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62 lines
2.0 KiB
Bash
Executable File
62 lines
2.0 KiB
Bash
Executable File
#!/bin/bash
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#
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# Copyright 2021 DeepMind Technologies Limited
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# Downloads, unzips and flattens the PDB database for AlphaFold.
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#
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# Usage: bash download_pdb_mmcif.sh /path/to/download/directory
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set -e
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if [[ $# -eq 0 ]]; then
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echo "Error: download directory must be provided as an input argument."
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exit 1
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fi
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if ! command -v aria2c &> /dev/null ; then
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echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
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exit 1
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fi
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if ! command -v rsync &> /dev/null ; then
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echo "Error: rsync could not be found. Please install rsync."
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exit 1
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fi
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DOWNLOAD_DIR="$1"
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ROOT_DIR="${DOWNLOAD_DIR}/pdb_mmcif"
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RAW_DIR="${ROOT_DIR}/raw"
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MMCIF_DIR="${ROOT_DIR}/mmcif_files"
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echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
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mkdir --parents "${RAW_DIR}"
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rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
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rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
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"${RAW_DIR}"
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echo "Unzipping all mmCIF files..."
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find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +
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echo "Flattening all mmCIF files..."
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mkdir --parents "${MMCIF_DIR}"
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find "${RAW_DIR}" -type d -empty -delete # Delete empty directories.
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for subdir in "${RAW_DIR}"/*; do
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mv "${subdir}/"*.cif "${MMCIF_DIR}"
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done
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# Delete empty download directory structure.
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find "${RAW_DIR}" -type d -empty -delete
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aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"
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