Hi Geoff,
Have you looked at pymatgen? It has a lot of useful features for crystal
structures and some also for molecules as well.
Gary
On Wed, Dec 28, 2016 at 11:26 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> Hi,
>
> I'm pretty excited that we have an initial draft of (python) workflow
> scripts. The idea is simple - Avogadro will pass off a molecule to a
> command-line script, which could be Python or anything else that handles
> JSON. The script hands back some JSON for a dialog, and when run, it
> returns a modified molecule to Avogadro.
>
> Undo and redo commands are created automatically.
>
> The initial example (attached) simply scales the Cartesian coordinates for
> all atoms. Another example will use a Python package to build nanotubes (
> https://scikit-nano.org).
>
> I want to ask the community if they have some ideas for use cases. For
> example, should the scripts be able to return numbers and/or text in
> addition to the molecule?
>
> * A "flatten molecule" command that makes everything planar, to ensure
> symmetry
> * A "make cluster" command that generates multiple copies of the current
> molecule along an axis
> * An RDKit module that generates conformers
> * An ASE module that inserts dopant atoms into octahedral vacancies
>
> Thoughts? We'd like to nail down the API and packaging so multiple scripts
> can be built up before release.
>
> -Geoff
>
>
>
>
>
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