On May 25, 2009, at 8:21 PM, Daniel Russel wrote:
> > On May 25, 2009, at 5:22 PM, Keren Lasker wrote: > >> this all makes sense yes. >> I am just not that is the most intuitive way to work > What is a more intuitive alternative. The current setup It works > quite a bit like the code for creating a centroid. > >> I would suggest adding functions for an external coordinate set and >> get transformation of RigidBodies as the internal coordinate system >> is an implementation detail. > I don't know what such would mean. Could you clarify? > > If someone gives you a bunch of particles, there isn't really a > single natural reference point. Different choices makes sense > depending on what you are doing with them. The code currently uses > the standard way of defining the position and orientation from > physics when using rigid bodies. > > I do agree that it probably makes sense to add a transform function > for rigid bodies to go with the one for IMP.atom.Hierarchy. yes ! this is exactly what I need for the optimization !! :)
> > >> On May 25, 2009, at 4:30 PM, Daniel Russel wrote: >> >>> As with any thing you want to use that is an offset from a value, >>> you need to keep track of the offset and subtract it when you set >>> the value. For ease with rigid bodies, compute the centroid in the >>> rigid body frame (or apply the inverse transform to map a point in >>> external coordinates) and then rotate the internal coordinates and >>> subtract them before setting when you want to set the >>> translational part of the coordinats later. Make sense? >>> >>> If you don't care what centroid you use, just use the rigid body >>> center (since it is currently a unwejghted centroid and will at >>> most change to a weighted centroid). >>> >>> >>> >>> On May 25, 2009, at 2:01 PM, Keren Lasker kerenl@salilab.org >>> wrote: >>> >>>> I know Daniel .... >>>> This is how I solved it now - but I would like to change the >>>> centroid of the rigid body after an optimization stage since it >>>> is part of a bigger optimization protocol. >>>> On May 25, 2009, at 1:54 PM, Daniel Russel wrote: >>>> >>>>> Assuming you want to transform, say, the input pdb, then just >>>>> get the transformation immediately following creation and >>>>> compose with that (since the initial transform has not moved the >>>>> object). >>>>> >>>>> >>>>> >>>>> On May 22, 2009, at 10:27 PM, Keren Lasker kerenl@salilab.org >>>>> wrote: >>>>> >>>>>> thanks - but what I want to do is different from RigidBodyMover >>>>>> as the transformation should be absolute and not relative. >>>>>> On May 22, 2009, at 9:40 PM, Dina Schneidman wrote: >>>>>> >>>>>>> it is rigid body internal coord. transformation. >>>>>>> you can move by composing it with your move. take a look at >>>>>>> RigidBodyMover.cpp propose_move func. >>>>>>> >>>>>>> On Fri, May 22, 2009 at 7:43 PM, Keren Lasker <kerenl@salilab.org >>>>>>> > wrote: >>>>>>>> >>>>>>>> Is the transformation given in set_transformation relative to >>>>>>>> a global >>>>>>>> internal coordinate system or to the rigid body internal >>>>>>>> coordinate system >>>>>>>> ? >>>>>>>> If the answer is that it is relative to the rigid body >>>>>>>> internal coordinate >>>>>>>> system -how can you move the rigid body to a specific >>>>>>>> position in space ? >>>>>>>> >>>>>>>> Thank you ! >>>>>>>> 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 >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >> >> _______________________________________________ >> 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