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
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
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
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.
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
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,
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
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
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