[bip] biopython

[Andrew Perry]

On Sun, Jul 5, 2009 at 6:55 PM, amrita bhu2005 <amritabhu2005 at yahoo.com>wrote:

>
> Dear all,
>
> I want to know that by using biopython programming is it possible to
> extract chemical shift information of amino acidsfrom BMRB or Ref-DB or not.
>
> Thanks,
> Amrita Kumari
> Research Scholar
> IISER Mohali
> Chandigarh-160019
> INDIA
>

You might take a look at CCPN. It has quite an extensive Python API for
reading many NMR formats ... you could probably use the standard Python
library urllib2 to pull down BMRB records (eg
http://www.bmrb.wisc.edu/cgi-bin/explore.cgi?format=raw&bmrbId=6448 , where
6448 is the BMRB entry number) , then parse them with CCPN.

http://www.ccpn.ac.uk/ccpn/software/downloads-v2/

Just a guess, but it looks like the BMRB ("nmrSTAR format") parser can be
found in the FormatConverter package, under:
ccpnmr/ccpnmr2.0/python/ccp/format/nmrStar

I haven't had a chance to use CCPN yet, but it appears to be maturing quite
nicely.

Hope this helps,

Andrew Perry
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