Jason Biggs
On Tue, Mar 9, 2021 at 10:49 AM Maciek Wójcikowski <mac...@wojcikowski.pl> wrote: > Hi Jean-Marc, > > I know you can draw them, but both SMILES and RDKit internally use two > bonds (up/down) directions to assign the bond stereo, which means that > there are not > Fortunately the RDKit also allows you to set bond stereo without using the bond directions, by setting the bond stereo flag to stereocis or stereotrans and then setting the stereoAtoms to say which atoms are cis or trans. Using bond directions for double bond stereo has always seemed rather archaic and confusing to me. Jason > enough bonds to define both double bonds configuration and have the middle > one undefined at the same time. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > wt., 9 mar 2021 o 13:14 Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr> > napisał(a): > >> Hi Maciek, >> >> I would find your example rather readable even without explicit H atoms. >> >> >> >> I drew it like that because I do not have the wavy wedge at hand. >> >> Thanks for your proposal, >> Best, >> >> Jean-Marc >> >> >> >> Le 09/03/2021 à 11:26, Maciek Wójcikowski a écrit : >> >> Hi, >> >> I'd say that for a tetrahedral stereo that is possible to remove all of >> Hs. But for double bonds it might not be as easy, or impossible for some >> edge cases - conjugated double bonds in particular. Here is one: >> >> [image: image.png] >> [H]\C(=C/C)C=C\C([H])=C\C >> >> >> ---- >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl >> >> >> wt., 9 mar 2021 o 10:47 Paul Emsley <pems...@mrc-lmb.cam.ac.uk> >> napisał(a): >> >>> On 09/03/2021 09:01, Jean-Marc Nuzillard wrote: >>> > Sure, testosterone may be drawn as >>> > [snip] >>> >>> OK :-) >>> >>> That's a top quality rendering by the way. How did you make it? >>> >>> Paul. >>> >>> >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> >> >> _______________________________________________ >> Rdkit-discuss mailing >> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> >> -- >> Jean-Marc Nuzillard >> Directeur de Recherches au CNRS >> >> Institut de Chimie Moléculaire de Reims >> CNRS UMR 7312 >> Moulin de la Housse >> CPCBAI, Bâtiment 18 >> BP 1039 >> 51687 REIMS Cedex 2 >> France >> >> Tel : 03 26 91 82 10 >> Fax : 03 26 91 31 >> 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html >> http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/ >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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