On 2018-01-17 10:25, Jason Biggs wrote:

For the case in question, I find that if I read in a mol file containing 2D coordinates, and I skip the sanitization step altogether, then the 3D embedding algorithms fail.

Well, yes, as I mentioned in the other thread: the only way you can get it to work reliably is if you start with 3D coordinates to begin with. Otherwise your users have to get in there every once in a while and decide which way to slice that cake they don't get to eat. ;)


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