Merge tag 'v2.3.2'

scripts/download_alphafold_params.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 AlphaFold parameters.
+#
+# Usage: bash download_alphafold_params.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}/params"
+SOURCE_URL="https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
+  --directory="${ROOT_DIR}" --preserve-permissions
+rm "${ROOT_DIR}/${BASENAME}"

scripts/download_bfd.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 BFD database for AlphaFold.
+#
+# Usage: bash download_bfd.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}/bfd"
+# Mirror of:
+# https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz.
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
+  --directory="${ROOT_DIR}"
+rm "${ROOT_DIR}/${BASENAME}"

scripts/download_mgnify.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 MGnify database for AlphaFold.
+#
+# Usage: bash download_mgnify.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}/mgnify"
+# Mirror of:
+# ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2022_05/mgy_clusters.fa.gz
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/v2.3/mgy_clusters_2022_05.fa.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+pushd "${ROOT_DIR}"
+gunzip "${ROOT_DIR}/${BASENAME}"
+popd

scripts/download_pdb70.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 PDB70 database for AlphaFold.
+#
+# Usage: bash download_pdb70.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}/pdb70"
+SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
+  --directory="${ROOT_DIR}"
+rm "${ROOT_DIR}/${BASENAME}"

scripts/download_pdb_mmcif.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, unzips and flattens the PDB database for AlphaFold.
+#
+# Usage: bash download_pdb_mmcif.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
+
+if ! command -v rsync &> /dev/null ; then
+    echo "Error: rsync could not be found. Please install rsync."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/pdb_mmcif"
+RAW_DIR="${ROOT_DIR}/raw"
+MMCIF_DIR="${ROOT_DIR}/mmcif_files"
+
+echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
+echo "If the download speed is too slow, try changing the mirror to:"
+echo "  * rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ (Europe)"
+echo "  * ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ (Asia)"
+echo "or see https://www.wwpdb.org/ftp/pdb-ftp-sites for more download options."
+mkdir --parents "${RAW_DIR}"
+rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
+  rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
+  "${RAW_DIR}"
+
+echo "Unzipping all mmCIF files..."
+find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +
+
+echo "Flattening all mmCIF files..."
+mkdir --parents "${MMCIF_DIR}"
+find "${RAW_DIR}" -type d -empty -delete  # Delete empty directories.
+for subdir in "${RAW_DIR}"/*; do
+  mv "${subdir}/"*.cif "${MMCIF_DIR}"
+done
+
+# Delete empty download directory structure.
+find "${RAW_DIR}" -type d -empty -delete
+
+aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"

scripts/download_pdb_seqres.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 PDB SeqRes database for AlphaFold.
+#
+# Usage: bash download_pdb_seqres.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}/pdb_seqres"
+SOURCE_URL="ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+
+# Keep only protein sequences.
+grep --after-context=1 --no-group-separator '>.* mol:protein' "${ROOT_DIR}/pdb_seqres.txt" > "${ROOT_DIR}/pdb_seqres_filtered.txt"
+mv "${ROOT_DIR}/pdb_seqres_filtered.txt" "${ROOT_DIR}/pdb_seqres.txt"

scripts/download_small_bfd.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 Small BFD database for AlphaFold.
+#
+# Usage: bash download_small_bfd.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}/small_bfd"
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+pushd "${ROOT_DIR}"
+gunzip "${ROOT_DIR}/${BASENAME}"
+popd

scripts/download_uniprot.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, unzips and merges the SwissProt and TrEMBL databases for
+# AlphaFold-Multimer.
+#
+# Usage: bash download_uniprot.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}/uniprot"
+
+TREMBL_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz"
+TREMBL_BASENAME=$(basename "${TREMBL_SOURCE_URL}")
+TREMBL_UNZIPPED_BASENAME="${TREMBL_BASENAME%.gz}"
+
+SPROT_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
+SPROT_BASENAME=$(basename "${SPROT_SOURCE_URL}")
+SPROT_UNZIPPED_BASENAME="${SPROT_BASENAME%.gz}"
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}"
+aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
+pushd "${ROOT_DIR}"
+gunzip "${ROOT_DIR}/${TREMBL_BASENAME}"
+gunzip "${ROOT_DIR}/${SPROT_BASENAME}"
+
+# Concatenate TrEMBL and SwissProt, rename to uniprot and clean up.
+cat "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" >> "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}"
+mv "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" "${ROOT_DIR}/uniprot.fasta"
+rm "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}"
+popd

scripts/download_uniref30.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 Uniclust30 database for AlphaFold.
+#
+# Usage: bash download_uniclust30.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}/uniref30"
+# Mirror of:
+# https://wwwuser.gwdg.de/~compbiol/uniclust/2021_03/UniRef30_2021_03.tar.gz
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
+  --directory="${ROOT_DIR}"
+rm "${ROOT_DIR}/${BASENAME}"

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='2.3.1',
+    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=[
+        'matplotlib',  # For notebook_utils_test.
+        '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',
+    ],
+)