(ccing to openbabel-discuss)
Hi Ryan,
The operations are aimed at use from the command-line and so I would
recommend using Python's subprocess. Otherwise, the only way to set
the options is to use an OBConversion object and set GENOPTION
"confab" as well as whatever other options apply. This isn't really
ideal either way.
Note that all of this is referring to the current development version
of Open Babel.
Regards,
Noel
On 23 February 2015 at 21:07, Renslow, Ryan S <ryan.rens...@pnnl.gov> wrote:
> Hi Noel
>
>
>
> I am a scientist at the Pacific Northwest National Laboratory, currently
> working with NWChem computational chemistry software.
>
>
>
> We are writing a python script to automate NWChem input file generation,
> with the goal of predicting metabolite NMR spectra, and I was wondering if
> you know how to easily implement your confab conformer generation method in
> a python script using pybel or the open babel python API?
>
>
>
> I saw on one of your posts on the Open Babel forum, that implementing
> “gen3D” can be done by using the following:
>
> gen3d = openbabel.OBOp.FindType("Gen3D")
> gen3d.Do(myOBMol)
>
>
>
> Is this sort of method applicable to confab as well? How would one pass
> confab parameters like “—ecutoff” for the energy cutoff?
>
> Or perhaps I am missing something and there is an easier way?
> Thank you!
>
>
>
> Cheers,
>
> Ryan Renslow
>
> Pacific Northwest National Laboratory
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