ww.linkedin.com/company/glpg>
[cid:image004.png@01DA5433.970407E0]
<https://www.youtube.com/c/GalapagosGlobal>
[cid:image005.png@01DA5433.970407E0] <https://www.glpg.com/>
Giovanni Tricarico
Principal Scientist Chemoinformatics
+32 15 6514 30
giovanni.tricar...@glpg.com<mailto:g
ain for your input.
From: James Wallace mailto:james.wall...@evotec.com>>
Sent: 22 March 2023 14:20
To: Giovanni Tricarico
mailto:giovanni.tricar...@glpg.com>>
Subject: RE: invalid core SMILES returned by RGroupDecompose
You don't often get email from
james.wall...@evotec.com<
n tautomer only].
Thanks
Giovanni Tricarico
Principal Scientist Computational Chemistry
[cid:image001.png@01D95CA8.7ECCEA80]
Galapagos
Generaal De Wittelaan L11 A3
2800 Mechelen
Belgium
T: +32 15 6514 30
www.glpg.com<http://www.glpg.com/>
This e-mail and its attachment(s) (if any) may cont
Indeed, the only two chemically valid configurations for this molecule seem to
be:
[cid:image001.png@01D92C36.B02214E0]
Impressive that rdkit can detect this kind of contradictions.
G
From: Kangway Chuang (CHUANGK4) via Rdkit-discuss
Sent: 19 January 2023 17:54
To: Ling Chan ; Gianmarco
Hello,
I've been experiment with the above module, and I am stuck with the cluster
object, I cannot find how to cut the tree at a specified distance and get the
list of cluster indices for the original molecules.
See below the code.
The 'Print()' function does show a tree and values for a
Hello Tristan,
I imagine you have seen Greg Landrum's post on sphere exclusion clustering:
https://greglandrum.github.io/rdkit-blog/similarity/tutorial/2020/11/18/sphere-exclusion-clustering.html
The initial MaxMin selection is very fast, especially Roger Sayle's
implementation, and not
!
Giovanni
From: Ivan Tubert-Brohman
Sent: 14 April 2022 12:58
To: Giovanni Tricarico
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] how to report SDF records for which
Chem.ForwardSDMolSupplier returns None?
You don't often get email from
ivan.tubert-broh...@schrodinger.com
for inspection.
Thanks
Giovanni
-Original Message-
From: Nils Weskamp
Sent: 13 April 2022 22:55
To: Giovanni Tricarico ;
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] how to report SDF records for which
Chem.ForwardSDMolSupplier returns None?
[You don't often get
Hello,
I am using rdkit to read data from SD files.
My goal is to extract both the molecules and their associated properties (which
for our purposes are separate entities) from the SDF.
[For 100% clarity: by 'properties' I don't mean calculated properties or atom
or bond properties, but the
Thank you Dan; it's done:
https://github.com/rdkit/rdkit/issues/5165#issue-1192683590
brg
Giovanni
From: Dan Nealschneider
Sent: 04 April 2022 23:48
To: Giovanni Tricarico
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] issue with V3000 SD files containing enhanced
Hello,
I am trying to process V3000 MolBlock's from some SD files, and I seem to
encounter issues when enhanced stereochemistry information is present,
depending on the source of the SD file.
To test that the molecule to SDF and back conversion within rdkit was working
OK, I ran this code:
Hello Theo,
I cannot immediately think of any other obvious way to check molecular
identity, but please note that my feedback was more about the chemistry aspects
than about rdkit.
Assuming that the methods you listed are the main/only available ones, I
suppose the only thing to do is try them
Hello Theo,
in my experience, something like approach 3 is quite safe (not sure how
computationally efficient in rdkit, but I suppose you'd rather have an accurate
slow method than a fast often wrong one, right?).
In short:
In the greatest majority of cases, the literal string match of
Hello,
very interesting.
I think it is worth raising a related point regarding the representation of
stereochemistry for such types of molecules, because it’s important not only to
validate them, but to interpret them correctly, too.
See this document:
ence my attempt to go back to fp.
From: Rajarshi Guha
Sent: 15 September 2021 17:39
To: Patrick Walters
Cc: Giovanni Tricarico ;
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] how to make a database fingerprint
*** CAUTION : External e-mail ***
Is it correct to use Mo
Hello,
based on this article:
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0195-1
I have been trying to make what they call a 'database fingerprint'.
The first step seems to require obtaining the frequencies of each fingerprint
bit in a database of molecules.
To do that, I
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