Kappa vs. BNGL
From BioNetWiki
Kappa and BNGL are essentially the same, except for a few small differences. A list of these differences is provided below.
Indistinguishable sites
In BNGL, a molecule is allowed to have a set of indistinguishable sites. This is not allowed in Kappa - each molecular component must have a unique name. Sites/components of a molecule that share the same name are taken to be indistinguishable in BNGL. Consider a monoclonal IgE antibody, which has two antigen-combining sites, which are the same for most intents and purposes. In the BNGL molecule type definition IgE(Ag,Ag), two sites are introduced that share the same name (Ag). Thus, these sites are taken to be indistinguishable. In Kappa, one would need to artificially distinguish the two sites, using a construct such as IgE(Ag1,Ag2).
Application conditions related to molecularity of a reaction and number of products of a reaction
In BNGL, reaction rules always contain application conditions related to the molecularity of a reaction and for reversible rules the number of products of a reaction. These application conditions are specified using dot-plus notation. For example, the plus sign in A(a)+B(b)->A(a!1).B(b!1) indicates that A and B associate only when the association reaction is bimolecular, i.e., the match of pattern A(a) and the match of pattern B(b) are not indirectly connected and part of the same species, the matches must be parts of separate species. Equivalent application conditions can be specified in Kappa, but at this time, this capability is an undocumented language feature. See the discussion here. The language feature is important for modeling many reaction systems, such as systems with polymerization-like reactions that have chain-elongation steps (intermolecular reactions) and ring-closure steps (intramolecular reactions). Note that the period or dot in the BNGL expression A(a!1).B(b!1) is gratuitous. The period or dot represents connectivity, but one can see that A and B are connected by the bond information in the expression, i.e., by the sharing of the bond index "!1" by the a and b components of A and B. This "inelegance of gratuitous notation" is avoided in Kappa, as Kappa does not include the period or dot notation. In Kappa, molecules in rule patterns are separated by commas, whereas in BNGL, molecules in rule patterns are separated by a plus sign or dot.
Implicit connectivity
In BNGL, one can specify that two molecules are connected without explicitly specifying how the two molecules are connected. This is not possible in Kappa. For example, both of the BNGL expressions below indicate that molecules A and C are connected, but only the latter has an equivalent in Kappa. The Kappa equivalent is A(c!1,b!2),B(a!2,c!3),C(b!3,a!1).
A().C()
A(c!1,b!2).B(a!2,c!3).C(b!3,a!1)
