Metadata-Version: 2.4
Name: pyaptamer
Version: 0.1.0a1
Summary: Python library for aptamer simulation
Author-email: German Center for Open Source AI <info@gcos.ai>
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.83
Requires-Dist: datasets>=4.0.0
Requires-Dist: lightning>=2.5.3
Requires-Dist: numpy>=2.0.2
Requires-Dist: pandas>=2.0.0
Requires-Dist: scikit-base
Requires-Dist: torch>=2.5.1
Requires-Dist: scikit-learn<1.8.0,>=1.3.0
Requires-Dist: skorch
Requires-Dist: imblearn
Requires-Dist: requests
Provides-Extra: dev
Requires-Dist: ruff>=0.12.0; extra == "dev"
Requires-Dist: pytest>=8.0.0; extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Dynamic: license-file

# pyaptamer - AI for aptamer discovery

### sponsored by ecoSPECS

The python library for easy aptamer design.

|  | **[Tutorials](https://github.com/gc-os-ai/pyaptamer/tree/main/examples)** · **[Issue Tracker](https://github.com/gc-os-ai/pyaptamer/issues)** · **[Project Board](https://github.com/orgs/gc-os-ai/projects/1)** |
|---|---|
| **Open&#160;Source** | [![BSD 3-clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://github.com/gc-os-ai/pyaptamer/blob/main/LICENSE) [![GC.OS Sponsored](https://img.shields.io/badge/GC.OS-Sponsored%20Project-orange.svg?style=flat&colorA=0eac92&colorB=2077b4)](https://gc-os-ai.github.io/) | |
| **Community** | [![!discord](https://img.shields.io/static/v1?logo=discord&label=discord&message=chat&color=lightgreen)](https://discord.gg/7uKdHfdcJG) [![!slack](https://img.shields.io/static/v1?logo=linkedin&label=LinkedIn&message=news&color=lightblue)](https://www.linkedin.com/company/german-center-for-open-source-ai/) |
| **CI/CD** | [![github-actions](https://img.shields.io/github/actions/workflow/status/gc-os-ai/pyaptamer/release.yml?logo=github)](https://github.com/sktime/pytorch-forecasting/actions/workflows/pypi_release.yml) |
| **Code** | [![!pypi](https://img.shields.io/pypi/v/pytorch-forecasting?color=orange)](https://pypi.org/project/pyaptamer/) [![!python-versions](https://img.shields.io/pypi/pyversions/pyaptamer)](https://www.python.org/) [![!black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/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, API is unstable and not 100% features are complete - contributions appreciated!

---

## 🛠️ Usage

Checkout [examples/](examples) to see how to use the current API.

---

## ⚡ Installation

### PyPI prerelease

```bash
pip install pyaptamer==0.1.0a1
```
NOTE: pyaptamer is in early development. The API is unstable and may change between releases.

### Development install

```bash
# 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](https://github.com/gc-os-ai/pyaptamer/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22good%20first%20issue%22)

and/or join the [discord](https://discord.gg/7uKdHfdcJG) and ping the developers,
you can also ask for longer projects here.

Please open an issue before making a PR about bug/feature.

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!](https://github.com/gc-os-ai/pyaptamer/issues)

---

#### Team

The package is maintained in collaboration between [ecoSPECS](https://ecospecs.de/en/) and the [German Center for Open Source AI](https://gcos.ai/).

* German Center for Open Source AI
    * Franz Kiraly ([@fkiraly](https://www.github.com/fkiraly)) - primary point of contact (package)
    * Simon Blanke ([@simonblanke](https://www.github.com/simonblanke))
* ecoSPECS
    * Dennis Kubiczek ([@KubiczekD](https://www.github.com/KubiczekD)) - primary point of contact (domain/aptamers)
    * Fatih Yolcu ([@fat1hy0](https://www.github.com/fat1hy0))
    * Jakob Birke ([@jabirke](https://www.github.com/jabirke))
    * Kerstin Moser ([@KerstinMoser](https://www.github.com/KerstinMoser))
* European Summer of Code contributors 2025
    * Matteo Pinna ([@nennomp](https://www.github.com/nennomp))
    * Satvik Mishra ([@satvshr](https://www.github.com/satvshr))
    * Siddharth ([@siddharth7113](https://www.github.com/siddharth7113))
