Re: [Rdkit-discuss] Turn off warning in Huckel calculations.

[Paolo T. <pao...@gm...>]

Dear Jan,

That warning is printed straight to stderr by the YAeHMOP code, so 
disabling Boost logging won't help.

If you are using the YAeHMOP code from Python, your best option is 
probably to catch stderr as I described here:

https://sourceforge.net/p/rdkit/mailman/message/36781695/

f = io.BytesIO()
with stderr_redirector(f):
     ...your YAeHMOP call(s)...
grabbed_stderr = f.getvalue().decode('utf-8')

The warnings should be grabbed by the redirector and should now be found 
in grabbed_stderr.

HTH, cheers
p.

On 10/12/2019 10:10, Jan Halborg Jensen wrote:
> I am using the new Huckel feature to find bonded atoms using bond 
> orders (https://github.com/jensengroup/xyz2mol : xyz2AC_huckel). This 
> means I am doing a calculation in a mol object with no bonds based xyz 
> coordinates I read in, including hydrogens.
>
> A calculation on water gives the following warning
> !!! Warning !!! Distance between atoms 2 and 1 (0.962107 A) is suspicious.
> !!! Warning !!! Distance between atoms 3 and 1 (0.962107 A) is suspicious.
>
> where atom 2 and 3 are Hs. I believe this warning is because there are 
> no bonds defined. Is there a way to turn off this warning?
>
> rdBase.DisableLog('rdApp.error’) doesn’t work.
>
> Best regards, Jan
>
>
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