>
> > Is there any reason why these should not become standard tools in
> chemistry
> > labs and classes and replace the current closed systems that so many
> people
> > are locked into?
> >
> > P
>
> The biggest barrier to general usage is setting up the job. Do these
> have user interfaces? If not, can Avogadro bump this up their priority
> list? I'll work on it from the cclib end.
>
> There are (at least) two sorts of interfaces:
* human interfaces for launching jobs and things like Avogadro and Bioclipse
are good for this
* machine interfaces for generating input.
Another interesting piece of software is ASE, which provides a common
> interface to setting up jobs for several of these programs. See
> https://wiki.fysik.dtu.dk/ase/index.html. Perhaps Avogadro can
> consider being a backend to this.
>
> This is a useful approach
I am interested in machine interfaces so that - say - we can automatically
compute all the covalent molecules in CrystalEye (I am at a grid meeting
where we are discussing this sort of grand challenge). Here we need a common
representation (CrystalEye emits CML) and a set of parameters
(parameter-sweep) to be applied to each molecule. In out current work we use
dictionaries to define the parameters and then use a templating tool
(Freemarker) to create the input for each program (this template only hase
to be written once and is roughly independent of the language driving the
job).
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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