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
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 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
>>
>>
>>
>>
>> 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/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
>>
>> [image: github.png] adelenelai
>>
>>
>>
>>
>>
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
___
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Re: [Rdkit-discuss] How to center atom labels vertically?
Hi Theo, The atom label placement in drawings turns out to be very tricky to do in a cross platform way. You're using the RDKit's old drawing code which we haven't been maintaining for a while now, I'd recommend either switching to using one of the convenience functions likes Draw.MolToImage() or using the Draw.MolDraw2DCairo() or Draw.MolDraw2DSVG() classes directly. I can maybe help with the decision which to use: once you've generated an image of the molecule, what do you want to do with it? -greg On Tue, Oct 20, 2020 at 1:32 PM theozh wrote: > Dear RDKit-ers, > > this sounds like a simple problem, however, I haven't found a link to the > corresponding documentation. > > When I draw a structure with: > > from.rdkit.Chem import Draw > > Draw.MolToQPixmap(mol) > > The non-Carbon atom labels are not centered to the bonds, but typically > shifted downwards. > How to center them also vertically? > > https://rdkit.org/docs/source/rdkit.Chem.Draw.MolDrawing.html > Here I don't see how to center atom labels vertically. Am I missing > something? > > Thanks for hints and the right link, > Theo. > > > > > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to preserve undefined stereochemistry?
Hi Adelene,
I have updated the gist
https://gist.github.com/ptosco/1e1c23ad24c90444993fa1db21ccb48b
to account for your questions.
Cheers,
p.
On Tue, Oct 20, 2020 at 2:08 PM Adelene LAI wrote:
> Hi Dave and Pablo,
>
>
> Thanks for your helpful replies.
>
>
> @Dave, issue created: https://github.com/rdkit/rdkit/issues/3514
>
>
> @Pablo, your gist shows that the internal representation of the mol does
> indeed factor in undefined stereo, contrary to the way it is depicted.
>
>
> But why then does this happen when I check if the 2 molecules are the same?
>
>
> smi =
> Chem.MolFromSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)C(=CC(C(=O)O)Br)CC(=O)O')
> isosmi =
> Chem.MolFromSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)/C(=C/C(C(=O)O)Br)/CC(=O)O')
> print(smi == isosmi)#True, expect False
> print(smi.HasSubstructMatch(isosmi)) #True, expect False
> print(isosmi.HasSubstructMatch(smi)) #True, expect False
> print(smi.HasSubstructMatch(isosmi) and isosmi.HasSubstructMatch(smi))
> #True,
> expect False
>
>
> However, converting smi and isosmi to canonical smiles and comparing them
> gives False, as expected:
>
> a =
> Chem.CanonSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)C(=CC(C(=O)O)Br)CC(=O)O')
> b =
> Chem.CanonSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)/C(=C/C(C(=O)O)Br)/CC(=O)O')
> a == b #False
>
>
> (If there are better ways to check if 2 molecules are equal, I'd be
> interested to know.)
>
> https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/9DF05ED7-A30E-4742-A568-9B3995689382%40dalkescientific.com/#msg29882815
> ?
>
>
> 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:* 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/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 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
>>
>>
>>
>>
>> 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/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
>>
>> [image: github.png] adelenelai
>>
>>
>>
>>
>>
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
Re: [Rdkit-discuss] How to preserve undefined stereochemistry?
Hi Dave and Pablo,
Thanks for your helpful replies.
@Dave, issue created: https://github.com/rdkit/rdkit/issues/3514
@Pablo, your gist shows that the internal representation of the mol does indeed
factor in undefined stereo, contrary to the way it is depicted.
