evmutation2 0.0.1__tar.gz

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evmutation2-0.0.1/LICENSE.txt

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+MIT License
+
+Copyright (c) 2026-present Thomas Hopf <thomas.hopf@gmail.com>
+
+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.

evmutation2-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: evmutation2
+Version: 0.0.1
+Project-URL: Documentation, https://github.com/thomashopf/evmutation2#readme
+Project-URL: Issues, https://github.com/thomashopf/evmutation2/issues
+Project-URL: Source, https://github.com/thomashopf/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.

evmutation2-0.0.1/README.md

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+# 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.

evmutation2-0.0.1/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "evmutation2"
+dynamic = ["version"]
+description = ''
+readme = "README.md"
+requires-python = ">=3.12"
+license = "MIT"
+keywords = []
+authors = [
+  { name = "Thomas Hopf", email = "thomas.hopf@gmail.com" },
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: Implementation :: CPython",
+]
+dependencies = [
+    "torch", "numpy", "einx", "einops", "lightning", "click",
+    "biopython>=1.84", "msgpack", "pandas", "requests", "loguru",
+    "jsonargparse[signatures]", "beartype", "environs", "jaxtyping",
+    "torchdata", "pyarrow",
+]
+
+[project.urls]
+Documentation = "https://github.com/thomashopf/evmutation2#readme"
+Issues = "https://github.com/thomashopf/evmutation2/issues"
+Source = "https://github.com/thomashopf/evmutation2"
+
+[tool.hatch.version]
+path = "src/evmutation2/__about__.py"
+
+[tool.hatch.envs.types]
+extra-dependencies = [
+  "mypy>=1.0.0",
+]
+[tool.hatch.envs.types.scripts]
+check = "mypy --install-types --non-interactive {args:src/evmutation2 tests}"
+
+[tool.coverage.run]
+source_pkgs = ["evmutation2", "tests"]
+branch = true
+parallel = true
+omit = [
+  "src/evmutation2/__about__.py",
+]
+
+[tool.coverage.paths]
+evmutation2 = ["src/evmutation2", "*/evmutation2/src/evmutation2"]
+tests = ["tests", "*/evmutation2/tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+  "no cov",
+  "if __name__ == .__main__.:",
+  "if TYPE_CHECKING:",
+]

evmutation2-0.0.1/src/evmutation2/__about__.py

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+# SPDX-FileCopyrightText: 2026-present Thomas Hopf <thomas.hopf@gmail.com>
+#
+# SPDX-License-Identifier: MIT
+__version__ = "0.0.1"

evmutation2-0.0.1/src/evmutation2/__init__.py

@@ -0,0 +1,3 @@
+# SPDX-FileCopyrightText: 2026-present Thomas Hopf <thomas.hopf@gmail.com>
+#
+# SPDX-License-Identifier: MIT