Re: [Rdkit-discuss] Chembience Postgres RDKit extension
Hello, I have added a Postgres-13/RDKit 2021.03-Version to my Chembience Postgres RDKit project (https://github.com/chembience/docker-postgres-rdkit-compile) Available Docker images are now *chembience/postgres-rdkit:postgres-13.rdkit-2021.03 (new)* chembience/postgres-rdkit:postgres-13.rdkit-2020.09 chembience/postgres-rdkit:postgres-12.rdkit-2020.03 chembience/postgres-rdkit:postgres-11.rdkit-2019.09 Best, Markus On Mon, Mar 8, 2021 at 8:49 AM Greg Landrum wrote: > That's really cool, thanks Markus! > > On Sat, Mar 6, 2021 at 7:34 PM Markus Sitzmann > wrote: > >> Hello, >> >> I have reworked the Postgres RDKit extension module of Chembience and >> made it a spin-off project of its own which is available at: >> >> https://github.com/chembience/docker-postgres-rdkit-compile >> >> It is now based on a fork of the Official Postgres Docker Image >> repository at GitHub just adding the compilation of the RDKit extension >> module to it. It allows for local compilation of the package, however, I >> also provide ready-to-pull Docker images at DockerHub of it. Currently >> available by docker pull are (they all are usable independently of any >> Chembience setup) : >> >> chembience/postgres-rdkit:postgres-13.rdkit-2020.09 >> chembience/postgres-rdkit:postgres-12.rdkit-2020.03 >> chembience/postgres-rdkit:postgres-11.rdkit-2019.09 >> >> My plan is to keep this project up-to-date if newer versions of RDKit or >> Postgres are released. >> >> I also have updated Chembience https://github.com/chembience/chembience >> to version 0.2.18 last week. This is mostly an upgrade to RDKit 2020.09 >> (before it becomes the "old" version) and Postgres 13 and relies already on >> the project above. >> >> Best. >> Markus >> >> ___ >> 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] Stereochemistry problem with spiro centre
Thanks Paolo - I should have found this before posting!
Cheers
James
On 9 May 2021, at 15:05, Paolo Tosco wrote:
Hi James,
IIRC that's a known open issue with the way spirocyclic pseudochiral centers
are handled:
https://github.com/rdkit/rdkit/issues/3490
Cheers,
p.
On Sun, May 9, 2021 at 10:15 AM James Davidson
mailto:j.david...@vernalis.com>> wrote:
Dear All,
I am having some issues with tetrahedral stereochemistry perception in RDKit
(2020.09.4) for a certain class of molecule.
Here’s an example (rendered using cdk-depict):
https://www.simolecule.com/cdkdepict/depict/bot/svg?smi=F%5BC%40H%5D1C%5BC%40%40%5D2(C1)C%5BC%40H%5D(Cl)C2=-1=-1=off=bridgehead=false=3.65=cip=0
If I try to work with this class of molecule in RDKit, it seems impossible(?)
to assign stereo information to the central, spirocyclic stereo centre.
Exporting back out as SMILES shows that the information is not present:
m = Chem.MolFromSmiles('F[C@H]1C[C@@]2(C1)C[C@H](Cl)C2')
print(Chem.MolToSmiles(m))
>>> F[C@H]1CC2(C1)C[C@H](Cl)C2
The spiro-atom is clearly being identified as a potential stereo-centre
(strangely, the CIP labels aren’t being generated for the other two centres –
just the parity info is returned):
centers = Chem.FindMolChiralCenters(m, includeUnassigned=True,
useLegacyImplementation=False)
print(centers)
>>> [(1, 'Tet_CW'), (3, '?'), (6, 'Tet_CCW')]
If I look at the atom properties for the central atom, I can see
_ChiralityPossible == 1, but I also see _ringStereochemCand == False.
Is this the problem?
Any help/advice greatly appreciated!
Kind regards
James
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Re: [Rdkit-discuss] Stereochemistry problem with spiro centre
Hi James,
IIRC that's a known open issue with the way spirocyclic pseudochiral
centers are handled:
https://github.com/rdkit/rdkit/issues/3490
Cheers,
p.
On Sun, May 9, 2021 at 10:15 AM James Davidson
wrote:
> Dear All,
>
>
>
> I am having some issues with tetrahedral stereochemistry perception in
> RDKit (2020.09.4) for a certain class of molecule.
