Add operator[] to Vector3D as that is kind of customary in C++
Add a few methods to randomize particles in the XYZdecorator
Use the inactive particle exception in particle.h
Make some clarifications in the documents about what show and other things should do. And remove the name from the Optimization state since it is never used. We may want to put the name into object so that everything has it, but the current system with a few random objects having it is kind of awkward.
Add a singleton score function that applies a unary function to the value of a single attribute.
Daniel Russel wrote: > Add operator[] to Vector3D as that is kind of customary in C++
True - there's no reason really to have get_component() in this case. (operator[] can be trivially renamed to __getitem__ in IMP.i.) I also got rid of the #ifdef - the preprocessor is evil... and SWIG can just as easily be asked to %ignore (or, in future, %rename) the method.
> Make some clarifications in the documents about what show and other > things should do. And remove the > name from the Optimization state since it is never used. We may want to > put the name into object so that everything has it, but the current > system with a few random objects having it is kind of awkward.
I don't really see the point in anything having a name, except for restraint sets (perhaps). Your patch didn't actually seem to completely kill OptimizerState::name_, so I modified it a little.
> Add a singleton score function that applies a unary function to the > value of a single attribute.
A unit test for this one would be great...
Ben
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Ben Webb -
Daniel Russel