Introduction

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

$ mkdir my_dgeba_pacm
$ cd my_dgeba_pacm
$ htpolynet fetch-example -n 4
$ ls
4-pacm-dgeba-epoxy-thermoset/
$ tree 4-pacm-dgeba-epoxy-thermoset
4-pacm-dgeba-epoxy-thermoset/
├── DGEPAC.yaml
├── lib
│   └── molecules
│       ├── inputs
│       └── parameterized
├── README.md
└── run.sh

The bash script run.sh is a suggested way to run a build, and it contains the commands to generate the input mol2 files for activated DGEBA and PACM.

#!/bin/bash -l
# A simple driver to demonstrate usage of HTPolyNet
#
# Cameron F. Abrams cfa22@drexel.edu

# activate the conda environment we configured to run htpolynet
conda activate mol-env

sysname="DGEPAC"
mollib='./lib/molecules'

# clean out any existing project directories and the library
rm -rf proj-* *log ${mollib}/parameterized/*

# Monomer structures:
# DGEBA
DGEBA="CC(C)(C1=CC=C(C=C1)OCC(O)C)C3=CC=C(C=C3)OCC(O)C"
obabel -:"$DGEBA" -ismi --gen2d -opng -O ${mollib}/inputs/DGE.png
obabel -:"$DGEBA" -ismi -h --gen3d -omol2 --title "DGE" | \
            sed s/"UNL1   "/"DGE    "/ | \
            sed s/"14 C "/"14 C1"/ | \
            sed s/"25 C "/"25 C2"/ | \
            sed s/"12 C "/"12 C3"/ | \
            sed s/"23 C "/"23 C4"/ | \
            sed s/"13 O "/"13 O1"/ | \
            sed s/"24 O "/"24 O2"/ > ${mollib}/inputs/DGE.mol2
# PACM
PACM="C1CC(CCC1CC2CCC(CC2)N)N"
obabel -:"$PACM" -ismi --gen2d -opng -O ${mollib}/inputs/PAC.png
obabel -:"$PACM" -ismi -h --gen3d -omol2 --title "PAC" | \
            sed s/"UNL1   "/"PAC    "/ | \
            sed s/"14 N "/"14 N1"/ | \
            sed s/"15 N "/"15 N1"/ | \
            sed s/"3 C "/"3 C1"/ | \
            sed s/"11 C "/"11 C1"/ > ${mollib}/inputs/PAC.mol2

# launch the build
htpolynet run -diag diagnostics.log ${sysname}.yaml &> console.log

So, if you have a mol-env conda enviroment, just issue ./run.sh to start the builds. The section “run” below walks through the build process, while the first three sections describe in detail how to create the monomer inputs and configuration file, with a special emphasis on explaining the syntax of the reactions.