Spoken by a man whose school fight song is Um Yah Yah...
Happy to do it. I'm putting some stuff together for BCCE, and I might as well
do all the testing on your latest versions.
Otis
Sent from my iPad
> On Mar 30, 2016, at 12:10 AM, Robert Hanson wrote:
>
> Otis, thanks so much for testing
Otis, thanks so much for testing this. It has to do with that needed
reversal of connection numbers and branches. There was still a bug in the
switching code. In the process of fixing that, I discovered a line I
dropped from the code that broke Jmol's ability to check stereochemistry in
one SMILES
shoot! Thanks for testing, Otis...
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Bob,
It’s not my implementation. I tested this on my page on my server for
4.4.4_2016.03.25 and 4.4.3_2016.03.05. Only 4.4.4_2016.03.25 is broken. Prior
to this I tested your page at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
(4.4.4_2016.03.14). It’s not broken there.
4.4.4_2016.03.25 bro
Yeah, today is "fix-it" day all day.
OK. The aspirin Java error is fixed. The other error has to do with the
fact that we are returning "\1" inside a string. I'll have to track down
where that is coming from. Can't work on this for a bit
Bob
On Thu, Mar 24, 2016 at 2:23 PM, Otis Roth
Typo: steps 4 and 5 are both from Jmol console.
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Mar 24, 2016, at 2:08 PM, Otis Rothenberger wrote:
>
> Bob,
>
> I was exploring a SMILES problem with the version you loaded yesterday.
>
> I just downloaded today's new version a fe
Why no difference? That's because if you are using strings like that, you
need to use \\ instead of \. All you are doing there is escaping the "4",
which doesn't do anything.
$ load "$prostacyclin i2"
$ show smiles
C[C@H](O)/C=C/[C@@H]1[C@@H]2[C@H]3O/C/4=C\(O)=O.C2\4.[C@H](O)1C3
$ var x
Otis,
I got it -- very interesting -- two obscure bugs, both relating to cationic
aromatic nitrogen. Wow. Good find! Fixed for both Jmol 12.1.35 and 12.0.32.
Uploading http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Jmol was generating an incorrect SMILES string for NAD+ both in the
Bob,
Some additional information to add some checks to this issue.
I pass the SMILES into Jmol Script from JavaScript, thus the // for / in
the DB. I thought I better check the console entry of SMILES on an example
that works. I was surprised by the results, but the NAD+ problem appears to
be
Bob,
This is not a huge problem. For what we are doing, we depend mostly on
internal consistency of our SMILES library, and Jmol SMILES give us
that. The only place we run into this problem is with a link that
optimizes a model in the window by making a Resolver call.
Otis
Otis Rothenberger
Sounds like a resolver issue. This is tricky, but not ambiguous.
C\2=C/C#C
indicates a trans connection ("down" to the other atom at connection 2; "up"
to the triple bond)
More explicitly you would have:
o...@h]1[c@H]/2[C@@]34N[C@@H]5C/C=C\C#C.C4CC1.C5CC3.C\2=C/C#C
but that first "/2" can be j
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