Commit 1109480e authored by Augustin-Zidek's avatar Augustin-Zidek
Browse files

Initial release of AlphaFold.

PiperOrigin-RevId: 384954738
parents
#!/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
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
# 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='2.0.0',
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',
'scipy',
'tensorflow',
],
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',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
],
)
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