Emergent Site example

[paulflang]

This is an implementation of the emergent site example discussed July 09.

I'm not planning to work further along that thread atm. But here are the open issues with the generated network for future reference:

• There is no R2 present in the output and increasing generator.transitions(2) to 3 takes forever.
• Idk why we have a bond_peptide [e_SiteR1R1 []] composite. This should not be possible, since their (co)domain does not match.
• We have a dimerization of non-polymerized R1 R1. This dimerization should only be possible after polymerization, which creates the required CN site (needed for further restriction to SiteR1R1). But I don't see the CN site in the output:

let bond [] in
    let i_SiteR1R1 [0.0] in
        (C [1.1], polymerization [e_C [], i_R1 [0.0], i_R1 [0.2], e_N [], 0.1])
    : let bond [] in
    let i_SiteR1R1 [0.0] in
        (
        C [1.1],
        (
            M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]],
            M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]]
        )
        )
    → let bond [] in
    let i_SiteR1R1 [0.0] in
        (
        C [1.1],
        let bond_peptide [0.1] in
            (
            M [i_aminoacid [e_N [], i_R1 [1.0], 0.0]],
            M [i_aminoacid [0.1, i_R1 [1.2], e_C []]]
            )
        )

[paulflang]

polymer.clone() is wrong here. First create a new variable polymer_free. Then you can use polymer_free.subst(&mut vec![name("e_SiteR1R1"), MorTm::var("s3")]) here.