The SMILES/SMARTS comparison in Jmol is great! As Bob says, you don't have
to worry about the origin of the SMILES strings (as long as they are valid,
of course), Jmol will get the comparison right every time.
One useful additional feature that is not mentioned in the interactive
scripting documentation page, is that Jmol can ignore stereochemical
information present in the strings using the /nostereo/ option, e.g.
var result = Jmol.evaluate(myJSmol, '"' + studentSMILES +
'".find("SMILES","/nostereo/' + correctSMILES + '")');
where 'studentSMILES' and 'correctSMILES' are variables containing SMILES
strings.
The /nostereo/ option must be documented in one of Bob's other demonstration
pages, I can't remember which one. It can be very useful because users
sometimes use dashed/wedged bonds where they are not needed.
Mike
From: Robert Hanson [mailto:[email protected]]
Sent: 22 January 2014 03:10
To: [email protected]
Subject: Re: [Jmol-users] Jmol 14.0.6 released
The nice thing about Jmol's SMILES comparisons is that it is totally
independent of what program was used to make the SMILES string in the first
place. There is no need for a "canonical" string for our purposes (as there
might be for database look-ups). Thus, it matches any matching structure,
regardless of method of construction. And it can detect isomerism. So it's
really a very convenient solution to this problem of checking answers.
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