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 > ------------------------------------------------------------------------------ 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
