[Biopython-dev] Pathway Module

[Cayte]

----- Original Message -----
S1:
 V = {A,B,C,D,E}
 E = {(A,C,E), (A,D,E), (B,C,E), (B,D,E)}


 > > Step is separate from reaction, because a reaction could occur in
> > more than one pathway.
>
> I'm not sure I see the rationale for this. It is true that a reaction
> can occur in several pathways, but unless there is information about a
> reaction that only applies to a specific pathway there is no need to
> keep a separate Step object - you can just let two different pathway
> objects reference the same reaction object.
>

   The information that applies to just one pathway is the branching and
sequence, the in links and out links to other steps..  Maybe you can tease
this information out of the products and substrates for each reaction, but I
thought of using explicit links from one step to the next step(s).

                                                 Cayte