Installation

atomworks can be installed in several ways, depending on your workflow and environment. Below are the recommended methods:

1. Installing via pip (recommended)

This is the easiest way to get started with atomworks.

pip install atomworks # base installation version without torch (for only atomworks.io)
pip install "atomworks[ml]" # with torch and ML dependencies (for atomworks.io plus atomworks.ml)
pip install "atomworks[dev]" # with development dependencies
pip install "atomworks[ml,dev]" # with all dependencies

2. Using the Standalone Apptainer

This is ideal for dataset parsing and generation in a controlled environment.

# Set up IPD-specific environment variables
source ./.ipd/setup.sh
# Use the provided apptainer image
./.ipd/atomworks.sif

2. Local Conda Environment

For development and testing:

git clone git@git.ipd.uw.edu:ai/atomworks.io.git
cd atomworks
make install  # or pip install -e "."

# Create a .env file (see .env.sample) with CCD and PDB paths as needed

To install in a fresh environment:

git clone git@git.ipd.uw.edu:ai/atomworks.io.git
cd atomworks
# Set up Gitlab credentials in your shell
echo 'export GITLAB_USER=<Gitlab_Username>' >> .bashrc
echo 'export GITLAB_TOKEN=<Gitlab_PAT_Token>' >> .bashrc
source .bashrc
make env
pytest tests

3. As a Dependency in Your Apptainer

Add atomworks.io/src to your apptainer’s PYTHONPATH:

export PYTHONPATH=$PWD/src:$PYTHONPATH

Or, if at IPD:

source ./.ipd/setup.sh

For new apptainers, see the apptainer.spec file for integration details.