HI JP,
you are welcome, thanks a lot for reporting the problem with a reproducible!
No need to bother filing a GitHub issue, I have already done that and also
submitted a fix:
https://github.com/rdkit/rdkit/pull/4282
Reionizing is good to make sure that charges are shuffled around if needed
and l
Hi Paolo!
Nice to hear from you -- and thanks for the lightning-fix+working example.
Very helpful as usual. (I don't imagine you need me to open a github issue
on this, but I'd be happy to if you think that is helpful/want to keep
a record).
Any thoughts on whether it is useful to reionize after
Hi JP,
the problem is caused by the reaction SMARTS that standardizes
pyridine *N*-oxides
being not very specific and also hitting your molecule, which is not
actually an *N*-oxide but rather a *N*-hydroxypyridinium ion.
I will submit a PR to fix the reaction pattern; in the meantime you can fix
t
Apologies I took my sweet time to reply, I went down the standardization
rabbit-hole and went through most of the material (thanks Matthew and
Francois, but also links from other notebooks). The recording of the
OpenScience session is excellent and crystal clear as usual Greg. I
enjoyed that.
I
Dear JP,
To confuse you even more, you can also have a look at the ChEMBL
open-source molecular standardizer:
https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py
No need to thank me. :D
On 18/06/2021 03:12, JP Ebejer wrote:
Dear all,
I
Hi JP,
On Thu, Jun 17, 2021 at 8:37 PM JP Ebejer wrote:
>
> I am trying to standardize(/normalize?) some molecules from different
> sources, to generate a set of descriptors for them. I have done this a
> number of times, and each time I find the process slightly confusing. I
> have the follow
Hi JP,
Lots of good questions, and it is quite an involved topic.
I'll let others who are more knowledgeable of the background answer
questions on the history and relationship between the tools.
One resource that may be helpful is the
https://github.com/chembl/ChEMBL_Structure_Pipeline repo, whi
Dear all,
I am trying to standardize(/normalize?) some molecules from different
sources, to generate a set of descriptors for them. I have done this a
number of times, and each time I find the process slightly confusing. I
have the following questions please, if you don't mind:
1. What is the
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