Dear Paolo,
Thanks for updating the gist - it's a really important resource for me and
probably future RDKit beginners too. Thanks.
I like your suggestion to add the unspecifiedBondStereoMeansUnknown flag to
SmilesParserParams. I think this way circumvents having to do a SS-match +
BondStereo replacement loop.
To clarify, will implementing the above effectively mean unspecified stereo
will be depicted as a crossed double bond too?
Because then, the only way to differentiate between stereo unspecified and
stereo unknown would be to run bond.GetStereo(), which would give STEREOANY or
STEREONONE respectively. I think this would be OK...unless depiction-folks have
alternative suggestions.
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
[github.png] adelenelai
________________________________
From: Paolo Tosco <paolo.tosco.m...@gmail.com>
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 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<mailto: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
[github.png] adelenelai
________________________________
From: Greg Landrum <greg.land...@gmail.com<mailto: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<mailto: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<mailto: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
[https://owa.uni.lu/owa/]
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://owa.uni.lu/owa/]<https://pubchem.ncbi.nlm.nih.gov/compound/139598257#section=2D-Structure>
or that single bond to be squiggly, as in CDK's depiction:
[https://owa.uni.lu/owa/]
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/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://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
[github.png] adelenelai
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