Hi Paul,
On Wed, Nov 20, 2019 at 5:32 PM Paul Zierep via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Hi,
> in the original paper of ECFPs (Rogers, D.; Hahn, M.
> “Extended-Connectivity Fingerprints.” *J. Chem. Inf. and Model.* *50*:742-54
> (2010).); it says, " that the
Hi guys,
I am trying to construct my own symmetrical RMS matrix (lower half) for
Butina clustering, by using GetBestRMS which considers symmetry.
I need to get the matrix with rms elements in correct order first. Here is
what I did for testing, by just using GetConformerRMSMatrix and
Hi,
in the original paper of ECFPs (Rogers, D.; Hahn, M. “Extended-Connectivity
Fingerprints.” *J. Chem. Inf. and Model.* *50*:742-54 (2010).); it says, "
that the relationship between fingerprint features and the substructures
may not always be one-to-one, " (especially for the FCFPs but also the
Thank you, Greg and Andrew, for your replies, and I'm glad to hear that
this is something that can be fixed within RDKit. I had almost forgotten I
had sent this email... :-)
Best,
Ivan
On Wed, Nov 20, 2019 at 12:17 AM Greg Landrum
wrote:
> Hi Ivan,
>
> I agree that there is a bug here, but I
Hi Taka,
So this bug is fix thanks.
Now I have two others issues:
1. This cell gives also an error:
dataset = rg.GetRGroupsAsColumns()
core = Chem.RemoveHs(dataset["Core"][0])
RDKit ERROR: [12:59:27] Explicit valence for atom # 6 N, 5, is greater than
permitted
Hi Guillaume,
I confirmed the issue.
RemoveHs does not work to invalid molecule.
So I updated my code example and uploaded gist.
Could you please check new version of my code?
https://gist.github.com/iwatobipen/77269b8a10eafe0e0cba8de5c1cae6ec
Any comments or suggestions will be appreciated.
Dear colleagues,
we would like to invite you on the 5th Drug Design workshop which
will be held 3-7 January 2020 in Olomouc (Czech Republic). It is focused
on practical applications of different chemoinformatic tools and
approaches for drug development. This might be interesting for
On 20/11/2019 02:00, Benjamin Datko wrote:
Hello Francois,
I am trying to replicate some of the functionality of
CreateDifferenceFingerprintForReaction [Ref 1] for my own
understanding on how the code works. The function
CreateDifferenceFingerprintForReaction allows for three difference
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