Thanks Stuart,
I've submitted an abstract to the Fall ACS, intending to see if there's
interest and will look at possible options after that.
John
On 9 May 2017 at 21:27, Chalk, Stuart <sch...@unf.edu> wrote:
> Bob, John and the group
>
> If there is interest in starting up an ‘Open CIP’ project I can offer
> space on the newly minted IUPAC GitHub account.
> Let me know if that would be of use and if so who would be the admin for
> the project. We can invite collaborators after that…
>
> Stuart
>
> On May 9, 2017, at 4:19 PM, John Mayfield <john.wilkinson...@gmail.com>
> wrote:
>
> With regards to an "Open" CIP -- I strongly suggest not going there. If
>> you are seriously interested in this, join/form an IUPAC project.
>
>
> For me the main motivation is to not reinvent the wheel, or perhaps not
> reinvent the wheel worse than it already was. The less people have to think
> and worry about CIP the better.
>
> Maybe an IUPAC project is the way to go there... but a stepping stone is
> to have a 'standard/verified' implementation (i.e. Open CIP) first. You've
> done well on your implementation and it may be one to recomend as a
> 'verified' version but if we do nothing in 2 years time someone else will
> come along and waste more time with the same bugs/corner cases.
>
> - You've still not done the iteration quite right, you only give 4 labels
> for this one: [C@]3([C@]1([H])CC[C@@]([H])(C)CC1)([C@]2([H])CC[C@@]([H])(
> C)CC2)CC[C@]([H])(C)CC3
> - What CIP labels do you get for CHEBI:51439
> <http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A51439>? I believe
> a correct implementation should never finish... or at least run of memory
> when building the digraph.
>
> On 9 May 2017 at 19:48, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> 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 <hans...@stolaf.edu>
>> 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 <hans...@stolaf.edu>
>>> 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
>>
>>
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