Change ambiguous variable names

Replac rxnNames with rxnList as model.rxnNames is different from
model.rxns, and model.rxns is used to select the subnetwork. Replac
metNames with metList, to avoid similar confusion.
Add the fields - rxnNames, rules and metCharge

Adds rxnNames, rules (which contains the binary representations whereas
grRules contains a string(cell) representation) and metCharge to the
subnetwork.