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> wrote:
>
>
> On Fri, Nov 12, 2010 at 9:22 AM, Otis Rothenberger
> <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 to the unpublished supposed additional @OHn and @TBn designations.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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