[Jmol-users] Possible Bug in compare with SMARTS

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

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://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