Introduction

Set up a clean working directory and pull the example YAML:

$ mkdir my_polystyrene
$ cd my_polystyrene
$ htpolynet fetch-example 1
Fetched 1-polystyrene.yaml  (run with: htpolynet run 1-polystyrene.yaml)
$ ls
1-polystyrene.yaml

Like example 0, this is a single self-contained YAML — no shell script, no pre-generated mol2. The styrene SMILES is in the constituents block and htpolynet materializes STY.mol2 itself at the start of the run. What this example adds over example 0 is the cure chemistry: a single C–C inter-monomer reaction (cure stage) and a corresponding cap reaction (cap stage) that restores the vinyl double bond on any monomer that did not react.

Note

With count: 1000 and a full cure loop, this is a noticeably longer build than example 0 (same monomer count, but the cure iterations dominate overall wall time). If you just want a smoke test, drop constituents.STY.count to ~200 before running.

The next page covers what the styrene “monomer” actually looks like in the config, and why we represent it in its saturated active form rather than as the natural vinyl.