From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: adding a new org-element? Date: Tue, 22 Mar 2016 11:07:21 -0400 Message-ID: References: <87mvpqx6m1.fsf@ucl.ac.uk> <87oaa6txzh.fsf@ucl.ac.uk> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:47668) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aiNu6-0004gI-2H for emacs-orgmode@gnu.org; Tue, 22 Mar 2016 11:07:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aiNu0-000527-7P for emacs-orgmode@gnu.org; Tue, 22 Mar 2016 11:07:29 -0400 Received: from mail-qg0-x234.google.com ([2607:f8b0:400d:c04::234]:33008) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aiNu0-000523-30 for emacs-orgmode@gnu.org; Tue, 22 Mar 2016 11:07:24 -0400 Received: by mail-qg0-x234.google.com with SMTP id 51so15079100qgy.0 for ; Tue, 22 Mar 2016 08:07:24 -0700 (PDT) In-reply-to: <87oaa6txzh.fsf@ucl.ac.uk> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Eric S Fraga Cc: Emacs orgmode 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 Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu