clean 2D and long alkyl chains

Hi,





When we have a compound with a long alkyl chain, such as CH₃(CH₂)₁₀OH, and we do a 2D clean, the cleaned compound is in its fully extended form, with a very large length and a very small width.





It would be nice to have an option to set the aspect ratio of the drawing to be within certain boundaries. In the example, you could fold the compound over on itself to halve the length and double the width.





-- Bob

Hi Bob,





Yes, I agree this would be nice however, it is not so obvious how to do this task if the molecule is not a long alkyl chain.


And there is an other problem: the cleaning algorithm is solved at molecule level. So it does not know about the canvas size.


Of course we can make an other clean method which takes some canvas size as a parameter, but actually I don't know how to solve this problem generally.





Do you have any idea how to solve it in a general way?





Volfi

I don't think you worry about the canvas size; you simply give it an optimal aspect ratio (length/width). You can provide it as one of the clean() options.





Yes, it's not obvious how to solve the problem if the compound doesn't have a long alkyl chain; but the long alkyl chain is usually what causes the problem, so I don't think you need to worry too much about other cases.

Actually we don't have capacity to implement this feature.


How important is this for you?


I will make a task for this but I cannot guarantee that this will be solved soon...

It is not high priority by any means.