Yes, exactly
On Thu, Apr 24, 2014 at 7:19 AM, Christos Kannas wrote:
> Hi Patrick,
>
> Thanks.
>
> So the correct would be, sodium should not have an explicit bond with the
> oxygen.
> From O=S(c1ccc(C(CCC))cc1)(O-[Na+])=O I should
> have O=S(c1ccc(C(CCC))cc1)([O-])=O.[Na+]
>
> S
Hi Patrick,
Thanks.
So the correct would be, sodium should not have an explicit bond with the
oxygen.
>From O=S(c1ccc(C(CCC))cc1)(O-[Na+])=O I should
have O=S(c1ccc(C(CCC))cc1)([O-])=O.[Na+]
Similar to the rest of my compounds.
And regarding nitrogen it already has 4 bonds with
It looks like the problem here is a covalent bond to the counter ion.
Pat
On Thu, Apr 24, 2014 at 6:04 AM, Christos Kannas wrote:
> Hi all,
>
> I'm having a dozen of compounds, where some of them have a charged atom
> (see the attached SMILES file).
>
> When I parse the file I get sanitization
Hi all,
I'm having a dozen of compounds, where some of them have a charged atom
(see the attached SMILES file).
When I parse the file I get sanitization errors on the compounds with the
charged atoms.
But when I view them with MarvinView 6.2.0 all goes fine.
I'm using an RDKit build from github,
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