Bind	Reference Home

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Bind is an uninstantiated function that is used to indicate intermediate complexes formed during a reaction, e.g.,

A + X ↔ Bind[A,E] ↔ B + E

for an enzymatic reaction. When Bind[A,B] is generated by interpret, the arguments will be alphabetized, i.e., Bind[B,A] will be converted to Bind[A,B]. If Bind[B,A] is sent to interpret, the order of the arguments will not be changed. The user should ensure that Bind[A,B] and Bind[B,A] are treated equivalently.

In general, it is not necessary to redefine Bind unless a specific format is required - in the above reaction, the intermediate species will be referred to as Bind[A,En][t], which is a perfectly valid species name in xCellerator.

The user should redefine Bind[..] if a specific format is desired for automatically generated complexes.

The following function will generate a complex name such as

        mybind[A_, B_]:= Module[{names,name},
                names=Sort[{A,B}];
                name = ToString[names[[1]]]<>
                "\[UnderBracket]"<>
                ToString[names[[2]]];
                Return[Symbol[name]];
        ]

If indices are used, the following function should be defined first:

        mybind[A_[i__], B_[j__]]:= mybind[A,B][i,j];

mybind[p[1,2],q[3]] will return

The user would then do the following to change the variable names to their preferred format:

        interpret[...]/.{Bind->mybind}