it sounds great. just one question: can we have both rigid body
hierarchy and molecular hierarchy defined at the same time?
On Tue, Dec 9, 2008 at 4:21 PM, Daniel Russel <> wrote:
> There is now some code to use SingletonModifiers and a ScoreState and
> ParticleRefiners to, for example, make sure that each residue defines a
> sphere which contains all its atoms and that derivatives are propagated
> properly. Such would probably also make a good model for rigid bodies as all
> we would have to write would be four very simple classes:
> - a RigidBodyDecorator which inherits from XYZDecorator and adds a
> quaternion
> - a RigidBodyComponentDecorator which inherits from XYZDecorator and adds a
> set of coordinates relative to its original frame
> - a TorquesFromRefinedSingletonModifier (like
> DerivativesFromRefinedSingletonModifier) which uses the derivatives of the
> particles produced by a particle refiner to apply torques to a rigid body
> - a TransformComponentsSingletonModifier which applies the transform in a
> RigidBodyDecorator particle to each of the RigidBodyComponentDecorator
> particles produced by a particle refiner
>
> Then they could be tied together just as in the residue cover example and
> the rigid bodies could be trivially defined through a molecular hierarchy or
> any other particle refiner you want to use.
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