Yes, the conformer search tools in Avogadro are the same as those in Open
Babel.
Funny you should mention ring conformers since that's something I'm
planning. Help would certainly be appreciated, since there are a few
approaches and I'd like to see what works best.
As for RDKit, the distance geometry method should inherently sample
different ring conformers.
Geoff
On Wed, Feb 25, 2015 at 7:23 PM Renslow, Ryan S <ryan.rens...@pnnl.gov>
wrote:
> Thank you Noel
> I will go down the path of using the subprocess support in Python.
>
> As a different, but related question, is it true that the open babel
> conformer search routines are the ones used in Avogadro?
> Finally, if you have time: Do you know of any python-accessible
> scripts/code that can generate ring conformers (like chair, boat, twisted,
> etc.)? It appears that neither confab in Open Babel nor RDkit functions can
> do this.
>
> Cheers,
> Ryan
>
> -----Original Message-----
> From: Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com]
> Sent: Wednesday, February 25, 2015 3:24 PM
> To: Noel O'Boyle
> Cc: Renslow, Ryan S; openbabel-discuss@lists.sourceforge.net
> Subject: Re: [Open Babel] pybel/openbabel and use of confab
>
> > The operations are aimed at use from the command-line and so I would
> > recommend using Python's subprocess.
>
> Well, I think you can employ them in Python directly. This is untested,
> but something like this would work:
>
> >> confab = openbabel.OBOp.FindType("confab") confab.Do(myOBMol,
> >> "options")
>
> where "options" is a space-delimited set of options.
>
> Looking at the code, it seems like none of the Op classes actually parse
> the option text, which seems like a bug (i.e., a never-implemented feature).
>
> As Noel said, the src/ops/opconfab.cpp code is more-or-less command-line
> driven and using the subprocess support seems to be the best current
> approach.
>
> -Geoff
>
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