The reaction rules editor pane is currently the only way to specify and edit a reaction rule.
Each reaction rule is specified on two lines, with reactants on the firsl line and products underneath. This way a modeler
can easily see the transformation of reactants to products.
Sites in white are fully unspecified (they can be bound or unbound, denoted by grey question mark under the site).
Sites in green must have either binding status defined
(bound to specific site - denoted by color bond with index, bound to arbitrary site - denoted by vertical line , unbound),
or state defined. The first rule describes binding of egfr monomer (site r is unbound) to free egf (site r is unbound).
The second rule describes phosphorylation of unbound Y1148 site (change of state from Y to P) on a receptor that is bound to
another receptor (site r is bound) but may be bound to a ligand (question mark under l site) and
site Y1068 may be in any state and may be either bound or not.
Reaction Rule edit/specification:
Note: If reaction rule has multiple identical molecules, they are enumerated to provide
one-to-one mapping from reactants to products. The match is established automatically, but can be reassigned
with a right click on a molecular shape.