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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