initial alphafold2

scripts/download_uniref90.sh

+#!/bin/bash
+#
+# 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.
+#
+# Downloads and unzips the UniRef90 database for AlphaFold.
+#
+# Usage: bash download_uniref90.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/uniref90"
+SOURCE_URL="ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+pushd "${ROOT_DIR}"
+gunzip "${ROOT_DIR}/${BASENAME}"
+popd

setup.py

+# 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.
+"""Install script for setuptools."""
+
+from setuptools import find_packages
+from setuptools import setup
+
+setup(
+    name='alphafold',
+    version='2.2.1',
+    description='An implementation of the inference pipeline of AlphaFold v2.0.'
+    'This is a completely new model that was entered as AlphaFold2 in CASP14 '
+    'and published in Nature.',
+    author='DeepMind',
+    author_email='alphafold@deepmind.com',
+    license='Apache License, Version 2.0',
+    url='https://github.com/deepmind/alphafold',
+    packages=find_packages(),
+    install_requires=[
+        'absl-py',
+        'biopython',
+        'chex',
+        'dm-haiku',
+        'dm-tree',
+        'docker',
+        'immutabledict',
+        'jax',
+        'ml-collections',
+        'numpy',
+        'pandas',
+        'scipy',
+        'tensorflow-cpu',
+    ],
+    tests_require=['mock'],
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: Apache Software License',
+        'Operating System :: POSIX :: Linux',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Topic :: Scientific/Engineering :: Artificial Intelligence',
+    ],
+)