[Biopython-dev] Pathway Module

[Cayte]

  I'm posting some sketchy ideas about what the Pathway modules may contain,
mostly to get the discussion going.  I used arrays because most of the
relations are many to many.    Maybe reaction should have a pathway array?
Step is separate from reaction, because a reaction could occur in more than
one pathway. These classes are scaffolding, so please don't hesitate  to
suggest better ideas.

There may be other information associate with reaction, like temperature,
but I haven't come across it yet in the WIT or EMP databases.  It looks like
a lot of the meat is in the enzyme structures.  In EMP, the structure of an
Enzyme looks straight forward because it is a flat two column file with the
first column the name of a field and the contents in the second.

                                                                       Cayte


class Reaction:
    self.substrates = []
    self.products = []
    self.enzymes = []
    self.factors = []

class PathStep:
    self.reaction = None
    self.inlinks = []
    self.outlinks = []

class Pathway:
    self.name = ''
    self.organisms = []
    self.steps = []