The files in this folder contain KEGG-specific information and are described here.

* DIFF_modified_equations.out:
		This contains a map of reaction IDs to their modified reaction equations.  
		These reactions have undergone some kind of manuual curation and are not identical to the original KEGG equations.
		
* SIMULATION_default_additional_reactions.out:
		These are reactions that are added by default to all model reconstructions as they have been deemed of high importance in previous model reconstructions.
		
* SIMULATION_metabolites_with_default_exchanges.out:
		Metabolites that by default can diffuse in and out of cells.
		
* SIMULATION_spontaneous_or_non_enzymatic.lst:
		A list of reactions from KEGG deemed either spontaneous or non-enzymatic based on the KEGG entry.
		
* SIMULATION_universe_rxn_before_metanetx.info:
		Contains list of reactions of interest, their original KEGG name, and the upper and lower bounds independently assigned.  Equations are not stored here; they are downloaded automatically from KEGG using its API at runtime.  Then, reactions with modified equations (see DIFF_modified_equations.out) have their equations substituted.
		
* WARNING_reactions_with_formulaless_cpds.out:
		A list of reactions with compounds that do not have any formula in KEGG.  Given that mass balance is important, these reactions are incorporated in models reconstructions only if the user explicitly specifies this to be their wish.