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#!/bin/bash
# Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is licensed under CC BY-NC-SA 4.0. To view a copy of
# this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/
#
# To request access to the AlphaFold 3 model parameters, follow the process set
# out at https://github.com/google-deepmind/alphafold3. You may only use these
# if received directly from Google. Use is subject to terms of use available at
# https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
set -euo pipefail
readonly db_dir=${1:-$HOME/public_databases}
for cmd in wget tar zstd ; do
if ! command -v "${cmd}" > /dev/null 2>&1; then
echo "${cmd} is not installed. Please install it."
fi
done
echo "Fetching databases to ${db_dir}"
mkdir -p "${db_dir}"
readonly SOURCE=https://storage.googleapis.com/alphafold-databases/v3.0
echo "Start Fetching and Untarring 'pdb_2022_09_28_mmcif_files.tar'"
wget --quiet --output-document=- \
"${SOURCE}/pdb_2022_09_28_mmcif_files.tar.zst" | \
tar --use-compress-program=zstd -xf - --directory="${db_dir}" &
for NAME in mgy_clusters_2022_05.fa \
bfd-first_non_consensus_sequences.fasta \
uniref90_2022_05.fa uniprot_all_2021_04.fa \
pdb_seqres_2022_09_28.fasta \
rnacentral_active_seq_id_90_cov_80_linclust.fasta \
nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta \
rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta ; do
echo "Start Fetching '${NAME}'"
wget --quiet --output-document=- "${SOURCE}/${NAME}.zst" | \
zstd --decompress > "${db_dir}/${NAME}" &
done
wait
echo "Complete"