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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