Re: [IMP-dev] More patches with a couple API changes

[Ben Webb <>]

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
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle