semvec/pypi-packages huggingface dataset:
duet-tools 1.0.1
Output management tools for LANL DUET program
License: MIT
Requires Python: >=3.10

# duet-tools

## Quick-Links

[Documentation](https://nmc-cafes.github.io/duet-tools/) - [PyPi Package](https://pypi.org/project/duet-tools/)

## What is duet-tools?

duet-tools is a Python package that provides a convenient interface for programmatically working with the inputs and outputs of the DUET program developed by [McDanold et al. (2023)](https://doi.org/10.1016/j.ecolmodel.2023.110425) at Los Alamos National Lab. Central to the package is the ability to calibrate the values in DUET outputs to match targets supplied by the user or national datasets.

The goals of duet-tools are to:

1. Write a DUET input file.
2. Read in DUET outputs for easy manipulation.
3. Calibrate DUET outputs by scaling the magnitude of the parameter values while retaining the spatial distributions from DUET.
4. Provide a platform for the future development of additional tools centered around DUET.

## Installation

quicfire-tools can be installed using `pip`.

### pip

```bash
pip install duet-tools
```

To use the [landfire](reference.md#duet_tools.landfire) module, install using the `landfire` extra using `pip`.

```bash
pip install duet-tools[landfire]
```

## Issues

If you encounter any issues with the quicfire-tools package, please submit an issue on the duet-tools GitHub
repository [issues page](https://github.com/nmc-cafes/duet-tools/issues).
bsbt 0.1.2
BSBT: Binding Sequence Benchmarking Tool - A Python package for benchmarking protein language models and predicting antibody-antigen binding.
License: MIT
Requires Python: >=3.8

# 🧬 BSBT – Antibody to Antigen Prediction

BSBT (Biological Sequence Binding Tool) is a Python package designed to **predict antigen sequences given antibody sequences**.  
The package is structured to allow easy experimentation and integration of **protein language models (PLMs)** or **large language models (LLMs)** in the future.

At the moment, BSBT provides a **mock implementation** using hardcoded antibody–antigen sequence mappings. This enables developers and researchers to test the pipeline structure before connecting it to real machine learning models.

---

## ✨ Features

- 🔹 Simple **antibody → antigen prediction** interface (`findAntigen`)
- 🔹 Current backend: **mock hardcoded mappings**
- 🔹 Future backend: **LLM or fine-tuned PLM integration**
- 🔹 Modular design (easy to extend, swap components)
- 🔹 Unit tests included (`pytest`-ready)

---

## 📦 Installation

You can install directly from PyPI (after publishing):

```bash
pip install bsbt