On Fri, Nov 12, 2010 at 10:38 AM, Otis Rothenberger
<osrot...@chemagic.com>wrote:
> Bob,
>
> I think "A" is all I need." Everything we do is based on issues related to
> the model in the Jmol window (I think? See below). This involves queries to
> a number of resources (check name, check image, get remote db molfile, check
> FIND in database SMILES vs model SMILES... ), but the query is always based
> on the SMILES generated by the model in the Jmol window.
>
> With two models in the window, I'm using the following logic:
>
> string for selected atoms in model 1.find("SMILES",string for selected
> atoms in model 2)
>
>
If "string" means "SMILES string", then I think you are using (B).
> To make that truly method A, do I need to change to:
>
> {selected atoms in model 1}.find("SMILES",string for selected atoms in
> model 2)
>
>
That's much better.
> ???
>
> Do you mean that you think you can actually detect cis/trans and enatiomers
> in octahedral systems?
>
>
>
Probably not. You would have to have a SMILES string that has the @OHn
designation, and Jmol won't create that at this point in time.
> Otis
>
> Otis Rothenbergerchemagic.com
>
>
> On 11/12/2010 10:39 AM, Robert Hanson 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 to the unpublished supposed additional @OHn and @TBn designations.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.
>
>
>
>
> ------------------------------------------------------------------------------
> 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
