Running an example

This guide will walk you through an example to run Syndirella’s pipeline through a jupyter notebook.

Attention

If you have a Windows OS, use Docker Desktop by following these steps before continuing:

  1. Create a Docker account.

  2. Install Docker Desktop.

  3. In Docker Desktop: go to Add Extensions.

  4. Search for Jupyter Notebook Scientific Python Stack Extension and install it.

  5. Open newly installed extension.

  6. Open a terminal in the JupyterLab interface.

  1. Install Syndirella.

conda create -n syndirella python=3.10
conda activate syndirella
pip install syndirella
pip install aizynthfinder
python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'  # run once, for Fragmenstein

Note: If cgrtools installation fails, try running:

conda install -c conda-forge c-compiler cxx-compiler
pip install --no-build-isolation cgrtools

Troubleshooting: If you encounter a TypeError: 'AttributeFilledMock' object is not iterable error, this is related to a PyRosetta dependency by Fragmenstein. To resolve this, you can download PyRosetta for academic and non-commercial use (see PyRosetta License).

pip install pyrosetta-installer
python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'

  1. Clone Syndirella repo.

git clone https://github.com/kate-fie/syndirella.git
cd syndirella

3. Open notebook in the syndirella environment at syndirella/example/run_syndirella_example/run_examples.ipynb which will take you through installation, looking at designs, running a handful of placements, and analysing outputs.