all-atom RMSD used to prune conformers in embedding code, docs say heavy-atom RMSD is used #1227

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greglandrum opened this Issue Dec 22, 2016 · 0 comments

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reported by JW Feng, here's the thread: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg06404.html

The docs say one thing, the code does another. One is wrong and should be fixed; either way the fix is not hard.

I believe that the right thing to do is calculate heavy-atom RMSD instead of all-atom RMSD, but this will change the results that are generated by the code, so I'm going to leave this open for a bit to see if any discussion pops up.

@greglandrum greglandrum added the bug label Dec 22, 2016
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