Thanks for the very fast response Otis. Yes, I had forgotten about the
problem with '\' characters, and your solution works perfectly.
Many thanks,
Mike
Dr Mike Casey
School of Chemistry
UCD
Dublin
01 716 2420
On 6 May 2016 at 16:15, Otis Rothenberger <osrot...@icloud.com> wrote:
> 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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