On Jul 10, 2009, at 12:33 AM, Daniel Russel wrote:
> Comments: > - The names should be more the questions that come up for me are > (1) if it is coordinate RMSD, are the molecules rigidly aligned > before it is computed (and with the hierarchies case, are they all > aligned together or separately) yes - this is a very simple function that assumes correspondence between the two structures. Solving the correspondence problem should be handled n a different function > > (2) is it coordinate RMSD or distance RMSD (maybe I've just been > around Vijay's lab too long, does anyone else use dRMSD?) this is RMSD. probably a dRMSD would be useful as well > > (3) it's not really clear what the distance between two collections > of Hierarchies (when do you average). > I think the most important distinction is (1). And I'm not sure > what the best way to convey it. Are there some conventional modifiers > that someone knows? "structural" and "positional"? > > - it probably should go in a new header distance.h as there are > likely to be many such functions along the way. It definitely > shouldn't be in pdb.h as they don't have to do with pdbs. > > - Also, they should probably return doubles instead of Float (since > that is just the storage type for attributes and doubles should always > be used for computations). > ok - I'll add these functions in distances.h and return doubles > > On Thu, Jul 9, 2009 at 2:09 PM, Keren Laskerkerenl@salilab.org > wrote: >> hi, >> >> are you all ok with me adding a function >> MPATOMEXPORT Float rmsd(const Hierarchy& m1 ,const Hierarchy& m2); >> IMPATOMEXPORT Float rmsd(const Hierarchies& mh1 ,const Hierarchies& >> mh2); >> >> to pdb.h or utility.h in IMP::atom ? >> >> thanks, >> Keren. >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev