Metadata-Version: 2.4
Name: antibody-utils
Version: 0.1.1
Summary: Utilities for antibody sequence and structure analysis.
Keywords: antibody,immunoglobulin,CDR,numbering,bioinformatics
Author: Benjamin Heathcote Williams
Author-email: Benjamin Heathcote Williams <benjaminhwilliams@users.noreply.github.com>
License-Expression: BSD-3-Clause
License-File: LICENCE
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Dist: gemmi
Requires-Dist: numpy
Requires-Dist: platformdirs ; extra == 'canonicals'
Requires-Dist: anarcii>=2 ; extra == 'numbering'
Maintainer: Oxford Protein Informatics Group
Maintainer-email: Oxford Protein Informatics Group <opig@stats.ox.ac.uk>
Requires-Python: >=3.11
Project-URL: Documentation, https://antibody-utils.readthedocs.io
Project-URL: Source, https://github.com/oxpig/antibody-utils
Project-URL: Issues, https://github.com/oxpig/antibody-utils/issues
Provides-Extra: canonicals
Provides-Extra: numbering
Description-Content-Type: text/markdown

# antibody-utils

[![Tests](https://github.com/oxpig/antibody-utils/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/oxpig/antibody-utils/actions/workflows/tests.yml)
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[![PyPI](https://img.shields.io/pypi/v/antibody-utils)](https://pypi.org/project/antibody-utils/)
[![Python versions](https://img.shields.io/pypi/pyversions/antibody-utils)](https://pypi.org/project/antibody-utils/)
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[![Licence: BSD-3-Clause](https://img.shields.io/badge/licence-BSD--3--Clause-blue)](LICENCE)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)

Utilities for antibody sequence and structure analysis: numbering, region
definitions, sequence comparison, VH/VL orientation and more.

antibody-utils is developed by the
[Oxford Protein Informatics Group](https://opig.stats.ox.ac.uk/).

## Installation

With [uv](https://docs.astral.sh/uv/), add antibody-utils to your project:

```console
uv add antibody-utils
```

Or with pip:

```console
pip install antibody-utils
```

To number raw sequences and structures with
[ANARCII](https://github.com/oxpig/ANARCII), install the `numbering` extra:

```console
uv add "antibody-utils[numbering]"
```

```console
pip install "antibody-utils[numbering]"
```

> [!TIP]
> ANARCII depends on PyTorch.  On Linux, the default PyTorch wheels from PyPI
> bundle CUDA libraries, a download of several gigabytes.  To get the build that
> suits your machine (CPU-only, or your CUDA or ROCm version):
>
> - With uv's pip interface, let uv detect your hardware:
>
>   ```console
>   uv pip install --torch-backend=auto "antibody-utils[numbering]"
>   ```
>
>   `uv add` has no such flag; in a uv project, point `torch` at the right
>   PyTorch index in your `pyproject.toml` instead, as described in
>   [uv's PyTorch guide](https://docs.astral.sh/uv/guides/integration/pytorch/).
>
> - pip cannot detect your hardware, so install PyTorch first from the
>   [PyTorch index](https://pytorch.org/get-started/locally/) for your platform,
>   e.g. CPU-only:
>
>   ```console
>   pip install torch --index-url https://download.pytorch.org/whl/cpu
>   pip install "antibody-utils[numbering]"
>   ```

## Documentation

See the [documentation](https://antibody-utils.readthedocs.io) for a user guide
and API reference.

## Citing

If you use antibody-utils in published work, please cite it and the methods
it implements; see [Citing](https://antibody-utils.readthedocs.io/en/latest/citing.html)
in the documentation.

## Contributing

See [CONTRIBUTING.md](CONTRIBUTING.md) for how to set up a development
environment, run the tests and propose changes.

## Licence

BSD 3-Clause; see [LICENCE](LICENCE).
