Introduction

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

$ mkdir my_pms
$ cd my_pms
$ htpolynet fetch-example -n 2
$ ls
2-polymethylstyrene/
$ tree 2-polymethylstyrene
2-polymethylstyrene/
├── lib
│   └── molecules
│       ├── inputs
│       └── parameterized
├── pMSTY.yaml
├── README.md
└── run.sh

The bash script run.sh is a suggested way to run the build, and it contains the commands to generate the input mol2 file for activated methylstyrene (i.e., ethylmethylbenzene, or “EMB”). A listing of run.sh appears below:

#!/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="pMSTY"
mollib='./lib/molecules'

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

# Generate a 2d picture and a 3d mol2 file for methylstyrene's activated
# form, ethylmethylbenzene (EMB) and rename reactive atoms
echo "C1=CC(C)=CC=C1CC" | obabel -ismi --gen2d -opng -O ${mollib}/EMB.png
echo "C1=CC(C)=CC=C1CC" | obabel -ismi --gen3d -h -omol2 --title "EMB" | \
      sed s/" 8 C "/" 8 C1"/ | \
      sed s/" 9 C "/" 9 C2"/ | \
      sed s/"UNL1"/"EMB "/ > ${mollib}/EMB.mol2

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

Note that we are activating the mol-env conda environment; that may not be necessary in your case, depending on how you configured your Python instance. Note the two obabel commands: the first simply draws the chemical structure of the monomer as PNG file, and the second generates the 3D structure in mol2 format. The sed commands are used to give unique atom names to atoms 8 and 9, and the default residue name UNL1 is replaced with EMB.

So running the build just requires launching the script:

$ ./run.sh &

Results will appear in the files diagnostics.log and console.log, and the project directory proj-0/.

The first invocation of htpolynet run performs all needed parameterizations and runs the first system build. These parameterizations appear in the library lib/molecules/parameterized/. All subsequent invocations of htpolynet run will use these parameterizations directly without re-performing them.

So, you could build multiple replicas by simply issuing more htpolynet run commands in series, for example:

$ htpolynet run -diag diagnositics-1 pMSTY.yaml &> console-1.log
$ htpolynet run -diag diagnositics-2 pMSTY.yaml &> console-2.log
$ htpolynet run -diag diagnositics-3 pMSTY.yaml &> console-3.log

These will generate three new replicas in proj-1/, proj-2/, and proj-3/, respectively.

Although this makes it seem quite simple to run htpolynet, the aim of the tutorial is to show how it works to a level of detail sufficient to allow a user to develop their own new systems. The remainder of this tutorial considers the major elements of htpolynet run and its usage. Next we consider how to generate the monomer inputs.