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

From: Beda Kosata
Subject: Re: [Bkchem-user] OASA, missing atoms in periodic_table.py
Date: Tue, 6 Apr 2010 14:56:36 +0200
User-agent: Thunderbird (X11/20090605)

Loic d'Anterroches wrote:
> OC wrote:
>> Loic d'Anterroches wrote:
>>> 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.
>> I'm not a chemist, but I bet it is:
>> "en" : electronegativity (Pauling). I notice that some values are not
>> exact (for example H 2.10 instead of 2.20) but it may be on purpose.
>> "els" : number of electrons in the neutral atom on the outer shell
>> "valency" : possible number of bonds
> Thanks, this was this valency where I was wondering the most. The
> numbers are all listed in ascending order, except for Carbone with 4
> first and 2.
> I will simply try and see what is coming out of it.
> Thanks!
> loïc


valency is sorted from the most common to the least common (see for
example "P").
A complete periodic table is part of the development version of OASA.
You can either get it from the tla sources
(http://bkchem.zirael.org/arch_en.html) or it was distributed with the
last preview version of BKChem (a separate release of OASA will be made
for the final version).
The algorithm for 2D layout is indeed not optimal as it does not take
other that local influences into account and thus allows overlap of
parts of the structure. AFAIK CDK
contains a more sophisticated algorithm, but I did not try it myself.

        Best regards


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Bedrich Kosata
Laboratory of Informatics and Chemistry
ICT Prague
Czech Republic

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