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Satvik Mishra 809ae7b4d7
[INVALID] AptaNet tests no longer fail on python version 3.13 (#219) 
fixes #218 by removing test restrictions on python 3.13. I also changed
the `__required__` attribute of `AptaNetPipeline` to no longer mention
that we support python 3.9 given we have no tests for that version in
the first place.
2025-12-15 01:39:38 +05:30
.github [MNT] [Dependabot](deps): Bump actions/checkout from 5 to 6 (#199) 2025-11-25 01:21:27 +01:00
build_tools [ENH] CI test to run jupyter notebooks (#74) 2025-09-05 10:30:00 +02:00
examples [FEATURE] Add cells for saving model weights in AptaTrans notebook, optimizer memory footprint of lightning training (#193) 2025-11-08 19:57:06 +01:00
pyaptamer [INVALID] AptaNet tests no longer fail on python version 3.13 (#219) 2025-12-15 01:39:38 +05:30
.gitignore [BUG] Remove .DS_Store files and add it to .gitignore (#207) 2025-12-11 13:50:08 +01:00
.pre-commit-config.yaml [BUG} Solves ruff errors for non-UNIX systems. (#96) 2025-08-14 21:40:18 +02:00
LICENSE [ENH] Readme and release content (#69) 2025-08-04 11:15:47 +02:00
pyproject.toml [BUG] AptaNetPipeline failing tests (#217) 2025-12-13 01:41:56 +05:30
README.md README - incompleteness pointers and typos (#86) 2025-08-06 08:17:56 +02:00

README.md

pyaptamer - AI for aptamer discovery

sponsored by ecoSPECS

The python library for easy aptamer design.

Tutorials · Issue Tracker · Project Board
Open Source BSD 3-clause GC.OS Sponsored
Community !discord !slack
CI/CD github-actions
Code !pypi !python-versions !black

🌟 Features

  • ✅ aptamer design and optimization algorithms
  • ✅ feature extraction from proteins and compounds
  • ✅ compatible with pdb and biopython
  • ✅ scikit-learn-like API - standardized and composable
  • 🛠️ Easily extendable with plugins
  • 📦 Minimal dependencies

NOTE: the package is in early development and not 100% feature complete - contributions appreciated!

🛠️ Usage


to be completed

⚡ Installation

Stable version from pip

NOTE: the package is not released yet on pypi - install from repo instead (unstable version)

pip install pyaptamer

Latest unstable version

# Clone the repository
git clone https://github.com/gc-os-ai/pyaptamer.git

# Install dependencies
pip install -e .  # latest version
# or editable developer install
pip install -e ".[dev]"

🤝 Contributing

Contributions are welcome! 🎉

How to start: find a good first issue

and/or join the discord and ping the developers, you can also ask for longer projects here.

Contributions and participation are subject to the GC.OS Code of Conduct.

🗺️ Roadmap

  • more complete set of aptamer design and protein feature algorithms
  • wider support for cif and/or biopandas
  • integration of first-principles simulation tools
  • Community feedback integration - suggest features on the issue tracker!

Team

The package is maintained in collaboration between ecoSPECS and the German Center for Open Source AI.