From: SourceForge.net <no...@so...> - 2009-09-20 10:34:28
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Feature Requests item #2858670, was opened at 2009-09-14 18:07 Message generated for change (Comment added) made by steinbeck You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2858670&group_id=20024 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: jchempaint Group: None Status: Open Priority: 5 Private: No Submitted By: pmatos (pauladematos) Assigned to: Christoph Steinbeck (steinbeck) Summary: Seven Membered ring preferably in different orientation Initial Comment: Hi, When trying to draw a seven membered ring and I call clean structure. It comes out on its side. One of the bonds should be flat on the bottom with a pointy one on top. See image attached. P ---------------------------------------------------------------------- >Comment By: Christoph Steinbeck (steinbeck) Date: 2009-09-20 12:34 Message: This is a general and much more profound problem with my SDG code - the final global rotation of the outcome to a generally accepted form is not performed. I don't think this is a problem - I just never found the time to do it. If you take a steroid with some side chains and clean it up, you will see what I mean :-) To overcome the problem, I suggest a quick fix for the worst problem first and then work on a clean solution. The quick-fix would be a 2D Kabsch-Alignment (CDK code) of the outcome of the SDG to give at leat the approximately correct solution. For a clean solution, we would need to assemble the accepted rules for putting the axes of structures and then implement those. ---------------------------------------------------------------------- Comment By: Stefan Kuhn (shk3) Date: 2009-09-15 12:42 Message: This is really a problem of the SDG. I assign this to Christoph, he might have an idea if it can be done easily or how hard it is. I have no idea about the SDG. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2858670&group_id=20024 |