The problem is that even if you fix it in the readers, the hydrogens
are ignored when passed to the code that does the kekulization. While
this means that we are able (better than most others) to handle files
(e.g. PDB) that don't have the hydrogens locations specified, none of
us realized that all
Hi Noel,
Thanks for the response.
Would it be hard to add a command line switch for the CML and/or SMILES
reader(s) to suppress any attempts to add implict hydrogens?
I have structures coming from QM calculations and thefore I know all
hydrogens and don't want any to be added (even my SMILES hav
Hi Oliver,
You are hitting an OB bug. The SMILES reader (among others) does not
set the implicit hydrogen correctly. I've done some work on sorting
this out, but it's kind of "on the long finger" now.
Regards,
- Noel
On 9 December 2014 at 19:53, Oliver Stueker
wrote:
> Hi,
>
> I'm trying to use
