Daniel Russel wrote: > - The constructors for the nonbonded lists no longer take the radius key > as an argument. They default to XYZRDecorator::get_radius_key and the > value can be set using the set_radius_key method
What if I wanted a particle to have more than one radius? It seems like this would make such a thing impossible. I can certainly imagine spheres with a 'hard' inner radius and a 'soft' outer radius, to allow partial penetration. And all atoms in Modeller have two radii.
> - More changes to the names of the hierarchy and molecular hierarchy > decorator functions to make them more consistent. Those should be stable > now
Is there a reason why these are not static methods? Seems like that would make more sense, and give a cleaner namespace, e.g. rather than IMP::hierarchy_get_by_attributes(), use instead IMP::HierarchyDecorator::get_by_attributes().
> - I added a function in log.h to control whether exception messages are > dumped to standard error in addition to being embedded in the exception. > The current default is yes. The python lib init code should probably set > it to false for python, but I don't know how to do that.
I can handle that - it's just a %init line in the SWIG wrapper. I'm not sure why it should ever be true, actually. Surely if I throw an exception and then catch it somewhere else in the code that exception is expected, and I shouldn't bother the user with it. Seems like only unhandled exceptions should be logged.
Other changes look fine to me, and will continue to work their way gradually into SVN when I have time to disentangle the patch.
Ben