But why then does this happen when I check if the 2 molecules are the same?
smi = Chem.MolFromSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)C(=CC(C(=O)O)Br)CC(=O)O')
isosmi =
Chem.MolFromSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)/C(=C/C(C(=O)O)Br)/CC(=O)O')
print(smi == isosmi)#True, expect False
print(smi.HasSubstructMatch(isosmi)) #True, expect False
print(isosmi.HasSubstructMatch(smi)) #True, expect False
print(smi.HasSubstructMatch(isosmi) and isosmi.HasSubstructMatch(smi)) #True,
expect False
However, converting smi and isosmi to canonical smiles and comparing them gives
False, as expected:
a = Chem.CanonSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)C(=CC(C(=O)O)Br)CC(=O)O')
b = Chem.CanonSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)/C(=C/C(C(=O)O)Br)/CC(=O)O')
a == b #False
(If there are better ways to check if 2 molecules are equal, I'd be interested
to know.)
https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/9DF05ED7-A30E-4742-A568-9B3995689382%40dalkescientific.com/#msg29882815
?
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
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/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
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/service.svc/s/GetFileAttachment?id=AAMkAGZmYjQwYmQ2LTcxODYtNDNhYi1hNTZlLTFiNDgxODA0MjNiZQBGAADhez7GVLyNT6vooKL2ihHhBwBuSX%2BNSPCHQainUEFyygsfAAAB%2B4B1AABuSX%2BNSPCHQainUEFyygsfAAGQzO9iAAABEgAQACo4Qhn9gSVGjyknvlrNy9g%3D=KzXvJGD5S0GSEPfNkS5fZYDFe7bcdNgIObv5ckhjF4wefmj-g3q1TT_E6gcW1r5xr5EjBUEwMBo.=True]
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://lh6.googleusercontent.com/qcj3x-KsughszG8tryquO6V-VDfqWT0oNF-LfA0jHbbue2pSzA69HqOAWsa_34FYyxQKfTdJv6gWeIsXW-hhNglMy4_rpf6l_x-Y3ufGRpuz_c1ZCK69k4VKVmE1Cq93rhdD7a7ij8U]
or that single bond to be squiggly, as in CDK's depiction:
[https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=CC(C)(C1%3DCC(%3DC(C(%3DC1)Br)O)Br)C(%3DCC(C(%3DO)O)Br)CC(%3DO)O=80=50=on=bridgehead=false=1.6=none]
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/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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Re: [Rdkit-discuss] How to preserve undefined stereochemistry?
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 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
>
>
>
>
> 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/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
>
> [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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Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] How to center atom labels vertically?
Dear RDKit-ers, this sounds like a simple problem, however, I haven't found a link to the corresponding documentation. When I draw a structure with: from.rdkit.Chem import Draw Draw.MolToQPixmap(mol) The non-Carbon atom labels are not centered to the bonds, but typically shifted downwards. How to center them also vertically? https://rdkit.org/docs/source/rdkit.Chem.Draw.MolDrawing.html Here I don't see how to center atom labels vertically. Am I missing something? Thanks for hints and the right link, Theo. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] How to preserve undefined stereochemistry?
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/service.svc/s/GetFileAttachment?id=AAMkAGZmYjQwYmQ2LTcxODYtNDNhYi1hNTZlLTFiNDgxODA0MjNiZQBGAADhez7GVLyNT6vooKL2ihHhBwBuSX%2BNSPCHQainUEFyygsfAAAB%2B4B1AABuSX%2BNSPCHQainUEFyygsfAAGQzO9iAAABEgAQACo4Qhn9gSVGjyknvlrNy9g%3D=KzXvJGD5S0GSEPfNkS5fZYDFe7bcdNgIObv5ckhjF4wefmj-g3q1TT_E6gcW1r5xr5EjBUEwMBo.=True]
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://lh6.googleusercontent.com/qcj3x-KsughszG8tryquO6V-VDfqWT0oNF-LfA0jHbbue2pSzA69HqOAWsa_34FYyxQKfTdJv6gWeIsXW-hhNglMy4_rpf6l_x-Y3ufGRpuz_c1ZCK69k4VKVmE1Cq93rhdD7a7ij8U]
or that single bond to be squiggly, as in CDK's depiction:
[https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=CC(C)(C1%3DCC(%3DC(C(%3DC1)Br)O)Br)C(%3DCC(C(%3DO)O)Br)CC(%3DO)O=80=50=on=bridgehead=false=1.6=none]
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/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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