[Rdkit-discuss] Question: Explaining bits from Morgan Fingerprints

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

Re: [Rdkit-discuss] [ext] Re: Taylor-Butina clustering

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

Re: [Rdkit-discuss] Taylor-Butina clustering

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

Re: [Rdkit-discuss] Javascript MinimalLib

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

Re: [Rdkit-discuss] Javascript MinimalLib

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

Re: [Rdkit-discuss] Substructure search for an aldehyde returns ketones and acids

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

[Rdkit-discuss] Taylor-Butina clustering

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