Thanks for the response.
My goal is to render visually pleasing models of biological polymers: polysaccharides, polypeptides, nucleic acids and lipids. I can generate the ‘flat’ 2D models alright, but you really can’t do this stuff in 2D (mannose and glucose are the same in 2D). So Haworth looked like a good place to start on flattish 3D. It’s instantly familiar and is widely used for polysaccharides, but if there is a better way to use the CDK to produce stereo/3D layouts that would be great. If it makes any difference, I don’t expect to build single giant molecules but rather a series of repeating units at the monomer level, and then visually link them into polymers of a few thousand units. Regards David M Bennett FACS _____ Polygamo – Programming Languages and Players for Games and Puzzles -- http://www.polyomino.com <http://www.polyomino.com/> From: John Mayfield <john.wilkinson...@gmail.com> Sent: Sunday, 23 January 2022 10:36 PM To: dpoly <da...@polyomino.com> Cc: cdk-user@lists.sourceforge.net Subject: Re: [Cdk-user] Layout for Haworth and Fischer projections We do not currently have this feature and I was always sceptical about adding it since there would be information loss for other tools since you can not reliably store them. ChemDraw (and maybe CML) can store them okay but not MOLfile (since it primarily stores stereochemistry with wedges). The code in StereoElementFactory is about working out stereochemistry from an input that is drawn but is not 100% since often it can be very ambiguous. John On Sun, 23 Jan 2022 at 10:27, dpoly <da...@polyomino.com <mailto:da...@polyomino.com> > wrote: Hi All New to CDK, but most impressed by what I see. I can build molecules just fine and depict them in ball and stick 2D (using my own rendering). Very nice! But I can’t figure out how to do layout for Haworth and Fischer projections. I found StereoElementFactory but really no idea how to use it. Any pointers much appreciated. Regards David M Bennett FACS _____ Polygamo – Programming Languages and Players for Games and Puzzles -- http://www.polyomino.com <http://www.polyomino.com/> _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net <mailto:Cdk-user@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/cdk-user
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