Re: [BlueObelisk-discuss] Jmol - CIP update

[Robert Hanson]

Jmol update. Rule 4 is complete. Just 1/80 structures -- Example 6, p. 1208
-- is not validating. But that's just because I have not worked on Rule 5,
and that structure is only resolved there.

Two other structures (Example 4, p. 1200 and O-methyl
(S)-(benzenesulfonothioate), P-93.2.5, page 1216 ) I believe are
incorrectly annotated in the SDF file. In the first case, it looks like an
error in choosing the reference configuration when the two branches have
different Rule-1 priorities; in the second, it looks like S=O is not
properly considered to be a single bond (so no duplicated S on O2). These
seem to me to be easy things to miss and, at least the second one, to fix.
Jmol has no problem now with the reference issue. It is handling all
components of Mata's description of Rule 4b. Again, the code for that is
highly recursive.

So I'm fairly certain that the overall approach I am using exactly
implements IUPAC 2013 Chapter 9 Rules 1-4 for all cases considered,
including S and P with lone pairs (but not imines yet). There are some
great examples there that are really demanding of an algorithm and caught
some rather subtle issues.

Now I'm definitely getting interested in what other algorithms are out
there and how they perform. Very interested in what you find, John. Are you
planning to test these other implementations using a standard validation
suite? I've put mine up at
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip, but
I think it's missing some key tests.

I'm hoping to finish Rule 5 sometime tomorrow or Thursday.

743 lines.

Bob


On Tue, Apr 25, 2017 at 11:26 AM, Robert Hanson  wrote:

> Basic Mata analysis is in. Still two structures (Examples 4 and 6, pp 1200
> and  1208) are not validating, but I know why. Haven't implemented
> multi-reference like/unlike checking or a final check for complex
> pseudochirality involving Mata analysis. Both should be simple enough.
> We'll see! All other structures are validating. I've asked IUPAC for their
> validation set.
>
> 699 lines.
>
> Bob
> ​
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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
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Re: [BlueObelisk-discuss] Jmol - CIP update

[Robert Hanson]

Basic Mata analysis is in. Still two structures (Examples 4 and 6, pp 1200
and  1208) are not validating, but I know why. Haven't implemented
multi-reference like/unlike checking or a final check for complex
pseudochirality involving Mata analysis. Both should be simple enough.
We'll see! All other structures are validating. I've asked IUPAC for their
validation set.

699 lines.

Bob
​
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