one other short thing.
If this is the code you are using for the distance matrix:
On Thu, Jul 17, 2014 at 12:18 AM, Matthew Lardy <mla...@gmail.com> wrote:
>
> dm=[]
> for i,fp in enumerate(zims_fps[:26000]): # only 1000 in the demo (in
> the interest of time)
>
> dm.extend(DataStructs.BulkTanimotoSimilarity(fp,zims_fps[1+1:26000],returnDistance=True))
> dm = array(dm)
>
Then at least part of the problem is that you are generating the full
matrix. I think you intend to have:
dm.extend(DataStructs.BulkTanimotoSimilarity(fp,zims_fps[i+1:26000],returnDistance=True))
in there.
That typo was in the original notebook that you used; I'm going to have to
figure out how to fix that.
-greg
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