Mike,
I can’t comment on your SMARTS question, but your first question relates to
escaping JavaScript strings. Hopefully, the first two lines (regular expression
replace) of my compare function are self explanatory:
function compSmiles(key, ans) {
key = key.replace(/\\/g, '\\\\');
ans = ans.replace(/\\/g, '\\\\');
return jmv("'" + key + "'.find('SMILES','" + ans + "') > 0");
}
If you need further explanation, let me know.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On May 6, 2016, at 11:00 AM, Mike Casey <mike.ca...@ucd.ie> wrote:
>
> 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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