Re: [Jmol-users] Problem with SMARTS searching using JSmol

[Robert H. <ha...@st...>]

Hmm, this is working as well:


x = Jmol.evaluate(jmolApplet0, "'CCCC'.find('SMARTS','[#6]')")

both in 13.2 and 13.3.  Could it just be a version issue? Please try 13.2.7
or 13.3.7

Bob



On Fri, Oct 18, 2013 at 8:00 AM, Robert Hanson <ha...@st...> wrote:

> Sorry for the delay in getting back to you, Mike. I've been totally
> focused on converting JSpecView to JavaScript. Much success, but not
> trivial by any means!!
>
>
>
> However, searching a string for a SMARTS string does not work, e.g.
> X  = Jmol.evaluate(myJSmol, '"CCCC".find("SMARTS","[#6]")'
>
> );    // X is ERROR
>
>
> This works fine in the app:
>
>
> $ print "CCCC".find("SMARTS","[#6]")
> 1
> 5
> 8
> 11
>
>
> and this in the JavaScript version of the console:
>
>
> print "CCCC".find("SMARTS","[#6]")
>
>
> 1
> 5
> 8
> 11
>
>
> So there must be a problem with Jmol.evaluate() itself. Stand by....
>
>
>
>
>
> On Wed, Oct 9, 2013 at 6:19 AM, Mike Casey <mik...@uc...> wrote:
>
>> Hi All,****
>>
>> ** **
>>
>> In the context of developing a tutorial site I need to compare user
>> generated (JSME) SMILES strings with the “correct” SMARTS strings without
>> loading the structure into JSmol (the intention is that the user can
>> subsequently opt to use JSmol to view the structure if they wish).  The
>> powerful SMILES and SMARTS features of JSmol seemed ideal for this purpose,
>> but I have run into some difficulties, as listed below.  ****
>>
>> ** **
>>
>> Searching an atom expression (when a structure is present in JSmol) for a
>> SMARTS string works, e.g.****
>>
>> X  = Jmol.evaluate(myJSmol, '{*}.find("SMARTS","[#6]")');    //Works as
>> expected****
>>
>> ** **
>>
>> However, searching a string for a SMARTS string does not work, e.g.****
>>
>> X  = Jmol.evaluate(myJSmol, '"CCCC".find("SMARTS","[#6]")');    // X is
>> ERROR****
>>
>> ** **
>>
>> On the other hand, calculating a molecular formula from a SMARTS string
>> (or an atom expression) does work, e.g.****
>>
>> X  = Jmol.evaluate(myJSmol, '"CCCC".find("SMARTS","MF")');  //X is C 4
>> Correct!!!****
>>
>> ** **
>>
>> I would be very grateful if anyone can identify what I am doing wrong, or
>> suggest an alternative approach.****
>>
>> ** **
>>
>> Mike****
>>
>> ** **
>>
>> Dr Mike Casey
>> School of Chemistry & Chemical Biology
>> University College Dublin
>> Dublin 4
>> Ireland ****
>>
>>
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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