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the unpublished supposed additional @OHn and @TBn designations.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
> Markus (Resolver) wrote several weeks ago indicating that the Resolver
> SMILES are only internally unique. He mentioned that Daylight never
> released their algorithm. I'm carrying them in our data base with the
> hope that in our mini-internal system I can use them to pick up isomer
> types in coordination complexes. This would not be a general algorithm,
> but it would allow detecting isomer types in our database for problem
> exercises.
>
> Otis
>
> Otis Rothenberger
> chemagic.com
>
>
> On 11/12/2010 7:50 AM, Robert Hanson wrote:
> > Ah, HA! Found it. It was in the SMILES reader translating indicated
> > stereochemistry to actual 3D positions when a new component mark "."
> > was followed by a stereochemistry indicator with H, "[...@h]", which was
> > followed immediately with the SECOND ring bond connection number. Wow.
> > That's obscure. One little line in the code.... Amazing. Good test, Otis!
> >
> > version=12.1.22_dev
> >
> > # bug fix: SMILES matching string with "....@h]1" reads stereochemistry
> > incorrectly
> >
> > http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
> >
> >
> >
>
>
>
>
> ------------------------------------------------------------------------------
> Centralized Desktop Delivery: Dell and VMware Reference Architecture
> Simplifying enterprise desktop deployment and management using
> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
> client virtualization framework. Read more!
> http://p.sf.net/sfu/dell-eql-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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
------------------------------------------------------------------------------
Centralized Desktop Delivery: Dell and VMware Reference Architecture
Simplifying enterprise desktop deployment and management using
Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
client virtualization framework. Read more!
http://p.sf.net/sfu/dell-eql-dev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
