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[Bkchem-user] OASA, missing atoms in periodic_table.py

From: Loic d'Anterroches
Subject: [Bkchem-user] OASA, missing atoms in periodic_table.py
Date: Sat, 03 Apr 2010 10:32:02 +0200
User-agent: Thunderbird (X11/20090817)


just a small request, Neodymium[1] is missing from periodic_table.py and
I do not understand the format of the periodic_table dictionnary to add
it. If I can get some details about the "en", "els" and "valency" keys,
then I can add the missing components. I have a database of about 50k
molecules and when drawing them, the molecules with atoms not in the
periodic_table are failing.

On a side note, the automated generation of the 2D coordinates is not
always optimal. I tried to find a something more robust and still open
source without success. Do you know some good implementations? If not,
do you know some good papers with algorithms to do the generation? We
really need something robust in open source, I have some experience
maintaining such engine (closed source) so I can help get something done
here. I would need to start from scratch or the OASA code not to have IP
conflict with my previous work. This is why I am interested by good papers.

Thanks a lot for this great work!

[1]: http://en.wikipedia.org/wiki/Neodymium

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