Bob,
I don't know if I hit all possible combinations, but I can't break the
trans SMILES listing. This is great.
I don't see the auto update. This could be related to my own message
callbacks. I don't even see SMILES changes on find unless I do atom
substitutions - as opposed to drags. As a said above, this seems to work
perfectly. Since this is my main concern (atom substitution), I'm a
happy camper. The drag/SMILES change sounds like great fun, however.
Otis
Otis Rothenberger
chemagic.com
On 11/14/2010 3:17 PM, Robert Hanson wrote:
Otis, I have something for you. Woke up this morning with an idea, and
it appears to have worked. Jmol now generates correct stereochemical
SMILES for trigonal bipyramidal and octahedral shapes. Odd that
Daylight didn't consider T-shaped and square pyramidal. Oh well! This
is still better than nothing, I think. The trick was in getting Jmol
to list the ligands in the proper order -- first a trans-pair, then
the others in the correct order.
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Anyway, please test. A simple way to do that is to use
LOAD http://chemapps.stolaf.edu/jmol/docs/examples-11/data/SF6.smol
-1 # just the first vibration
wireframe only;label
{atomno=3}.element = "Br"
{atomno=5}.element = "I"
{atomno=6}.element = "Cl"
x = {*}.find("SMILES")
print x
print {*}.find("SMILES",x)
# and variations on that theme. Also, this is sort of fun:
set modelkitmode
delete atomIndex=6
set picking dragAtom
set echo top left
echo @{ {*}.find("SMILES")}
# now drag atoms around and watch the top left echo update automatically!
Bob
On Fri, Nov 12, 2010 at 9:39 AM, Robert Hanson <hans...@stolaf.edu
<mailto:hans...@stolaf.edu>> wrote:
On Fri, Nov 12, 2010 at 9:22 AM, Otis Rothenberger
<osrot...@chemagic.com <mailto:osrot...@chemagic.com>> wrote:
Bob,
Thanks for the quick repair job!
Follow-up question: By my testing, the SPn SMILES notation allows
complete FIND/compare ability for simple square planar
complexes. Does
the order of the ligands in the octahedral SMILES carry the
same punch?
I've had success with simple tests, but there's a lot more to
test here,
so I though I'd go directly to the SMILES master.
There are two kinds of finds:
A) {structure}.find("SMILES", smilesString)
B) smilesString1.find("SMILES", smilesString2)
for (A), all stereochemical notation is implemented -- allenyl,
tetrahedral, square planar, trigonal bipyramidal, and octahedral.
for (B), allenyl, tetrahedral, and square planar are fully
implemented. Trigonal bipyramidal requires that the two axial
ligands be listed first and last; in the case of octahedral, we
require that the two designated "axial" groups be listed first and
last.
No reason for this other that I did not finish the job and have no
access to the unpublished supposed additional @OHn and @TBn
designations. I think I could easily enough implement octahedral
checking as long as any two diametrically opposed groups are given
first and last.
Not 100% sure I can get Jmol to produce accurate SMILES for *any*
octahedral or trigonal bipyramidal compound.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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