Bob,
I'll send you the complete code on this if you want, but I'll simply get
to the bottom line on a curious compare issue in this note. When I
appended your isomer check to my existing identity check, I did the
SMILES checks as follows:
(sm2.find('SMILES',sm1)> 0)
Previously, I was using a compare function that seemed strange to you in
your earlier note to me. I think it's important to note that sm1 and sm2
above are SMILES generated by Jmol from two models in the same frame.
Since the above worked in the two model identity (and isomer) check, I
decided to change the compare function (the strange one) that I was
using in another routine (a model construction tutorial). In this
routine, a single model in the window was being compared to a SMILES
created by JME. In this routine, sm2 is the SMILES that came from Jmol
and sm1 is the SMILES that came from JME. The routine worked for models
with no stereochemistry. But for models with a chiral carbon, the
routine got it backwards. So,
For the strange compare function: var x =
compare({*},{*},'SMILES',sm2,'stddev');if (x == 'NAN'), A-OK for chiral
and non-chiral comparisons.
For (sm2.find('SMILES',sm1)> 0), A-OK for non-chiral. But chiral
backwards - i.e. R matched S and S matched R.
I do understand that the SMILES/SMILES condition is a match and the
compare statement condition is a non-match.
I started using the strange compare before the SMILES to SMILES
comparison was documented. To my way of thinking, the two approaches are
saying the same thing. I just doubled up on the single model {*} so the
compare function would have the correct number of arguments.
In trying to track down the problem, I sent the SMILES generated by Jmol
for (R)-2-chlorobutane to the NIH translate server. R returned S and S
returned R
So I sent (2R,3S)-2,3-dimethylpentanal. RS returned RR and RR returned RS!!
I don't know how reliable NIH translate is. I was getting returned
molfiles for input SMILES rather than returned unique SMILES because I
can read 3D model stereochemistry much better than SMILES stereochemistry.
Finally, I sent the JME SMILES for (R)-2-chlorobutane to NIH. The return
was (R)-2-chlorobutane.
On the one hand, there seems to be something wrong with Jmol generated
SMILES, but then Jmol should get it wrong consistently.
I'll triple check this stuff tomorrow, but I think the above is an
accurate description.
Otis
--
Otis Rothenberger
chemagic.com
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