Set up GRASP models¶

Set up models¶

Convert mechanisms¶

The purpose of this module is to convert an enzyme mechanism given in terms of elementary reactions into the pattern format currently accepted by GRASP.

set_up_grasp_models.set_up_models.convert_mechanisms.convert_er_mech_to_grasp_pattern(file_in, file_out, promiscuous=False, inhib_list=None, activ_list=None)¶

Given an input file with a mechanism in the form of elementary reactions, converts it to a GRASP pattern file.

Parameters

file_in (str) – path to the input file with elementary reactions mechanism.
file_out (str) – path to the output file with GRASP pattern.
promiscuous (bool) – to indicate whether reaction is promiscuous or not.
inhib_list (Optional[list]) – list of inhibiting metabolites.
activ_list (Optional[list]) – list of activating metabolites.

Returns

None

set_up_grasp_models.set_up_models.convert_mechanisms.generate_mechanisms(file_in_model, mech_in_dir, pattern_out_dir, hard_coded_mechs=None)¶

Given the GRASP input excel file, goes through the mechanisms defined in the kinetics sheet and checks if a .txt file with the same name exists in the pattern_out_dir, if not it checks the mech_in_dir for a .txt file with the mechanism name and converts it to a patter file to be stored in the pattern_out_dir.