Dear JP, On Mon, Apr 4, 2011 at 6:27 PM, JP <[email protected]> wrote: > Sorry for the repeated emails/questions.
No worries, that's what the list is for. :-) > I am a bit confused about the RMS usage in RDKit. > > When comparing two different structures you can easily get an RMSD > score (as the delta takes the difference between the coordinates from > one structure to the other - > http://en.wikipedia.org/wiki/Root_mean_square_deviation_(bioinformatics)). > > But how does the RMS work? As far as I can see it is a value based on > one structure only (http://en.wikipedia.org/wiki/Root_mean_square). > There must be a numerical relationship between the two. > > How do these two relate and how are they used in RDKit. > Specifically I am interested in pruneRmsThres in > http://rdkit.org/Python_Docs/rdkit.Chem.rdDistGeom-module.html#EmbedMultipleConfs The use of RMS in the names of functions/function arguments in the RDKit should probably be viewed as a bug. It's a lazy shorthand for RMSD (root mean squared distance). Unfortunately actually fixing the nomenclature would change the API, which would breaking a lot of code, so we may be stuck with it as is. I can/should certainly fix the doc strings to make this more clear. -greg ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
