Base installation

A fully-featured install of polymerist into a fresh virtual environment (called “polymerist-env” here, but can be renamed to whatever you like) can be obtained by running the following shell commands:

mamba create -n polymerist-env python=3.11
mamba activate polymerist-env
pip install polymerist
mamba install -c conda-forge openff-toolkit mbuild openbabel "packmol<=20.15.1"

The final mamba install is done as a one-liner (rather than in parts) to reconcile any discrepancies between packmol versions between the 3 conda-only packages required (namely the openff-toolkit, mbuild, and openbabel).

The packmol pin is to ensure solvation utilities work correctly; this will save you headaches, any later versions give inscrutable PDB errors where there previously were none.

Installing the ‘openff-toolkit <https://github.com/openforcefield/openff-toolkit`_ will take _at least_ a few minutes, and will make the terminal output quite busy; remain calm, that’s normal!

Test installation

To test that the installation worked, you can trying to run the following snippet in python:

mamba activate polymerist-env; python
>>> import polymerist as ps
>>> print(ps.pascal(5))
    1
   1 1
  1 2 1
 1 3 3 1
1 4 6 4 1

Extended install

An extended install with Jupyter Notebook support, molecular visualization capability, and chemical database querying capability can be obtained with similar commands. Testing of installation is analogous to the python code above.

mamba create -n polymerist-env python=3.11
mamba activate polymerist-env
pip install polymerist[interactive,chemdb]
mamba install -c conda-forge openff-toolkit mbuild openbabel "packmol<=20.15.1"

Conda install (NOT recommended)

As mentioned, the openff-toolkit install above is pretty slow with mamba; with conda, it will be glacial Nevertheless, we provide equivalent conda installation instruction here for users who are too stubborn to use mamba instead. These will perform the same installation, just much more slowly:

conda create -n polymerist-env python=3.11
conda activate polymerist-env
pip install polymerist[interactive,chemdb]
conda install -c conda-forge openff-toolkit mbuild openbabel "packmol<=20.15.1"