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.
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.
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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.
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Depends which way I hold my screen :p. Some of this comes down to personal preference, for example Roger insists pyrroles should have the NH at the top, I say at the bottom, wikipedia and google images agree with me.
You can now fix coordinates so it's possible to make any ring shape you like.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
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.
Still is the case with the new SDG. John, what do you think?
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=C1CCCCCC1&abbr=on&suppressh=true&showtitle=false&zoom=2.5&annotate=none
Depends which way I hold my screen :p. Some of this comes down to personal preference, for example Roger insists pyrroles should have the NH at the top, I say at the bottom, wikipedia and google images agree with me.
You can now fix coordinates so it's possible to make any ring shape you like.