the form 2.0 metabolite_id.

Parameters

• expression – metabolite with respective stoichiometric coefficient, “2.0 metabolite_id”

• sense – whether the metabolite is consumed (-1) or produced (1)

Returns

The stoichiometric coefficients

parse_reaction(reaction_str)

Given a reaction string in the form A_c + B_c <-> P_c, parses it to retrieve its reversibility (True or False) and stoichiometry in the form of a dictionary {metabolite_id : stoichoimetric_coefficient}.

Parameters

reaction_str – a reaction string in the form A_c + B_c <-> P_c

Returns

reaction reverisibility (True or False), and stoichiometry dictionary

Populate DB

Contains a bunch of functions to load data into the database. It is mostly used by the unit tests.