The most general solution to this problem boils down to one of graph
isomorphism:
http://en.wikipedia.org/wiki/Graph_isomorphism
James
On Apr 16, 2009, at 8:13 PM, rui wrote:
> Dear all,
>
> I want to pull out the sugar binding proteins from the pdb, however,
> there are so many different names for the ligand ( GAL, GLC,
> RIP... ) and it's not easy to get a complete list. If I want to pull
> out some fragments based on a specific geometry ( for instance, the
> glucose has C1 C2 C3 C4 C5 C6, and I want to use the geometry for
> instance, O5,C1, O1, C2 and O2 to pull out all the ligands that
> contains this kind of geometry. Is there any straightforward way to
> do it?
>
> Thanks a lot.
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