yes - this looks good, as long as it follows with examples for protein rigid bodies, usage of that in optimization, maybe also something about relevant score-states. Also - there is this issue of moving a rigid body that does not really does anything unless a flag is set - maybe it would be good to explain the mechanism of rigid body movements. Also - for optimization it might be useful to mention the RigidBodyMover. On Jan 26, 2010, at 1:56 AM, Daniel Russel wrote:
> Is this a better overview of rigid bodies text? The previous one was > not well structured. > > A rigid body particle describes a set of particles, known > as the members, which move rigidly together. Since the > members are simply a set of particles which move together > they don't (necessarily) define a shape. For example, > the members could include representations of the geometry > at several different representations. As a result, methods > that use rigid bodies also take a Refiner. This refiner > is used to map from the rigid body to the set of particles > defining the geometry of interest. > > The initial orientation of the rigid body is computed from > the coordinates, masses and radii of the particles > passed to the constructor, based on diagonalizing the > inertial tensor (which is not stored, currently). > > A rigid body stores the a set of local coordinates for each > member and an algebra::Transformation3D mapping between > the local coordinates and the actual location of the member. > > It is often desirable to randomize the orientation of a rigid > body: > \verbinclude randomize_rigid_body.py > > > On Jan 25, 2010, at 3:33 PM, Keren Lasker wrote: > >> thanks Daniel. >> Is there a function for each of those ? if so it would be useful to >> explicitly have it in the documentation. >> and specifically for my current requirement - what is the function >> for getting the set of particles which defines the highest >> resolution description of the shape, if the rigid body is not >> defined by atom::Hierarchy. >> ? >> On Jan 26, 2010, at 1:27 AM, Daniel Russel wrote: >> >>> On Jan 25, 2010, at 3:20 PM, Keren Lasker wrote: >>> >>>> To get the particles within a rigid body, it is better using >>>> IMP::core::get_leaves or get_members, >>> Maybe :-) They do different things (that might happen to have the >>> same result sometimes). >>> >>> >>>> i.e.: does get_members return the leaves or the children of the >>>> RigidBody ? >>> neither, it returns all particles which move rigidly with the >>> rigid body. >>> >>> Basically, when you have a shape that happens to be rigid, there >>> are many sets of particles associated with it >>> - all particles which movie rigidly with the shape (the rigid >>> members) >>> - the set of particles which defines the highest resolution >>> description of the shape (which, if the rigid body is created from >>> a molecular hierarchy, would be the leaves) >>> - the set of particles which defines the coarsest description of >>> the shape. Typically this is just the rigid body particle itself >>> with a radius >>> - the set of particles defining the residues in the rigid body >>> - the particles defining the sphere hierarchy used for collision >>> detection between that rigid hierarchy and another rigid hierarchy >>> (which would be members, if they existed) >>> etc. >>> >>> Depending on what you want to do, you will need different ones of >>> these sets. >>> >>> _______________________________________________ >>> 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