My mistake. The way to do this is
n = {*}.molecule.max
On Thu, Jun 30, 2016 at 9:57 AM, Philip Bays <pb...@saintmarys.edu> wrote:
> Otis:
>
> I confirm your observation using Safari. But in Firefox, n = 2. Safari
> can’t count?
>
>
>
> On Jun 30, 2016, at 12:29 AM, Otis Rothenberger <osrot...@icloud.com>
> wrote:
>
> Bob,
>
> Go to your test2.htm page and load hexanal from PubChem (not Resolver).
> Enter model kit mode and use delete bond to break hexanal into 3 parts.
> Exit model kit mode and use the console to enter n={*}[0].molecule;show n.
> You’ll get n = 1. As an aside n={*}[-1].molecule;show n yields n = 3
>
> Maybe this is a Safari thing. I worked on this some more today, and I’m
> seeing erratic n=1 in other cases not involving obvious presence of partial
> charge.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On Jun 29, 2016, at 10:53 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> I still don't get what the problem is.
>
> On Wed, Jun 29, 2016 at 2:21 PM, Otis Rothenberger <osrot...@icloud.com>
> wrote:
>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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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>>
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>>
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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
>
>
> ------------------------------------------------------------------------------
> 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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> http://sdm.link/attshape_______________________________________________
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>
>
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>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
> ------------------------------------------------------------------------------
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> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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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
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