[gmx-users] g_clustsize method

David van der Spoel spoel at xray.bmc.uu.se
Wed May 20 19:26:42 CEST 2009

Jacob Spooner wrote:
> It would be very advantageous for me to have a g_clustsize that 
> could implement the Jarvis-Patrick method instead of single linkage.
> Would this be very difficult to achieve? Or would it be easy enough to 
> use source code from g_cluster and do a sort of transplant? Thank
> you for you help

Maybe these two programs could be merged altogether, or at least the 
double code combined in a separate source file or so. Note that it is a 
good idea to check whether the algorithms have been implemented 
correctly anyway.

>>>> David van der Spoel <spoel at xray.bmc.uu.se> 5/19/2009 10:06 PM >>>
> Jacob Spooner wrote:
>> I am planning on using g_clustsize to do some condensation analysis.  I looked at g_cluster and see that it has a number of method options including single linkage and jarvis patrick.  Is it true that g_clustsize has only the single linkage option? I took a look at the source code but this type of thing is not my strength.
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> Yes. Is that not sufficient?

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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