Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

, 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 thin

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

Hi Bob, On 9 April 2017 at 13:42, Robert Hanson 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

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

Please read back in the discussion Henry, I've linked multiple comparisons - and am planning on doing a more comprehensive one for the next ACS (I'll add Gaussview to the list). ChemDraw's is more advanced than ChemDoodle's. CIP should not be used for finding stereocenters, canonicalizing, or

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

Noel pointed out I only sent this back to Bob. On 10 April 2017 at 08:40, John Mayfield <john.wilkinson...@gmail.com> wrote: > On 9 April 2017 at 23:53, Robert Hanson <hans...@stolaf.edu> wrote: > >> [13CH@@]12C3C1.C2=CC3 > > > Well if you make it valid (Open)

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

On 11 April 2017 at 04:37, Robert Hanson wrote: > 2) What did you get for the other test case, that one checks you have the >> ordering ranking for atomic masses. >> >>> CC[C@@](CO)([H])[14CH2]C >> >> > R. > There you go, that should also be S, ordering is: *CO, *[14CH2]C,

Re: [BlueObelisk-discuss] OK, bragging -- CIP

Thanks for the acknowledgments, let me know where Wolf and I can send the invoices for our consulting fees. ;-) - John On 21 April 2017 at 12:47, Robert Hanson wrote: > 570 lines; 40 methods. > https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/ >

Re: [BlueObelisk-discuss] another CIP question

d to rank ligands. This means that > in the examples in this figure, pairs 1,2 and 2,1 (the order is not > important) should be simultaneously compared in both ligands and the number > of l and u pairs evaluated [image: Inline images 1] On 19 April 2017 at 20:37, John Mayfield <john.w

Re: [BlueObelisk-discuss] Cohen-Ingold-Prelog rules into Jmol

> > Doh sent too soon Hi Bob, > I've been working with Jmol for 10 years and only yesterday realized it > was pretty trivial to write this Then you haven't written it correctly :-). It takes the first 20 pages of this document (

Re: [BlueObelisk-discuss] Jmol - CIP update

On 29 April 2017 at 20:54, Robert Hanson wrote: > 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 >

Re: [BlueObelisk-discuss] Jmol - CIP update

> > 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

Re: [BlueObelisk-discuss] Proposed amendment to CIP Rule 1b

On 17 May 2017 at 18:01, Robert Hanson wrote: > ? Missing this reference. Better algorithm than what? Or you mean just in > general, if you get a null result, at least you are just missing something. > Either case, I think, you need a better algorithm. :) > As I said before,

Re: [BlueObelisk-discuss] Proposed amendment to CIP Rule 1b

Hi Bob, Daniel says he'd seen another example in ChEBI essentially the same as this where if you add Rule 1b it breaks the tie when it shouldn't. John On 16 May 2017 at 00:25, John May wrote: > I need to think more about it tomorrow, I think your logic is correct

Re: [BlueObelisk-discuss] Jmol - CIP update

And the CHEBI one? :p On 9 May 2017 at 22:43, Robert Hanson wrote: > Thanks, again, John. That fix is checked in. I had forgotten to check for > r and s at other than the root atom. > > That reminds me to say that the BB validation suite is missing a lot of > good tests