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

[Jochen J. <joc...@fi...>]

Hi Robert!

Thank you so much, that nailed it!
This solution works for JSmol v16, but not v14, which I was using so far. But that is fine, I was about to update anyhow to the latest version.

I know that the geometry of the first molecule is *at least* strange. This was generated by a structure generator based on some theoretical data and is not expected to be a good fit. This geometry probably messes up JSmol's perception of aromatic, some also mess up OpenBabel’s perception of aromaticity…

I wanted to be able to do an automatic superposition with the reference, based on the MCS calculated by RDKit. This is expected not to be nice for bad fits. And probably this is why you have an odd feeling about it. But, it is working really fine now!

Thank you,
Jochen


On 30 May 2025, at 15:28, Robert Hanson via Jmol-users <jmo...@li...> wrote:

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...<mailto: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<https://ddec1-0-en-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2fsmarts.plus&umid=56eca403-cc5d-4f2b-afe2-593605a38c72&rct=1748629818&auth=1bcda6227c1853a98db9a85322c3ec3db27ad845-7645cc26a4d44abe738db6cc56aaf55d7ebbc097>, 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
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