I'll check on what's up with the partial charges. No effect on
{molecule=1}.find("MF"), I'm fairly certain.
On Wed, Jun 29, 2016 at 8:50 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> {*}.find("MF") will report the MF you want. No need to go through the
> propery. But I hear you. Yes, probably moleculeInfo should do that. It's a
> simple fix.
>
>
>
> On Wed, Jun 29, 2016 at 1:35 AM, Otis Rothenberger <osrot...@icloud.com>
> wrote:
>
>> Bob,
>>
>> First, AAARGH! Finally.
>>
>> Here’s what messes up [n = {*}[0].molecule;show n] in Jmol - Otis.htm and
>> Test2.htm
>>
>> PubChem provides SDF's with partial charges and without partial charges.
>> Actually, they are always there, but some are listed
>>
>> > <PUBCHEM_MMFF94_PARTIAL_CHARGES>
>> 0
>>
>> If the PubChem file actually lists non-zero charges, then cutting the
>> resulting molecule up in Jmol makes [n = {*}[0].molecule;show n] behave
>> erratically.
>>
>> I load by default from PubChem, and a McLafferty Rearrangement model kit
>> problem using hexanal that I was setting up started this whole email chain
>> with the mf problems. I just kept working with PubChem hexanal while I was
>> trying to find the “funky” behavior on my page. It was just dumb luck that
>> I noticed the PubChem relationship.
>>
>> OK, now that I can use n = {*}[0].molecule, I need to get the mf array
>> over to JavaScript. What’s the best route - message callback?
>>
>> Finally, it seems to me that if CH2 is in the Jmol window, then a simple
>> extraction of mf should be CH2 - not CH4. I’m just saying. This, of course,
>> is a small molecule guy’s opinion!
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.org
>> http://chemagic.org
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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