Hi Greg and Shani,
Please correct me if I understood something wrong, but isn't Shani
trying to create 3D coordinates in that example code? To me this looks
like the old issue with respecting double bond stereochemistry in
embedding, which should have been fixed with #4346? Oddly enough, the
example code produces correct stereochemistry for
smiles = {'Cis':'C1C/C=C\\CCCCCCCC1', 'Trans':'C1C/C=C/CCCCCCCC1'}
which are the molecules used in the test case of #4346.
Cheers,
Juuso
On Thu, Jan 27, 2022 at 2:56 PM Greg Landrum <[email protected]> wrote:
>
> 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 <[email protected]> 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
>>
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