I have only just returned to active use of Jmol, so I apologise if the
following questions have been dealt with in the two years that I have not
been paying attention.
First a SMILES issue. I use Jmol.evaluateVar (Jmol 14.4.4 2016-04-22) to
check whether a structure drawn by a student in JSME (2013-06-09) is
correct, but get odd behaviour when comparing SMILES strings for geometric
isomers of alkenes. The following examples, in which actual SMILES strings
are shown, rather than variable names, for clarity, are indicative.
C/C=C\C.find("SMILES", C/C=C/C) does not give a match, as expected, but
C/C=C/C.find("SMILES", C/C=C\C) DOES give a match!
In passing, it seems that the most recent distribution of JSME seems to
have lost the ability to generate SMILES strings with stereochemical
information for alkenes.
Searching for partial structures using SMILESstring.find("SMARTS",
SMARTSstring) worked perfectly with an older version of Jmol (13.2.7), but
v14.4.4 is different. For example, checking for the presence of an alcohol
functional group using
CCCO.find("SMARTS", [#6,H]C([OH])([#6,H])[#6,H])
gave a match in the old version, but not in the new one. It is necessary
to add explicit hydrogens on the O and the carbinol C to get a match in
v14.4.4.
Am I missing something, or are these real issues? The SMILES & SMARTS
features in Jmol are extremely useful, and I look forward to any comments
or suggestions.
Mike Casey
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