Hi Bob,
Sorry, my question was not clear. It arose form the perspective of
providing feedback to a learner who was being tested on his/her
understanding of the concept of aromaticity. E.g. a learner could be asked
to draw any aromatic structure, or a bicyclic aromatic structure, or a
five-membered ring that was aromatic, etc. Jmol could then be used to
analyse the SMILES of the learner-drawn structure and 'intelligent'
feedback could be provided that identified if the answer was correct, or,
if not, why the answer was incorrect. I suspect that most Jmol users are
interested in a Yes/No answer to the detection of aromaticity, but it would
be very nice to leverage your existing algorithm to provide a little more
information that would be helpful in educational contexts.
>From one of your earlier postings I assumed that your algorithm for
detecting 'strict' aromaticity must be checking the supplied structure
against a set of criteria (cyclic, uninterrupted pi system, planar, 4n + 2
electrons), so that it might be possible for the algorithm (optionally) to
return 'flags' (meets, or does not meet, each criterion) that could then be
used to generate the appropriate feedback to the learner. I have now read
your pdf on how the Jmol SMILES aromaticity algorithm works and, broadly
speaking, it does seem to function in that manner. So, following the steps
listed in your pdf document, and thinking particularly about the STRICT
directive, would it be possible to create an option for the function to
return a set of diagnostics, as follows?
1. Criterion 1: Does the structure contain at least one ring?
2.a., 2.c. (and 4.?) Criterion 2: Does the structure contain a ring(set) in
which all the ring atoms are involved in the pi system? (I'm not sure
what kinds of structures the algorithm is seeking to exclude in Step 4, but
I think it relates to Criterion 2.)
2.b. & 3. Criterion 3: Does the structure contain a ring(set) that meets
Criterion 2, and is planar?
2.c. & 3. Criterion 4: Does the structure contain a ring(set) that meets
Criteria 2 & 3, and involves 4n+2 electrons, or 4n electrons?
I haven't studied the Jmol code, so I may be mistaken about parts of the
algorithm, but I hope the general idea is clear. In much the same way as
the algorithm already assigns each ring a value of -1, 1 or 2, could a more
comprehensive set of flags be returned for the whole structure? By
extending the existing algorithm in this way, correct answers could be
identified, as now, but errors could be diagnosed and more detailed
feedback provided for incorrect responses.
Many thanks for all your work Bob. I'm pleased to read that you are
preparing a paper on the SMILES and SMARTS functionality of Jmol; those
powerful capabilities are great and are not available in any other open
resource, as far as I know, so they deserve to be fully reported.
Mike
Dr Mike Casey
School of Chemistry
UCD
Dublin
01 716 2420
On 14 May 2016 at 02:38, Robert Hanson <hans...@stolaf.edu> wrote:
> Mike, not sure what you want to consider a "criterion" but you can do all
> sorts of tests. The key is something called "directives" which instruct
> Jmol to use different options for aromatic. Can you give us some options of
> what you are interested in testing?
>
> On Fri, May 13, 2016 at 3:06 AM, Mike Casey <mike.ca...@ucd.ie> wrote:
>
>> Many thanks Bob, I'll check Jmol 14.6.0 when you release it.
>>
>> I like the option to check for aromatic structures using general
>> criteria, it will provides another good method for checking student
>> conceptual understanding. For analysis of incorrect student answers it
>> would be really useful to know which criteria were not met - any chance of
>> being able to retrieve that information? Presumably your algorithm checks
>> each criterion, so the info is available, though providing that additional
>> information might be tedious for you to implement. However, the ability to
>> interrogate the Jmol result and give detailed feedback to learners would be
>> excellent.
>>
>> Sorry, I'm never satisfied. ;)
>>
>> Best regards,
>> Mike
>>
>> Dr Mike Casey
>> School of Chemistry
>> UCD
>> Dublin
>> 01 716 2420
>>
>> On 13 May 2016 at 06:42, Robert Hanson <hans...@stolaf.edu> wrote:
>>
>>> I am just completing a total overhaul of Jmol's SMILES and SMARTS
>>> processing for a paper I am writing.
