[BlueObelisk-SMILES] Fwd: Whew! This is tricky! SMILES /C=C/ question.

[Robert H. <ha...@st...>]

---------- Forwarded message ----------
From: Robert Hanson <ha...@st...>
Date: Mon, Jun 7, 2010 at 11:11 AM
Subject: Re: [BlueObelisk-SMILES] Whew! This is tricky! SMILES /C=C/
question.
To: Craig James <cra...@em...>


Thank you all. I think I'm all set. Craig, you are EXACTLY correct, and with
that bit of information I have Jmol reading any God-awful SMILES using / ...
/ and properly checking for consistency. Hooray!

Geof, the SMARTS processor in Jmol (just checked in) is now reading all
these variations correctly for all stereochemistry. It uses Craig's clear
and concise description.

Craig, about that OpenSMILES documentation:

You use "allenyl" there where you mean "alkenyl" --- allenyl, of course, is
the central carbon of C=C=C. I suggest adding a section on ring bonds.
Specifically how one can use

  Br/1...........C\1=......

because the first one says "connection 1(C) is above Br" and the second says
"connection 1(Br) is below C". This is all consistent and proper...And it's
important when there are "cross-links" between components separated with
".". Since we only need one of those, not both, we can say:

  Br1...........C\1=......

or

  Br/1...........C1=......

just not

  Br/1...........C/1=......


As for that impossible structure, you're just forgetting that you can
combine two fragments. Yes, it's impossible if you allow no use of ".", but
with that, we can handle cyclooctatetraene. The "." allows the needed
switching parity between the two fragments.

C/1=C\C=C/2.C\1=C/C=C\2

That gives the proper structure at the Daylight DEPICT site.

:)

Now to encode that into my SMILES generator, and I will have it!




Bob



I hope that all of these questions are answered in the OpenSMILES
> documentation:
>
> http://opensmiles.org/spec/open-smiles-3-input.html#3.9.3
>
> The key is this sentence: "The 'visual interpretation' of the 'up-ness' or
> 'down-ness' of each single bond is relative to the carbon atom, not the
> double bond, so the sense of the symbol changes when the fluorine atom moved
> from the left to the right side of the allenal carbon atom."
>
> Once you understand this (that the up/down is relative to the CARBON atom,
> not the double bond), it answers all of your questions.
>
> You might also find this interesting.  It's a fundamental shortcoming in
> cis/trans in SMILES, an impossible structure:
>
> http://opensmiles.org/spec/open-smiles-6-extensions.html#6.3
>
> Craig
>
>
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-- 
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



-- 
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