Re: adding a new org-element?

[John Kitchin <jkitchin@andrew.cmu.edu>]

Eric S Fraga writes:

> On Tuesday, 22 Mar 2016 at 07:34, John Kitchin wrote:
>
> [...]
>
>> the elisp link is a good idea, but I am looking into an idea for a
>> chemical markup language where you might have a $(molecule + data)$ and
>> reaction descriptions $(molecule -> new molecules)$ that become
>> machine-readable as well.
>
> Sounds nice and I would probably find a use for this!  With elisp, you
> could of course define functions (reaction ...), (molecule ...),
> etc.  Ummmm something to think about for me now that term is finishing
> :-)

I also did something like that here:
http://kitchingroup.cheme.cmu.edu/blog/2016/01/17/Side-by-side-figures-in-org-mode-for-different-export-outputs/

which worked ok as long as everything fits into a block and you don't
want things inline. That implementation had some limitations, like no
communication between the blocks, and the need to load different
functions for different exports. The latter could be fixed the way
org-links are exported by backend specific outputs.

I could define a lisp helper lib with those definitions, and a link that
would provide some functionality (e.g. view the molecule, or compute
some property) and export.

The main reason for wanting a new element is just to be able to map over
them. With links, I have to map over all the links, and check if the
type is what I want. It's not terrible, but... It is also somewhat
tedious still to refontify some link types, e.g. ir org-ref I make the
cite, ref and label links specific colors, and show the full cite links
if there are descriptions. Also, I am looking for alternatives to my
\(mis\|ab\| \)use of links for this kind of stuff ;)

I was inspired by this paper:
http://pubs.rsc.org/en/Content/ArticleLanding/2001/NJ/b008780g#!divAbstract
that uses an XML based approach for "Development of chemical markup
language (CML) as a system for handling complex chemical content" and
I wondered what this would look like if I wrote the paper in org-mode
and used a lisp markup for the data.


>
> The nice thing about elisp is having the full power of lisp. even if it
> is emacs lisp ;-)
>
> Anyway, keep us posted!


--
Professor John Kitchin
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@johnkitchin
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