Bob,
I should gave given you two more data points on the PubChem issue. I'm sure you
know the first: If PubChem comes in with charges, these charges are appended to
the Jmol molfile extraction.
Second, If a Jmol extracted molfile containing these PubChem charges is loaded
into Jmol, this load carries with it the {*}[0].molecule problem.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jun 29, 2016, at 8:52 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> 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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> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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