Neurosnap SDK

Neurosnap SDK is a collection of utilities for bioinformatics, structural biology, and cheminformatics workflows, with strong support for amino acid sequences and molecular structures.

This a package developed by Keaun Amani at neurosnap.ai. You are welcome to use this code and contribute as you see fit. We are currently working on expanding this package as well to add support for more common functions.

Installation

# current stable version
pip install -U --no-cache-dir neurosnap

# latest version
pip install -U --no-cache-dir git+https://github.com/NeurosnapInc/neurosnap.git

# latest version + ClusterProt dependencies
pip install -U --no-cache-dir "neurosnap[clusterprot] @ git+https://github.com/NeurosnapInc/neurosnap.git"

# latest version + Kluster dependencies
pip install -U --no-cache-dir "neurosnap[kluster] @ git+https://github.com/NeurosnapInc/neurosnap.git"

# latest version + development dependencies
pip install -U --no-cache-dir "neurosnap[dev] @ git+https://github.com/NeurosnapInc/neurosnap.git"

Documentation

Official documentation can be found here: https://neurosnap.ai/docs/.

Building documentation

To build documentation, enter your virtual environment and run make docs from the root of the repository.

Then, open docs/build/html/index.html in a web browser.

Tutorials

Various interactive jupyter notebooks can be found in the example_notebooks directory of this repository. For additional tutorials check out the Official Neurosnap Blog or join our discord server.

Contributions

We welcome contributions to this package. If you have a feature that you want to code or have added, submit a pull request or an issue.

# setup virtual environment & activate it
python -m venv .venv && source .venv/bin/activate
# install package locally as editable and with dev dependencies
pip install --editable .[dev]

Citations

If you found this SDK helpful, please feel free to cite it using the following.

@misc{amani-2024,
	author = {Amani, Keaun and Amirabadi, Danial Gharaie},
	title = {{Neurosnap SDK}},
	year = {2024},
	url = {https://github.com/NeurosnapInc/neurosnap},
}

TODO:

• Consolidate some of the code that's shared and used across EvoEF2 and PDB2PQR.
• Also split those functions to have separate calls for the following:
  • add_hydrogens(structure, ...)
  • optimize_hydrogens(structure, ...)
  • assign_protonation_states(structure, ...)
  • assign_pqr(structure, ...)