>
> Here’s an example (rendered using cdk-depict):
>
>
>
>
> https://www.simolecule.com/cdkdepict/depict/bot/svg?smi=F%5BC%40H%5D1C%5BC%40%40%5D2(C1)C%5BC%40H%5D(Cl)C2=-1=-1=off=bridgehead=false=3.65=cip=0
>
>
>
> If I try to work with this class of molecule in RDKit, it seems
> impossible(?) to assign stereo information to the central, spirocyclic
> stereo centre.
>
> Exporting back out as SMILES shows that the information is not present:
>
>
>
> m = Chem.MolFromSmiles('F[C@H]1C[C@@]2(C1)C[C@H](Cl)C2')
>
> print(Chem.MolToSmiles(m))
>
>
>
> >>> F[C@H]1CC2(C1)C[C@H](Cl)C2
>
>
>
> The spiro-atom is clearly being identified as a potential stereo-centre
> (strangely, the CIP labels aren’t being generated for the other two centres
> – just the parity info is returned):
>
>
>
> centers = Chem.FindMolChiralCenters(m, includeUnassigned=True,
> useLegacyImplementation=False)
>
> print(centers)
>
>
>
> >>> [(1, 'Tet_CW'), (3, '?'), (6, 'Tet_CCW')]
>
>
>
> If I look at the atom properties for the central atom, I can see
> _ChiralityPossible
> == 1, but I also see _ringStereochemCand == False.
>
> Is this the problem?
>
>
>
> Any help/advice greatly appreciated!
>
>
>
> Kind regards
>
>
>
> James
> --
>
> PLEASE READ - This email is confidential and may be privileged. It is
> intended for the named addressee(s) only and access to it by anyone else is
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> contents of this email or any action taken (or not taken) in reliance on it
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> a secure method of communication and the Company cannot accept
> responsibility for the accuracy or completeness of this message or any
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> Company accepts no responsibility. If verification of this email is sought
> then please request a hard copy. Unless otherwise stated, any views or
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> those of the Company.
>
> Vernalis (R) Limited (no. 1985479)
> Granta Park, Great Abington
> Cambridge, CB21 6GB, United Kingdom
> Tel: +44 (0)1223 895 555
> --
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> Rdkit-discuss mailing list
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>
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[Rdkit-discuss] Stereochemistry problem with spiro centre
Dear All,
I am having some issues with tetrahedral stereochemistry perception in RDKit
(2020.09.4) for a certain class of molecule.
Here's an example (rendered using cdk-depict):
[cid:image002.png@01D744AE.E7C7ACA0]
https://www.simolecule.com/cdkdepict/depict/bot/svg?smi=F%5BC%40H%5D1C%5BC%40%40%5D2(C1)C%5BC%40H%5D(Cl)C2=-1=-1=off=bridgehead=false=3.65=cip=0
If I try to work with this class of molecule in RDKit, it seems impossible(?)
to assign stereo information to the central, spirocyclic stereo centre.
Exporting back out as SMILES shows that the information is not present:
m = Chem.MolFromSmiles('F[C@H]1C[C@@]2(C1)C[C@H](Cl)C2')
print(Chem.MolToSmiles(m))
>>> F[C@H]1CC2(C1)C[C@H](Cl)C2
The spiro-atom is clearly being identified as a potential stereo-centre
(strangely, the CIP labels aren't being generated for the other two centres -
just the parity info is returned):
centers = Chem.FindMolChiralCenters(m, includeUnassigned=True,
useLegacyImplementation=False)
print(centers)
>>> [(1, 'Tet_CW'), (3, '?'), (6, 'Tet_CCW')]
If I look at the atom properties for the central atom, I can see
_ChiralityPossible == 1, but I also see _ringStereochemCand == False.
Is this the problem?
Any help/advice greatly appreciated!
Kind regards
James
PLEASE READ - This email is confidential and may be privileged. It is intended
for the named addressee(s) only and access to it by anyone else is
unauthorised. If you are not an addressee, any disclosure or copying of the
contents of this email or any action taken (or not taken) in reliance on it is
unauthorised and may be unlawful. If you have received this email in error,
please notify the sender or postmas...@vernalis.com. Email is not a secure
method of communication and the Company cannot accept responsibility for the
accuracy or completeness of this message or any attachment(s). Please check
this email for virus infection for which the Company accepts no responsibility.
If verification of this email is sought then please request a hard copy. Unless
otherwise stated, any views or opinions presented are solely those of the
author and do not represent those of the Company.
Vernalis (R) Limited (no. 1985479)
Granta Park, Great Abington
Cambridge, CB21 6GB, United Kingdom
Tel: +44 (0)1223 895 555
___
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