Hi Adelene, Greg,
I have updated my gist fixing my gross vocabulary mistake ("undefined" to
"unspecified") and I have also added an example of the crossed bond
depiction by changing the BondStereo attribute to STEREOANY.
@Adelene: I think you touched an interesting point here. There are indeed
cases where it would be nice to address the SMILES ambiguity (no way to
symbolically discriminate "unspecified" from "unknown") more efficiently
than by doing a time-consuming (and potentially error-prone)
substructure match and BondStereo replacement on all input molecules,
particularly if you have a large number of those.
I propose to do that by adding a unspecifiedBondStereoMeansUnknown
(suggestion on a better name welcome) flag to SmilesParserParams - I
believe that would be useful to many.
Cheers,
p.
On Wed, Oct 21, 2020 at 8:00 AM Adelene LAI <adelene....@uni.lu> wrote:
> Hi Greg, Hi Paolo,
>
>
> @Paolo - thanks for the updated gist!
>
>
> @Greg - thanks for this detailed explanation. I think it makes sense to
> equate unspecified with unknown stereochem. I can't think of any obvious
> caveats to this convention change for now (but maybe others in the
> community can?).
>
>
> When you say "have unspecified double bonds be marked as unknown", you
> mean have unspecified double bonds be represented by crossed bonds too?
>
>
> If so, would this loop you're suggesting be computationally
> not-too-expensive when working with 1000s of molecules?
>
>
>
>
> Thanks and good morning!
>
>
> Adelene
>
>
>
> Doctoral Researcher
>
> Environmental Cheminformatics
>
> UNIVERSITÉ DU LUXEMBOURG
>
>
> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
>
> 6, avenue du Swing, L-4367 Belvaux
>
> T +356 46 66 44 67 18
>
> [image: github.png] adelenelai
>
>
>
>
>
> ------------------------------
> *From:* Greg Landrum <greg.land...@gmail.com>
> *Sent:* Wednesday, October 21, 2020 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. Unspecified means that you haven't said anything about
> what the stereo is; unknown means that you've actively provided the
> information that you don't know what the stereochemistry is; known is clear.
>
> The RDKit only draws crossed bonds in molecule drawings when the
> stereochemistry of the double bond is unknown.
>
> The problem here is that in standard SMILES there is no way to actively
> specify that you don't know the stereochemistry of a double bond (the same
> thing applies to stereocenters). You can either provide information about
> the stereochemistry by using "/" and "\" bonds, or you provide no
> information. So the SMILES C/C=C/C produces a double bond with known
> stereochemistry but CC=CC produces a double bond with unspecified
> stereochemistry.
>
> If, based on what you know about the SMILES that you are parsing, you
> would like to change the convention and have unspecified double bonds be
> marked as unknown, it's straightforward to write a script that loops over
> the molecule and makes that change (watch out for ring bonds).
>
> -greg
> [1] Perhaps "mistake" isn't the right word. It's confusing
>
> On Tue, Oct 20, 2020 at 1:54 PM Paolo Tosco <paolo.tosco.m...@gmail.com>
> wrote:
>
>> 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 <adelene....@uni.lu> wrote:
>>
>>> 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
>>> that way when converted to a Mol, but this doesn't seem to be the case:
>>>
>>>
>>> > mol =
>>> Chem.MolFromSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)C(=CC(C(=O)O)Br)CC(=O)O')
>>> > mol
>>>
>>> One would expect that C=C to either be crossed, as in PubChem's
>>> depiction:
>>>
>>> https://pubchem.ncbi.nlm.nih.gov/compound/139598257#section=2D-Structure
>>>
>>>
>>> <https://pubchem.ncbi.nlm.nih.gov/compound/139598257#section=2D-Structure>
>>>
>>>
>>> or that single bond to be squiggly, as in CDK's depiction:
>>>
>>> But it's not just a matter of depiction, as it seems internally, mol is
>>> equivalent to its stereochem-specific sibling (Entgegen form)
>>>
>>>
>>> CC(C)(C1=CC(=C(C(=C1)Br)O)Br)/C(=C/C(C(=O)O)Br)/CC(=O)O
>>>
>>>
>>>
>>> I've tried sanitize=False, but it doesn't seem to have any effect. I
>>> would prefer not having to manually SetStereo(Chem.BondStereo.STEREOANY)
>>> for every molecule with undefined stereochem (not sure how I would even go
>>> about that...).
>>>
>>>
>>> Possibly related to:
>>>
>>>
>>> https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570
>>>
>>>
>>>
>>> <https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570>
>>>
>>> https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAHOi4k3revAu-9qhFt0MpUpr0aADQ9d8bV2XT6FurTEKimCQng%40mail.gmail.com/#msg36365128
>>> o = Chem.MolFromSmiles('C/C=C/C')
>>>
>>>
>>> <https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570>
>>> https://www.rdkit.org/docs/source/rdkit.Chem.EnumerateStereoisomers.html
>>>
>>> https://github.com/openforcefield/openforcefield/issues/146
>>>
>>>
>>>
>>>
>>> Any help would be much appreciated.
>>>
>>>
>>> Thanks,
>>>
>>> Adelene
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Doctoral Researcher
>>>
>>> Environmental Cheminformatics
>>>
>>> UNIVERSITÉ DU LUXEMBOURG
>>>
>>>
>>> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
>>>
>>> 6, avenue du Swing, L-4367 Belvaux
>>>
>>> T +356 46 66 44 67 18
>>>
>>> [image: github.png] adelenelai
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
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