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

[Noel O'Boyle]

On 6 April 2010 13:56, Beda Kosata <address@hidden> wrote:
> 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
>>
>
> Hi,
>
> 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
> (http://sourceforge.net/apps/mediawiki/cdk/index.php?title=Main_Page)
> contains a more sophisticated algorithm, but I did not try it myself.

Regarding structure diagram generation, please see
http://baoilleach.blogspot.com/2008/10/cheminformatics-toolkit-face-off.html
and 
http://blueobelisk.shapado.com/questions/2d-structure-generation-background-and-techniques.

>        Best regards
>
>                Beda
>
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>>
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>
> --
> Bedrich Kosata
> Laboratory of Informatics and Chemistry
> ICT Prague
> Czech Republic
>
>
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