getPdbUpdate.pl dates getPdbUpdate.pl latest getPdbUpdate.pl 20020708
1) LWP::UserAgent, a Perl module for downloading files from the World Wide Web. LWP::UserAgent is part of the libwww-perl module, which is available from CPAN. Please see the link in the SEE ALSO section.
2) wget, a common Unix utility for downloading files from the World Wide Web. wget is also available for most Windows operating systems. Please see the link in the SEE ALSO section.
1) Get a list of valid update dates:
getPdbUpdate.pl dates
In this mode, the program will only retrieve and print a list of all valid update dates.
2) Get the files from the latest update:
getPdbUpdate.pl latest
In this mode, the program will retrieve all files associated with the latest update. The files will be saved in some or all of the following directories underneath your current working directory:
<yyyymmdd>/added <yyyymmdd>/modified <yyyymmdd>/obsolete <yyyymmdd>/models_added <yyyymmdd>/models_modified <yyyymmdd>/models_obsolete
3) Get the files from any given update:
getPdbUpdate.pl <yyyymmdd>
e.g.: getPdbUpdate.pl 20020708
In this mode, the program will retrieve all files associated with the specified update date. Again, the files will be saved in the same directory structure, e.g.:
20020708/added 20020708/modified 20020708/obsolete 20020708/models_added 20020708/models_obsolete
ls-lR wgettest.temp <yyyymmdd>/added.pdb <yyyymmdd>/added.sf <yyyymmdd>/added.nmr <yyyymmdd>/modified.pdb <yyyymmdd>/modified.sf <yyyymmdd>/modified.nmr <yyyymmdd>/obsolete.pdb <yyyymmdd>/obsolete.sf <yyyymmdd>/obsolete.nmr <yyyymmdd>/models_added.pdb <yyyymmdd>/models_modified.pdb <yyyymmdd>/models_obsolete.pdb
If any of these files are present prior to running this program, they will be overwritten! A safe option would be to create a new directory first, and then run getPdbUpdate.pl, e.g.:
mkdir newpdbfiles cd newpdbfiles getPdbUpdate.pl latest
2) If an added file (e.g. pdb1f5d.ent.Z from added.pdb) was obsoleted after the specified update date (20001212), then the program will issue a warning, and save the file in the obsolete directory (20001212/obsolete) on local disk instead of the added directory.
3) As of 1 July 2002, all theoretical models were moved to a dedicated area of the PDB FTP archive, and effectively all access to them was removed from the PDB Web interface. If a file (e.g. pdb1pln.ent.Z) represents a theoretical model, the program will issue a warning, and save the file in one of the models directories on local disk.
4) By default, the program will access the main PDB FTP servers at SDSC. Alternatively, another mirror FTP site may be specified as a second command line argument, e.g.:
getPdbUpdate.pl latest ftp://rutgers.rcsb.org/PDB/pub/pdb/
Version history:
Version Date Comments
1.1 2002-09-13 Moved from LWP::Simple to LWP::UserAgent
to support proxies (e.g. from behind a firewall)
1.0 2002-07-16 First release
perl getPdbUpdate latest
2) Be aware that only LWP::UserAgent::mirror, but not wget, preserves the original time stamps of the files being downloaded. getPdbUpdate.pl is intended only for your personal use, and hence this limitation may be of little consequence to you. Please note that files downloaded by getPdbUpdate.pl should not be served to the public through any kind of mirror site.
http://www.rcsb.org/pdb/ -- Protein Data Bank (PDB) home page ftp://ftp.rcsb.org/pub/pdb -- PDB FTP site http://www.rcsb.org/pdb/cgi/resultBrowser.cgi?Date::update=1 -- Last PDB Update ftp://ftp.rcsb.org/pub/pdb/software -- download page for this script and documentation
http://www.cpan.org/modules/by-module/LWP/ -- libwww-perl download page http://www.gnu.org/software/wget/wget.html -- wget home page
Copyright 2002
The Regents of the University of California
All Rights Reserved
Permission to use, copy, modify and distribute any part of this PDB software for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies. Those desiring to incorporate this PDB Software into commercial products or use for commercial purposes should contact the Technology Transfer Office, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345. In no event shall the University of California be liable to any party for direct, indirect, special, incidental, or consequential damages, including lost profits, arising out of the use of this PDB software, even if the University of California has been advised of the possibility of such damage. The PDB software provided herein is on an "as is" basis, and the University of California has no obligation to provide maintenance, support, updates, enhancements, or modifications. The University of California makes no representations and extends no warranties of any kind, either implied or express, including, but not limited to, the implied warranties of merchantability or fitness for a particular purpose, or that the use of the pdb software will not infringe any patent, trademark or other rights.