[Jmol-users] Problem with SMARTS searching using JSmol

[Mike C. <mik...@uc...>]

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