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 Lasker<>
wrote:
hi,
are you all ok with me adding a function
MPATOMEXPORT Float rmsd(const Hierarchy& m1 ,const Hierarchy& m2);