Re: [BlueObelisk-discuss] Jmol - CIP update

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

OK, 967 lines. This now includes chiral bridgehead nitrogens and is just
missing a small piece of code for integrating M/P and seqCis/seqTrans into
Rule 4b. The algorithm is solid. No particular issues other than that. Does
not implement atom-number averaging for mancude rings, but does remove
Kekule dependencies for aromatic rings. This last bit required a slight
additional "friendly amendment" to Rule 1b, which I don't think was crafted
with aromatics in mind. Pseudocode is still pretty much the same as
initially described. There are no issues with multi-center dependencies.

Validates on the full 236-compound Chapter 9 validation suite from ACD/Labs
except:

var skip = ({27 229}) || // ignore -- BB has E/Z only; missing chirality
           ({95 96 98 99 100 101 102 103 104 108 109 110 111 112 200}) ||
// trigonal planar, square planar, or hypervalent
           ({32 33})  || // helicene
           ({212 213})|| // chiral conformation 1,4-benzene in a ring
           ({38})  || // ignoring -- Mancude for cyclopentadienyl -- will
require some thought
 ({170}) // failing (mixed Rule 4b)

In the process, I have found four erroneous assignments in IUPAC Blue Book
2013. These are being checked by IUPAC. There's actually quite a large
errata page for that book already.

With regards to an "Open" CIP -- I strongly suggest not going there. If you
are seriously interested in this, join/form an IUPAC project.

Bob


On Sat, Apr 29, 2017 at 2:54 PM, Robert Hanson <ha...@st...> wrote:

> OK, final update for a while. (816 lines, Wolf. I have no idea how that
> compares to yours or others' algorithms.)
>
> Open-source, validated IUPAC 2013 preferred IUPAC name (PIN)
> stereochemical designations.
>
> Jmol.___JmolVersion="14.15.2" // 4/29/17
>
>  -- 816 lines
>  -- validation data are at https://sourceforge.net/p/jmol
> /code/HEAD/tree/trunk/Jmol-datafiles/cip/
>  -- validates for 160 structures (some duplicates; both cip_examples.zip
> and stereo_test_cases.sdf)
>  -- validates for all cases considered:
>    -- simple R/S and E/Z
>    -- small-ring removal of E/Z
>    -- parallel-strand Rule 4b and Rule 5 (Mata)
>    -- pseudochiral r/s and m/p
>    -- odd and even cumulenes
>    -- atropisomers
>    -- P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
>    -- imine and diazine E/Z chirality
>
> The algorithm will fail for some more complex nested aspects of Rule 4b. I
> decided to be satisfied for now with only those examples in IUPAC Blue Book
> 2013 Chapter 9. My understanding is that even ACD/Labs did not fully
> implement Rules 4 and 5 much beyond that.
>
> Working version in JavaScript can be tested at
> https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
> Binary and source at https://sourceforge.net/projects/jmol/files/Jmol/
>
> A great challenge for April!
>
> Bob
>
>
>
> On Thu, Apr 27, 2017 at 12:21 AM, Robert Hanson <ha...@st...>
> wrote:
>
>> Rule 5 is done. Fully validating using the first validation set that
>> Mikko sent me (86 compounds, roughly, some 2D/3D duplicates). I'm sure
>> there are more cases it needs testing with, though.
>>
>> My algorithm implementation handles Rules 4 and 5 lexicographically so
>> that a simple Array.sort(String[]) does the job. Kind of interesting,
>> perhaps.
>> ​
>> 763 lines, Wolf.
>>
>> 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
>
>


-- 
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