Hi Greg,
Thanks! My Python is really rusty at the moment, so I am always unsure if
I am just not going through the steps in the most efficient manner, or if
the path that I am following is far from ideal. Granted I would prefer to
write this in Java, but I should probably move back towards C++ when I do
stuff like this.
The code snippet you pointed to worked great for me! I hear you about
random picking being about just as good. I'd prefer to have a method for
this, but I understand that random is in itself a method. :)
In the past I have used a diversity algorithm by Gobbi & Lee to filter
hitlists, and it has worked really well for me in the past. Rather than
re-write that I wanted to give the diversity pickers in RDKit a whirl first.
Thanks again Greg,
Matt
On Wed, Jul 16, 2014 at 9:19 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> 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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