Re: [Rdkit-discuss] Seg fault importing rdkit.Chem on Mac 10.13.2 and Python 3.6.3

[JW Feng via Rdkit-discuss]

Thanks, my colleague Katrina Lexa found that python 3.6.1 worked.  Conda
version is 4.4.6

conda create --name test-rdkit --channel https://conda.anaconda.org/rdkit rdkit
python=3.6.1

Best,

JW

___
JW Feng, Ph.D.
Denali Therapeutics Inc.
151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650)
270-0628

On Wed, Jan 3, 2018 at 11:55 PM, Greg Landrum 
wrote:

> I'm going to guess that it's this problem: https://github.com/rd
> kit/rdkit/issues/1617
> and that the solution is to downgrade conda to v4.3.25 (conda install
> conda=4.3.25).
>
> This problem has proven much more frustrating to fix for the mac (linux
> and windows are now fine) than expected, but Brian and I continue to try.
>
> -greg
>
>
> On Tue, Jan 2, 2018 at 9:46 PM, JW Feng via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
>> Hi,
>>
>> I want to check to see if others encountered this problem before filing a
>> new issue on github.  I got a seg fault trying to import rdkit.Chem.  I am
>> using Python 3.6.3 on Mac OS 10.13.2 (High Sierra).  Below is a screenshot
>> showing how I reproduced the seg fault error.  RDKit was installed using
>> this conda command "conda install --channel
>> https://conda.anaconda.org/rdkit rdkit"
>>
>>
>> [image: Inline image 1]
>>
>> Python 2.7 works just fine.
>>
>> Thanks,
>>
>> JW
>>
>>
>> ___
>> JW Feng, Ph.D.
>> Denali Therapeutics Inc.
>> 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080
>> 
>>  |
>> (650) 270-0628
>>
>> 
>> --
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>>
>>
>
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Re: [Rdkit-discuss] Diversity picker

[Tim Dudgeon]

I think the MaxMinPicker can do what you want.
A blog on using this can be found here: 
https://rdkit.blogspot.co.uk/2017/11/revisting-maxminpicker.html



On 03/01/18 19:53, Sundar wrote:

Hi RDKit users,

Is it possible to pick a subset of (diverse) compounds that have less 
than a particular Tanimoto coefficient (for eg. 0.7) from a larger set 
using RDKit.
The current version of the Diverse Picker picks a diverse set based on 
a "number of compounds" instead of Tanimoto score.


Thanks
Jubilant


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Re: [Rdkit-discuss] Diversity picker

[David Cosgrove]

Hi Jubilant,
If you cluster your compounds using the Buttina-Taylor method at a
threshold of 0.7 then the cluster seeds or centroids will be at least 0.7
apart which is the effect you are looking for. There is no need to specify
the number of clusters in advance.
Regards,
Dave


On Wed, 3 Jan 2018 at 19:54, Sundar  wrote:

> Hi RDKit users,
>
> Is it possible to pick a subset of (diverse) compounds that have less than
> a particular Tanimoto coefficient (for eg. 0.7) from a larger set using
> RDKit.
> The current version of the Diverse Picker picks a diverse set based on a
> "number of compounds" instead of Tanimoto score.
>
> Thanks
> Jubilant
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
-- 
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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