I would like to propose getting rid of the trajectory log in the model
as we can do the same sort of thing using State classes. Since these
aren't part of the Model, they would be much more flexible and
customizable. I currently have such a state for writing chimera BILD
files that I can submit at some point.
And I would propose removing the ModelData OptimizedIndexIterator (or
whatever it is called). The API is funny and it doesn't provide any
functionality which can't be achieved other ways using more or less
the same number of lines of code.