OK. That's fine. Point me to the algorithm. I'll say no more.
On Mon, Apr 10, 2017 at 7:10 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Sorry, but I have to call you out on this, especially as this is the
> Blue Obelisk mailing list.
>
> I've no problem anyone reimplementing anything for fun or profit, but
> I have to disagree with the suggestion that having an N'th
> implementation of the same algorithm is progress, or good for this
> community. At a recent meeting at the EBI, I think there were at least
> 7 attendees who had written versions of this algorithm. The whole goal
> of the Blue Obelisk is to pool our expertise to develop common
> resources, to avoid exactly this situation.
>
> - Noel
>
> On 9 April 2017 at 23:53, Robert Hanson <hans...@stolaf.edu> wrote:
> > "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-
> cyclopropylethyl)-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
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> ------------------------------------------------------------
> ------------------
> >>>>>>> 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
> >>>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> 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
> >
>
--
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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