Hello,
My question may be simple. But I think others could benefit from having this skill, and I'm not quite sure how to separate these files once I get them. So I was looking through a molecular dynamics paper and I noticed that the authors used a lot of PDB files so I wanted to take those files and retrieve them with curl (c uniform resource locater).
If I just call this command then in my terminal I can see all the PDB files from the protein data bank that I am interested in, where the curly braces specify different files in the basic file extension.
$ sudo curl "http://files.rcsb.org/view/{1PPE,1AVW,1BRC,1CGI,1TGS,1TAB,2PTC,2SIC,1DFJ,2SNI,1UGH,1CHO,1
ACB,2TEC,4HTC,1CSE,1MAH,1FSS,1BRS,1DFJ}.pdb"
If I create an empty file named "enzyme_inhibitor_complexes, and redirect the output sequentially with " >> " (instead of overwriting the file multiple times with " > " which would not be good!) so that 1PPE is dumped into enzyme_inhibitor_complexes, then 1AVW, and finally 1DFJ, then I can dump all the information from the pdb files into the enzyme_inhibitor_complexes file one after another.
$ curl "http://files.rcsb.org/view/{1PPE,1AVW,1BRC,1CGI,1TGS,1TAB,2PTC,2SIC,1DFJ,2SNI,1UGH,1CHO,1
ACB,2TEC,4HTC,1CSE,1MAH,1FSS,1BRS,1DFJ}.pdb" >> enzyme_inhibitor_complexes
But now I want to separate the files into their own pdb files, such as 1PPE.pdb, 1AVW.pdb, 1BRC.pdb, and so forth. I would rather not have all the files in one big file. I felt that I had to do that compromise to collect all the pdb information.
For example, if I just wanted to download and save one of the files, then that would be easy.
$ curl "http://files.rcsb.org/view/1CGI.pdb" -o 1CGI.pdb,
where "-o" designates the output file.
It seems like it would be useful to use a scripting perl or python "for loop", but I don't know how I would make one for this "curl" application.
Obviously, it's more tedious to learn how to do this than downloading all the files individually from my web browser, but if I can learn how to do this, then I would save a lot of time in the long run as I work with pdb files in my bioinformatics career.
Thank you! Your help is much appreciated!
- Adron
This is simple to do in a bash for-loop, using wget.
for id in 1PPE 1AVW 1BRC (etc)
do
wget https://files.rcsb.org/download/57db3a6b48954c87d9786897.pdb
done
No need for post processing, you get all the files separately.
This is simple to do in a bash for-loop, using wget.
for id in 1PPE 1AVW 1BRC (etc)
do
wget https://files.rcsb.org/download/57db3a6b48954c87d9786897.pdb
done
No need for post processing, you get all the files separately.
download the attached file
make it executable
chmod 755 pdbdwn.bash
it your bash shell does not reside in /bin/bash
edit the first line accordingly
call it as:
pdbdwn.bash 1UDE 5ksz
you may use upper or lowercase characters, the file will be found, and it will be saved with the casing as you typed
i.e. if you give 5KSZ your file will be in 5KSZ.pdb.gz, but is you typed 5kSz your file will be 5kSz.pdb.gz
best wishes
rogelio
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