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From: David Cosgrove
Sent: Thursday, October 22, 2020 12:46:54 PM
To: Adelene LAI
Cc: Greg Landrum; Paolo Tosco; rdkit-discuss
Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry?
Hi Adelene,
In SMILES, there’s no way
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> *From:* Paolo Tosco
> *Sent:* Wednesday, October 21, 2020 10:56:24 AM
> *To:* Adelene LAI
> *Cc:* Greg Landrum; rdkit-discuss
>
> *Subject:* Re: [Rdkit-discuss] How t
66 44 67 18
[github.png] adelenelai
From: Paolo Tosco
Sent: Wednesday, October 21, 2020 10:56:24 AM
To: Adelene LAI
Cc: Greg Landrum; rdkit-discuss
Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry?
Hi Adelene, Greg,
I have updated my
> 6, avenue du Swing, L-4367 Belvaux
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> *From:* Greg Landrum
> *Sent:* Wednesday, October 21, 2020 6:15:58 AM
> *To:* Adelene LAI
> *Cc:* rdkit-di
20 6:15:58 AM
To: Adelene LAI
Cc: rdkit-discuss
Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry?
Paolo's gist includes a vocabulary mistake[1] that I think is confusing things
here.
In the RDKit the stereochemistry of a double bond can be unspecified, unknown,
or known. U
Paolo's gist includes a vocabulary mistake[1] that I think is confusing
things here.
In the RDKit the stereochemistry of a double bond can be unspecified,
unknown, or known. Unspecified means that you haven't said anything about
what the stereo is; unknown means that you've actively provided the
formatics
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> UNIVERSITÉ DU LUXEMBOURG
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> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
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> 6, avenue du Swing, L-4367 Belvaux
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> T +356 46 66 44 67 18
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> *From:* P
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From: Paolo Tosco
Sent: Tuesday, October 20, 2020 1:52:12 PM
To: Adelene LAI
Cc: rdkit-discuss
Subject: Re: [Rdkit-discuss] How to preserve undefined stereochemistry?
Hi Adelene,
this gist
https://gist.github.com/ptosco
Hi Adelene,
this gist
https://gist.github.com/ptosco/1e1c23ad24c90444993fa1db21ccb48b
shows how to add stereo annotations to RDKit 2D depictions, and also how to
access the double bond stereochemistry programmatically.
Cheers,
p.
On Tue, Oct 20, 2020 at 12:24 PM Adelene LAI wrote:
> Hi
Hi RDKit Community,
Is there a way to preserve undefined stereochemistry aka unspecified
stereochemistry when doing MolFromSmiles?
I'm working with a bunch of molecules, some with stereochemistry defined, some
without.
If stereochemistry is undefined in the SMILES, I would like it to stay
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