Bob,
There is a general aromatic problem that I'm having with find SMILES
that's easiest to explain with a specific scenario. If I load benzene
and run "var x={*}.find('SMILES');echo @x," I get:
c1=cc=cc=c1
If I use model kit mode to make 1,3-cyclohexadiene, the same "var
x={*}.find('SMILES');echo @x" produces
c1=cc=ccc1
I'm now stuck in lower case "c" mode on this ring no matter what I do to
the ring. If I break a ring bond while the ring is no longer aromatic
and reform the bond, I go back to upper case "C"
There are really two issues here:
1) Jmol creates Kekule SMILES in lower case, and this does not seem to
be standard. As long as compare is Jmol/Jmol, this is not a problem. And
in fact, NIH Resolver which uses aromatic SMILES (c1ccccc1), recognizes
the Jmol lower case Kekule SMILES for benzene.
2) Getting stuck in lower case mode, however, is a problem and seems to
be a bug.
I have a feeling that calculate/reset aromatic may offer one solution to
the problem, but I'm not sure it can be used in a general sense to
"unaromatise" an aromatic ring. If this is not a bug, an alternative is
to use JavaScript toUpperCase() on s, c, n, and o, but that has ugly
side affects.
Otis
--
Otis Rothenberger
chemagic.com
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