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30 changes: 30 additions & 0 deletions LICENSE
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BSD 3-Clause License

Copyright (c) 2025 - present, The pyaptamer developers.

All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
93 changes: 76 additions & 17 deletions README.md
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### Repository of the "AI for drug discovery" project with GC.OS and ecoSPECS
# pyaptamer - AI for aptamer discovery

Project board: https://github.com/orgs/gc-os-ai/projects/1
### sponsored by ecoSPECS

Issue tracker: https://github.com/gc-os-ai/pyaptamer/issues
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 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) |

#### Team
## 🌟 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

```python

##### GC.OS
to be completed
```

Franz Kiraly ([@fkiraly](https://www.github.com/fkiraly)) - primary point of contact and tech contributor
---

Simon Blanke ([@simonblanke](https://www.github.com/simonblanke)) - advisory, optimization algorithms
## ⚡ Installation

### Stable version from pip

##### ecoSPECS
```bash
pip install pyaptamer
```

Dennis Kubiczek ([@KubiczekD](https://www.github.com/KubiczekD)) tech lead and primary point of contact:
### Latest unstable version

Jakob Birke ([@jabirke](https://www.github.com/jabirke)) - contributor and domain expert
```bash
# Clone the repository
git clone https://github.com/gc-os-ai/pyaptamer.git

Kerstin Moser ([@KerstinMoser](https://www.github.com/KerstinMoser)) - stakeholder, head of R&D
# Install dependencies
pip install -e . # latest version
# or editable developer install
pip install -e ".[dev]"
```

---

##### ESoC
## 🤝 Contributing

Franz Kiraly ([@fkiraly](https://www.github.com/fkiraly)) - primary point of contact for ESoC
Contributions are welcome! 🎉

Avinab Neogy ([@avinab-neogy](https://www.github.com/avinab-neogy)) - ESoC contributor
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)

Matteo Pinna ([@nennomp](https://www.github.com/nennomp)) - ESoC contributor
and/or join the [discord](https://discord.gg/7uKdHfdcJG) and ping the developers,
you can also ask for longer projects here.

Satvik Mishra ([@satvshr](https://www.github.com/satvshr)) - ESoC contributor
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

Siddharth ([@siddharth7113](https://www.github.com/siddharth7113)) - ESoC contributor
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))
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