Hi Shani,
This is a limitation of the RDKit's 2D coordinate generation code.
The workaround is to use the RDKit's coordgen integration to generate 2D
coordinates. You can toggle this on by doing:
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
That will, in general, give nicer 2D coordinates anyway.
Best regards,
-greg
On Thu, Jan 27, 2022 at 10:37 AM Shani Zev <levishan...@gmail.com> wrote:
> Hi everyone,
> I'm trying to create coordinates for a molecule containing a TRANS double
> bond in a ring. However, while I try to create coordinate from the mol
> object, the structure that was created is CIS and not TRANS.
> I check both options (cis and trans) and check that bond
> specificity correctly using FindPotentialStereo, then I use MolToMolBlock
> in order to create coordinate, and both structures (cis and trans) are
> created as CIS.
> any ideas/suggestions?
>
> thanks in advance,
> Shani
>
> For example my code:
>
> import rdkit
> from rdkit import Chem
> from rdkit.Chem import AllChem
> print(rdkit.__version__)
>
> smiles = {'Cis':'C/C1=C\CCCCCCCC1', 'Trans':'C/C1=C/CCCCCCCC1'}
> for key in smiles:
> mol = Chem.MolFromSmiles(smiles[key])
> mol = Chem.AddHs(mol)
> AllChem.EmbedMolecule(mol)
> si = Chem.FindPotentialStereo(mol)
> for element in si:
> print(f' {key} Type: {element.type}, Descriptor:
> {element.descriptor} ')
> print(Chem.MolToMolBlock(mol), file=open(str(key)+'.mol', 'w+'))
>
> *the output: *
>
> 2021.09.4
> Cis Type: Bond_Double, Descriptor: Bond_Cis
> Trans Type: Bond_Double, Descriptor: Bond_Trans
>
> _______________________________________________
> 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
