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#!/bin/bash
# Script to download files from RCSB http file download services.
# Use the -h switch to get help on usage.
if ! command -v curl &> /dev/null
then
echo "'curl' could not be found. You need to install 'curl' for this script to work."
exit 1
fi
PROGNAME=$0
BASE_URL="https://files.rcsb.org/download"
usage() {
cat << EOF >&2
Usage: $PROGNAME -f <file> [-o <dir>] [-c] [-p]
-f <file>: the input file containing a comma-separated list of PDB ids
-o <dir>: the output dir, default: current dir
-c : download a cif.gz file for each PDB id
-p : download a pdb.gz file for each PDB id (not available for large structures)
-a : download a pdb1.gz file (1st bioassembly) for each PDB id (not available for large structures)
-x : download a xml.gz file for each PDB id
-s : download a sf.cif.gz file for each PDB id (diffraction only)
-m : download a mr.gz file for each PDB id (NMR only)
-r : download a mr.str.gz for each PDB id (NMR only)
EOF
exit 1
}
download() {
url="$BASE_URL/$1"
out=$2/$1
echo "Downloading $url to $out"
curl -s -f $url -o $out || echo "Failed to download $url"
}
listfile=""
outdir="."
cif=false
pdb=false
pdb1=false
xml=false
sf=false
mr=false
mrstr=false
while getopts f:o:cpaxsmr o
do
case $o in
(f) listfile=$OPTARG;;
(o) outdir=$OPTARG;;
(c) cif=true;;
(p) pdb=true;;
(a) pdb1=true;;
(x) xml=true;;
(s) sf=true;;
(m) mr=true;;
(r) mrstr=true;;
(*) usage
esac
done
shift "$((OPTIND - 1))"
if [ "$listfile" == "" ]
then
echo "Parameter -f must be provided"
exit 1
fi
contents=$(cat $listfile)
# see https://stackoverflow.com/questions/918886/how-do-i-split-a-string-on-a-delimiter-in-bash#tab-top
IFS=',' read -ra tokens <<< "$contents"
for token in "${tokens[@]}"
do
if [ "$cif" == true ]
then
download ${token}.cif.gz $outdir
fi
if [ "$pdb" == true ]
then
download ${token}.pdb.gz $outdir
fi
if [ "$pdb1" == true ]
then
download ${token}.pdb1.gz $outdir
fi
if [ "$xml" == true ]
then
download ${token}.xml.gz $outdir
fi
if [ "$sf" == true ]
then
download ${token}-sf.cif.gz $outdir
fi
if [ "$mr" == true ]
then
download ${token}.mr.gz $outdir
fi
if [ "$mrstr" == true ]
then
download ${token}_mr.str.gz $outdir
fi
done
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