Not optimizing will result in a lousy conformer. The default should not
generate poor bond lengths or angles. I’m less concerned about torsions.
-Dave
> On Jun 14, 2018, at 5:20 PM, Geoffrey Hutchison
> wrote:
>
> Hi,
>
> One of the GSoC projects this summer is an improved fragment-based
> I know that Open Babel already has several charge models, but none are
> documented currently, and so I have no clue what to do with them except
> calculate the values and write them out.
That's probably a matter for me to improve the documentation.
Generally people assign charges for force
Hi,
One of the GSoC projects this summer is an improved fragment-based coordinate
generation method. While that's going, I've been reading a lot of papers on 3D
coordinate generation.
As near as I can tell, no other program attempts to do a conformer search as
part of the 3D generation.
Hi Mohammad,
Just to take a step back, could you describe how users of Open Babel will
benefit from this? That is, what they might use these charges for? I know
that Open Babel already has several charge models, but none are documented
currently, and so I have no clue what to do with them except
I forgot to say that the background to all of this is that I was writing up
docs describing the handling of aromaticity in Open Babel, and when I got
to the section describing DeleteAtom() I found that the behaviour was not
how I thought.
- Noel
On 14 June 2018 at 07:03, Noel O'Boyle wrote:
>
Hi all,
I've sent in a pull request (
https://github.com/openbabel/openbabel/pull/1847) regarding to DeleteAtom()
and aromaticity, and Geoff asked me to bring it up here.
Currently, when you delete an atom (to be exact, it's actually
Begin/EndModify that I'm changing), the flag that indicates
