Yep, I’m aware .. but it wouldn’t take too much work to at least ignore
“<“ and “>” in the Open Babel parser. 🙂
In the meantime, my Python scripts will strip them from the SMILES strings
before passing them to Open Babel.
-Geoff
On Aug 14, 2022 at 4:42:25 AM, David Cosgrove <davidacosgrov...@gmail.com>
wrote:
> Hi Geoff,
> You should bear in mind that the dative bond syntax is an RDKIt extension
> to SMILES so is not guaranteed to be parsed correctly by other
> cheminformatics toolkits.
> Dave
>
>
> On Sun, 14 Aug 2022 at 00:42, Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
>
>> mol = Chem.MolFromSmiles("C12=CC=CC=[N]1->[*]<-[N]3=C2C=CC=C3")
>>
>>
>> Hmm. I forgot the SMILES syntax of dative bonds. That's a nice idea.
>>
>> I actually decided to use the noFreeType=True option, add a highlight as
>> the "metal" and remove the * from the depiction.
>>
>> The initial set is at:
>> https://github.com/OpenChemistry/fragments/tree/main/ligands
>>
>> Thanks!
>> -Geoff
>>
>>
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
> --
> David Cosgrove
> Freelance computational chemistry and chemoinformatics developer
> http://cozchemix.co.uk
>
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
