efmlrs.util package

Submodules

efmlrs.util.convert_matrix module

efmlrs.util.convert_matrix.get_denominators(smatrix)

Gets greatest denominator of each row in stoichiometric matrix :param smatrix: list of lists of stoichiometric matrix :return: list of greatest denominators for each row

efmlrs.util.convert_matrix.get_int_smatrix(smatrix, greatest_denominators)

Converts stoichiometric matrix from fractions to integer by multiplying each row with greatest denominator. :param smatrix: list of lists of stoichiometric matrix :param greatest_denominators: list of greatest denominators for each row :return: list of lists of converted stoichiometric matrix

efmlrs.util.convert_matrix.get_min_smatrix(int_smatrix)

Gets greatest divisor for each row and divides each row through greatest divisor. Converts matrix from list of lists to sympy matrix. :param int_smatrix: list of lists of stoichiometric matrix with integers as coefficients :return: sympy matrix of stoichiometric matrix with smallest coefficients

efmlrs.util.convert_matrix.run(smatrix)

Converts stoichiometric matrix from fractions to integer by multiplying each row with greatest denominator. For each row in stoichiometric matrix reduces coefficients to smallest number by dividing each row through greatest divisor. Converts matrix from list of lists to sympy matrix. :param smatrix: list of lists of stoichiometric matrix :return: sympy matrix of stoichiometric matrix with smallest coefficients

efmlrs.util.data module

Collection of small helper scripts.

efmlrs.util.data.bounds_print(bounds)

efmlrs.util.data.convert_df2matrix(smatrix_df)

efmlrs.util.data.convert_float2fraction(matrix)

efmlrs.util.data.convert_fraction2float(matrix)

efmlrs.util.data.convert_matrix2df(smatrix)

efmlrs.util.data.efmlrs_finish_compressions()

efmlrs.util.data.efmlrs_finish_decompressions()

efmlrs.util.data.efmlrs_start_compressions()

efmlrs.util.data.efmlrs_start_decompressions()

efmlrs.util.data.read_mfile(name)

efmlrs.util.data.read_rfile(name)

efmlrs.util.data.read_rvfile(name)

efmlrs.util.data.read_sfile(name)

efmlrs.util.data.read_sfile_int(name)

efmlrs.util.data.reversibilities4printing(reversibilities)

efmlrs.util.data.write_all(smatrix, reactions, reversibilities, metabolites, name)

efmlrs.util.data.write_cmp_int_matrix(core_name)

efmlrs.util.data.write_efms(name, efms)

efmlrs.util.data.write_info(core_name, reversibilities, outer_counter)

efmlrs.util.data.write_init_mfile(name, metabolism)

efmlrs.util.data.write_init_rfile(name, reactions)

efmlrs.util.data.write_initial_files_no_bounds(core_name, reactions, reversibilities, metabolites)

efmlrs.util.data.write_initial_files_with_bounds(core_name, reactions, reversibilities, metabolites)

efmlrs.util.data.write_mfile(name, metabolism)

efmlrs.util.data.write_rfile(name, reactions)

efmlrs.util.data.write_rvfile(name, reversibles)

efmlrs.util.data.write_sfile(name, smatrix)

efmlrs.util.data.write_sfile_float(name, smatrix)

efmlrs.util.data.write_uncmp_int_matrix(core_name)

efmlrs.util.log module

Collection of small scripts for creating log file.

efmlrs.util.log.log()

efmlrs.util.log.log_add()

efmlrs.util.log.log_close()

efmlrs.util.log.log_del()

efmlrs.util.log.log_delete(rea1, rea2)

efmlrs.util.log.log_delete_meta(meta)

efmlrs.util.log.log_delete_rea(rea)

efmlrs.util.log.log_init(name)

efmlrs.util.log.log_keep()

efmlrs.util.log.log_merge(remove, keep, keep_factor)

efmlrs.util.log.log_merge_many(remove, keep, remove_factor, factors, force=False)

efmlrs.util.log.log_merge_rea(rea)

efmlrs.util.log.log_module()

efmlrs.util.log.log_strip(rea)

efmlrs.util.log.log_time()

efmlrs.util.log.merge_reaction_names(R1_keep, R2_remove)

Module contents