Introduction

The first step is to get to a clean working directory, and then use htpolynet fetch-example to set up this example.

$ mkdir my_polystyrene
$ cd my_polystyrene
$ htpolynet fetch-example 1
$ ls
1-polystyrene.sh

fetch-example copies the shell script 1-polystyrene.sh into the current directory. Running it creates the 1-polystyrene/ project directory tree, generates the monomer mol2 file, and writes the htpolynet configuration file:

$ bash 1-polystyrene.sh
$ ls 1-polystyrene
lib/  pSTY.yaml
$ tree 1-polystyrene
1-polystyrene/
├── lib
│   └── molecules
│       ├── inputs
│       │   ├── STY.mol2
│       │   └── STY.png
│       └── parameterized

The 1-polystyrene/lib/molecules/inputs/ directory now contains the monomer structure file STY.mol2. The build is launched from inside 1-polystyrene/:

$ cd 1-polystyrene
$ htpolynet run -diag diagnostics.log pSTY.yaml &> console.log &