Introduction

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

$ mkdir my_vinyl_ester
$ cd my_vinyl_ester
$ htpolynet fetch-example -n 3
$ ls
3-bisgma-styrene-thermoset/
$ tree 3-bisgma-styrene-thermoset
3-bisgma-styrene-thermoset
├── GMASTY.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 bisGMA and styrene.

#!/bin/bash -l

mollib='./lib/molecules'
conda activate mol-env
rm -rf proj-* *log ${mollib}/parameterized/*

STYRENE="C1=CC=CC=C1CC"
obabel -:"$STYRENE" -ismi --gen2d -opng -O ${mollib}/inputs/STY.png
obabel -:"$STYRENE" -ismi -omol2 -h --gen3d --title "Styrene-active" | \
   sed s/" 7 C "/" 7 C1"/ | \
   sed s/" 8 C "/" 8 C2"/ | \
   sed s/"UNL1"/"STY "/ > ${mollib}/inputs/STY.mol2

# Components of BisGMA = HIE+GPA+HIE
# Bisphenol-A
PHENOL="C1=CC=C(O)C=C1"
BPA="CC($PHENOL)($PHENOL)C"
obabel -:"$BPA" -ismi --gen2d -opng -O ${mollib}/inputs/BPA.png -xp 600
obabel -:"$BPA" -ismi --gen3d -h -omol2 --title "Bisphenol A" \
         | sed s/"UNL1"/"BPA "/ \
         | sed s/" 7 O "/" 7 O1"/ \
         | sed s/"14 O "/"14 O2"/ \
         > ${mollib}/inputs/BPA.mol2

# 2-hydroxypropyl isopropyl ester
HIE="CC(C(=O)OCC(O)C)C"
obabel -:"$HIE" -ismi --gen2d -opng -O ${mollib}/inputs/HIE.png -xp 600
obabel -:"$HIE" -ismi --gen3d -h -omol2 --title "2-hydroxypropyl isopropyl ester" \
         | sed s/"UNL1"/"HIE "/ \
         | sed s/"10 C "/"10 C2"/ \
         | sed s/" 2 C "/" 2 C1"/ \
         | sed s/" 7 C "/" 7 C3"/ \
         | sed s/" 9 C "/" 9 C4"/ \
         > ${mollib}/inputs/HIE.mol2

htpolynet run -diag diagnostics.log GMASTY.yaml &> console.log

Note that we are actually generating three different monomeric species: styrene, bisphenol A (BPA), and 2-hydroxypropyl isopropyl ester (HIE). This is because we are going to tell HTPolyNet to build the bisGMA molecule by reacting the esters onto the phenolic hydroxyls on BPA.

As in the other two tutorials, if you have a mol-env conda enviroment, just issue ./run.sh to start the build.