x = Jmol.evaluateVar(.....)
On Thu, Jun 30, 2016 at 10:43 AM, Otis Rothenberger <osrot...@icloud.com>
wrote:
> Excellent. That works.
>
> Related to the mf array this leads to, what’s the best way to hand a
> JmolScript array to a page JavaScript function? The only way I know how to
> do this is with Message Callback. Is there a more direct way?
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On Jun 30, 2016, at 10:33 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> 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
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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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>>>>> everyone, including kids. Get more information and register today.
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>>>>> Jmol-users mailing list
>>>>> Jmol-users@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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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>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
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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
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape_______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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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>>
>>
>> Philip Bays
>> Emeritus Professor of Chemistry
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape
>> _______________________________________________
>> Jmol-users mailing list
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape_______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
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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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