Re: [Jmol-users] Possible Bug in compare with SMARTS

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

Jochen, you have just pushed the limit too far for what Jmol will consider
to be aromatic.

$ print this.search( "*/noaromatic/*
[#6]-[#8]-[#6]1:[#6]:[#6]2:[#6](:[#6]:[#6]:1-[#8]-[#6])-[#7](-[#6]1-[#6]-23-[#6]-[#6]-[#7]2-[#6]-3-[#6]-[#6](-[#6]-1)-[#6](-[#6]-2)=[#6]-[#6]-[#8]-[#6])")

({0:19 22 24:28})

But there is still something odd. I think "/strict/" should work. I'll keep
looking at it.




On Fri, May 30, 2025 at 3:02 PM Jochen Junker <joc...@fi...>
wrote:

>
> Hi!
>
> I am using JSMol 14.02 and I am seeing unexpected behavior with the
> compare command. Attached are two scripts, bug.txt demonstrates the problem
> and works.txt shows a situation where everything works fine. The smarts are
> generated by RDKit, and I have verified them to be correct via
> https://smarts.plus, also RDKit uses them just fine.
>
> I get the error message:
> script ERROR: invalid argument
> ----
>          compare { 2.1 } { 1.1 } search "
>
> [#6]-[#8]-[#6]1:[#6]:[#6]2:[#6](:[#6]:[#6]:1-[#8]-[#6])-[#7](-[#6]1-[#6]-23-[#6]-[#6]-[#7]2-[#6]-3-[#6]-[#6](-[#6]-1)-[#6](-[#6]-2)=[#6]-[#6]-[#8]-[#6])-[#6]-[#6]
> " rotate >> translate <<
>
> This looks like a bug in the handling of SMARTS by compare in JSMol. The
> error can be reproduced by pasting the attached scripts into the JSMol
> console.
>
> I appreciate any help with this.
>
> Best Regards,
> Jochen
>
>
>
>
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-- 
Robert M. Hanson
Professor of Chemistry, Emeritus
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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