Re: Code question: Partitioning the patch contents into water and non-water

From: David Hardy (
Date: Fri Aug 17 2007 - 10:24:18 CDT

Hi Vincent,

The Molecule object has an is_water(atomID) method. Also, I believe
that waters are assigned atomIDs in the order O, H1, H2, but you
might want to verify this.


On Aug 17, 2007, at 4:01 AM, Vincent Kraeutler wrote:

> Hi,
> I'm currently looking into customized water-water interactions. So one
> thing I need to do is to partition the atoms contained in a patch into
> water and non-water. From what I can tell so far, this seems to be
> non-trivial, i.e. it looks like the atoms contained in a given patch
> come in no particular order.
> I would be deeply grateful if anyone could answer the following
> questions:
> i) Are the atoms in a patch sorted in any particular way? (I think
> they
> are not, but I'm not sure). If so, which one?
> ii) If I need to sort the atoms, I suppose it would be best to perform
> the sort right after atom migration and before the assignment to
> compute
> objects. Could you suggest where (in the code) I would best do that?
> (I'm currently looking at PatchMgr.* and friends with limited success)
> iii) How would I go about distinguishing water from non-water
> atoms? Or
> even just solvent from solute atoms? Is there an explicit way to do
> it,
> or would I have to go via topological information?
> Thanks & cheers,
> v.

David J. Hardy, PhD
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois

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