Hi RDKit,
How does one input the number of bits to the ShapeTanimotoDist function?
The docs indicate the default is
*rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE,
*but I tried some other values and this gave unexpected results.
Specifically: when increasing to higher bit values, th
Dear RDKit community,
I am trying to explain the Explaining bits from Morgan Fingerprints as
described in the RDKit getting started guide here (
http://www.rdkit.org/docs/GettingStartedInPython.html#explaining-bits-from-morgan-fingerprints
).
I want to get the SMILES for each bit from morgan FP o
Hi Francesca,
adding to David's comment, we do have some material for beginners that also
covers and applies Butina clustering that may be useful:
https://github.com/volkamerlab/teachopencadd/blob/master/teachopencadd/talktorials/T005_compound_clustering/talktorial.ipynb
Best, Andrea
Hi Francesca,
The Taylor-Butina clustering is not hierarchical. It is a type of sphere
exclusion algorithm. A useful image for the results would be the
"centroid" of each cluster, possibly followed by the other cluster
members. You will need to generate the images from the original input
molecu
Brilliant, thanks. I will take note of how to do it myself in future 🙂.
Best,
Dave
On Wed, 21 Jul 2021 at 12:32, Greg Landrum wrote:
> Hi Dave,
>
> It's not in the JS interface yet, but I'll add it now.
>
> -greg
>
>
> On Mon, Jul 19, 2021 at 4:57 PM David Cosgrove
> wrote:
>
>> Hi,
>>
>> In
Hi Dave,
It's not in the JS interface yet, but I'll add it now.
-greg
On Mon, Jul 19, 2021 at 4:57 PM David Cosgrove
wrote:
> Hi,
>
> In this blogpost
> https://greglandrum.github.io/rdkit-blog/technical/2021/05/01/rdkit-cffi-part1.html,
> Greg mentions the CFFI function get_json(). Is that
Yeah, this is exactly the case where using qmol_from_ctab() should help.
Below is a short example demonstrating this by querying my local ChEMBL
instance. Notice that the first form of the query, which uses
mol_from_ctab() matches what you describe: the results include amides,
esters, etc. The sec
Hi,
I managed to performe Taylor-Butina clustering on a dataset of 193 571
fragments retrieved from ZINC20.
I used the indications in this link
https://www.macinchem.org/reviews/clustering/clustering.php
Actually, I've never used RDKit before and never did a cluster analysis, so I'm
really new t
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