>>> At least in the version I will be releasing this weekend as Jmol 14.6.0,
>>> I see this:
>>>
>>> $ print "CCCO".find("SMARTS",
>>> "[#6,H]C([OH])([#6,H])[#6,H]").format("JSON")
>>>
>>> [ 1,2,3 ]
>>>
>>> So that bug is fixed.
>>>
>>> One significant change in the way Jmol SMILES and SMARTS will work is
>>> that I have implemented "strict" aromatic testing, which does a Hueckel 4+2
>>> analysis the way that is taught in organic chemistry. -- cyclic pattern of
>>> sp2 atoms, planar, 6 electrons.The default for Jmol is "find the flat
>>> plane", but now that I have built in the capability to do the 4+2
>>> aromaticity test, I think it makes sense to go to that.
>>>
>>> $ load $cyclobutadiene
>>> C4H4
>>>
>>> $ print {*}.find("SMARTS","a")
>>> ({})
>>> $ load $azulene
>>> C10H8
>>>
>>> $ print {*}.find("SMARTS","a")
>>> ({0:9})
>>> $
>>>
>>> So, Mike, do check out the version I release this week end.
>>>
>>> Bob
>>>
>>>
>>>
>>> On Wed, May 11, 2016 at 11:11 AM, Mike Casey <mike.ca...@ucd.ie> wrote:
>>>
>>>> Hi All,
>>>>
>>>> Any thoughts on the change in the way substructure searches are carried
>>>> out using .find("SMARTS", SMARTSstring), described in the previous email?
>>>> Unless I am missing something, there seems to be a big change in the
>>>> behaviour of such searches, and any help would be most welcome.
>>>>
>>>> With thanks,
>>>> Mike
>>>>
>>>>
>>>>
>>>>
>>>> Dr Mike Casey
>>>> School of Chemistry
>>>> UCD
>>>> Dublin
>>>> 01 716 2420
>>>>
>>>> On 6 May 2016 at 18:03, Mike Casey <mike.ca...@ucd.ie> wrote:
>>>>
>>>>> Thanks Bob.
>>>>>
>>>>> I was already replacing \ with \\ in the expected string, but, as you
>>>>> say a second escape is necessary. The student-generated string comes from
>>>>> JSME, so Otis's tactic is a good solution in that case.
>>>>>
>>>>> Mike
>>>>>
>>>>>
>>>>>
>>>>> Dr Mike Casey
>>>>> School of Chemistry
>>>>> UCD
>>>>> Dublin
>>>>> 01 716 2420
>>>>>
>>>>> On 6 May 2016 at 17:55, Robert Hanson <hans...@stolaf.edu> wrote:
>>>>>
>>>>>> Ah, yes. Escaping those back-slashes may be the issue.
>>>>>>
>>>>>> $ load $2-butene
>>>>>> C4H8
>>>>>>
>>>>>> $ print {*}.find("SMILES","C/C=C/C")
>>>>>> ({0:11})
>>>>>> $ print {*}.find("SMILES","C/C=C\C")
>>>>>> ({0:11})
>>>>>> $ print {*}.find("SMILES","C/C=C\\C")
>>>>>> ({})
>>>>>>
>>>>>> So, you see, the real problem is that we are not getting an error
>>>>>> message from that second version. I will see if I can get that happening,
>>>>>> although in this particular mode, what will probably be returned is an
>>>>>> empty atom set, not a string error.
>>>>>>
>>>>>> Note that if doing this in JavaScript, you probably have to escape
>>>>>> TWICE:
>>>>>>
>>>>>> Jmol.evaluateVar(jmolApplet0, "{*}.find('SMILES','C/C=C\\\\C')")
>>>>>>
>>>>>> *Array [ ]*
>>>>>>
>>>>>>
>>>>>> because it has to go through two stages of conversion.
>>>>>>
>>>>>> Bob
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>
>>>>
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>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Department 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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>>
>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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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> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
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>
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