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.
