On May 25, 2009, at 8:21 PM, Daniel Russel wrote:
On May 25, 2009, at 5:22 PM, Keren Lasker wrote:What is a more intuitive alternative. The current setup It works quite a bit like the code for creating a centroid.this all makes sense yes. I am just not that is the most intuitive way to workI 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 <> 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 <> 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 < > 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 https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev