Metadata-Version: 2.4
Name: evmutation2
Version: 0.0.2
Project-URL: Documentation, https://github.com/evedesignbio/evmutation2#readme
Project-URL: Issues, https://github.com/evedesignbio/evmutation2/issues
Project-URL: Source, https://github.com/evedesignbio/evmutation2
Author-email: Thomas Hopf <thomas.hopf@gmail.com>
License-Expression: MIT
License-File: LICENSE.txt
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: Implementation :: CPython
Requires-Python: >=3.12
Requires-Dist: beartype
Requires-Dist: biopython>=1.84
Requires-Dist: click
Requires-Dist: einops
Requires-Dist: einx
Requires-Dist: environs
Requires-Dist: jaxtyping
Requires-Dist: jsonargparse[signatures]
Requires-Dist: lightning
Requires-Dist: loguru
Requires-Dist: msgpack
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pyarrow
Requires-Dist: requests
Requires-Dist: torch
Requires-Dist: torchdata
Description-Content-Type: text/markdown

# EVmutation2

[![PyPI - Version](https://img.shields.io/pypi/v/evmutation2.svg)](https://pypi.org/project/evmutation2)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/evmutation2.svg)](https://pypi.org/project/evmutation2)

-----

## Table of Contents

- [Installation](#installation)
- [License](#license)

## Installation

```console
pip install evmutation2
```

## License

`evmutation2` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.

## External Code

### alphafold3-pytorch

We gratefully acknowledge lucidrain's AlphaFold3 reimplementation (https://github.com/lucidrains/alphafold3-pytorch)
which we use in modified form for the encoder part of our model:

> MIT License
>
> Copyright (c) 2024 Phil Wang
>
> Permission is hereby granted, free of charge, to any person obtaining a copy
> of this software and associated documentation files (the "Software"), to deal
> in the Software without restriction, including without limitation the rights
> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
> copies of the Software, and to permit persons to whom the Software is
> furnished to do so, subject to the following conditions:
>
> The above copyright notice and this permission notice shall be included in all
> copies or substantial portions of the Software.
>
> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
> SOFTWARE.

### OpenFold

We also gratefully acknowledge code from OpenFold included in parts of this codebase where noted:

> Copyright 2021 AlQuraishi Laboratory
> Copyright 2021 DeepMind Technologies Limited
>
> Licensed under the Apache License, Version 2.0 (the "License");
> you may not use this file except in compliance with the License.
> You may obtain a copy of the License at
>
>      http://www.apache.org/licenses/LICENSE-2.0
>
> Unless required by applicable law or agreed to in writing, software
> distributed under the License is distributed on an "AS IS" BASIS,
> WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
> See the License for the specific language governing permissions and
> limitations under the License.

### BioNemo

We also gratefully acknowledge code from BioNemo:

> Copyright (c) 2022, NVIDIA CORPORATION.  All rights reserved.
>
> Licensed under the Apache License, Version 2.0 (the "License");
> you may not use this file except in compliance with the License.
> You may obtain a copy of the License at
>
>     http://www.apache.org/licenses/LICENSE-2.0
>
> Unless required by applicable law or agreed to in writing, software
> distributed under the License is distributed on an "AS IS" BASIS,
> WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
> See the License for the specific language governing permissions and
> limitations under the License.