[R] how to download pdb structure files?
csardi at rmki.kfki.hu
Sun Oct 28 20:09:06 CET 2007
On Sun, Oct 28, 2007 at 11:25:06AM -0700, Ben Bolker wrote:
> Baoqiang Cao-2 wrote:
> > Dear All,
> > I'd like to know if there is anyway to download a certain structure file
> > from http://www.pdb.org/. I tried the following but failed:
> > tmp <-
> > download.file(url="ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb",
> > destfile="pdb100d.ent.gz")
> > trying URL 'ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb'
> > Error in download.file(url =
> > "ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb", :
> > cannot open URL
> > 'ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb'
> > Any tips to fix it please? Thanks in advance.
> > Best,
> > Baoqiang
> I don't know that this is possible within R. I would try obtaining wget
> and using
> wget -r to fetch the files ...
If you don't know then you might try to read the documentation. Then it takes
about five seconds to get the right syntax:
Hint: you can use gzfile to decompress the file on th fly, while reading
it into R.
> View this message in context: http://www.nabble.com/how-to-download-pdb-structure-files--tf4707557.html#a13456168
> Sent from the R help mailing list archive at Nabble.com.
Csardi Gabor <csardi at rmki.kfki.hu> MTA RMKI, ELTE TTK
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