"re" implementing is a great way to find additional bugs and compare
strategies. This (to this point) took me two days. And if I started with a
"libRS" in Java, I would still have to modify it extensively to fit Jmol.
That said, I wouldn't mind taking a look at how other have implemented it.
In the mean time, is it OK for me to continue this discussion without libRS?
Q: What do you say for the stereochemistry of [13CH@@]12C3C1.C2=CC3 ?
On Sun, Apr 9, 2017 at 1:53 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> We need libRS. Everyone reimplementing these rules is some type of madness.
>
> On 9 Apr 2017 7:05 p.m., "Robert Hanson" <hans...@stolaf.edu> wrote:
>
>> OK, I don't get the logic of this:
>>
>>
>> Rule 1 (a) Higher atomic number precedes lower;
>> (b) A duplicated atom, with its predecessor node having the same label
>> closer
>> to the root, ranks higher than a duplicated atom, with its predecessor
>> node
>> having the same label farther from the root, which ranks higher than any
>> nonduplicated-atom-node (proposed by Custer, ref. 36)
>>
>> Rule 2 Higher atomic mass number precedes lower;
>>
>>
>> Seriously? root distance is checked before isotope. Sure seems odd to me.
>> Why would that distance check not be after atomic number and mass??
>>
>> Whatever...
>>
>> Bob
>>
>>
>>
>>
>> On Sun, Apr 9, 2017 at 12:11 PM, Robert Hanson <hans...@stolaf.edu>
>> wrote:
>>
>>> OK, so I am reading Chapter 9 now to see the gory details. I didn't know
>>> about the root-distance check, and so now
>>>
>>> 1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclop
>>> ropylethyl)-pentan-3-yl]methan-1-ol.mol
>>>
>>> is working. So all of this is easy enough. That's probably it for
>>> independent stereochemistry. Where there is a dependency of one
>>> stereochemical determination from another -- R/S after E/Z; E/Z after R/S,
>>> E/Z after E/Z, R/S after R/S -- obviously that takes some sort of more
>>> general iteration.
>>>
>>> I think I will have to tackle that another day.
>>>
>>> Bob
>>>
>>>
>>>
>>>
>>>
>>> On Sun, Apr 9, 2017 at 11:03 AM, John Mayfield <
>>> john.wilkinson...@gmail.com> wrote:
>>>
>>>> Good good,
>>>>
>>>> Fake news before fake news - a paper published in the CCG journal by
>>>> the CCG.
>>>>
>>>> John
>>>>
>>>> On 9 April 2017 at 16:51, Robert Hanson <hans...@stolaf.edu> wrote:
>>>>
>>>>> No, John. Don't worry. I just happened to look at that page prior to
>>>>> designing my own.
>>>>>
>>>>> On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <
>>>>> john.wilkinson...@gmail.com> wrote:
>>>>>
>>>>>> Hi Bob,
>>>>>>
>>>>>> On 9 April 2017 at 13:42, Robert Hanson <hans...@stolaf.edu> wrote:
>>>>>>
>>>>>>> [I actually do know it is Cahn; pulled "Cohen" without thinking from
>>>>>>> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>>>>>>>
>>>>>>
>>>>>> Was that the algorithm you implemented because it's not correct - it
>>>>>> doesn't (and can't) handle ghost atoms. Trying to track down the example
>>>>>> but Daniel Lowe constructed a small reproducible example to demonstrate
>>>>>> why
>>>>>> this can never work.
>>>>>>
>>>>>> John
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
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>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
--
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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