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)
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)
???
Do you mean that you think you can actually detect cis/trans and
enatiomers in octahedral systems?
Otis
Otis Rothenberger
chemagic.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 <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access to the unpublished supposed additional @OHn and @TBn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.
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