Not at the moment. It is relatively easy to change the code to support
it (by adding an arbitrary prefix to the keys) and I can do that if
desired.
On Dec 9, 2008, at 4:33 PM, Dina Schneidman wrote:
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