To try to get things moving a bit, here are the first few changes I plan on submitting for people to make high level comments: - adding the introduction.dox file - adding the XYZRDecorator that has been mentioned numerous times (it now supports setting the radius attribute name) - Simplify connectivity restraint to only support sets of size 1. You can using ParticleRefiners if you want larger sets (as in Frank's paper) - add io support for the model. It is in a header called core/ model_io.h. In contrast to how it was in the introduction, the methods are just called write/read rather than write_yaml as the yaml bit is an implementation detail that there is no reason to expose and we may want to change the format at some point

slightly later - change the nonbonded list to use the XYZRDecorator radius by default - add an is_nan function (this probably should go in kernel) so we don't have the funny looking x != x in places and the intent of the code is easier to understand. - rearrange the BondedLists. I think the best idea there is to replace BondedListScoreState with a simple ParticlePairsContainer (since that is all it is) and provide a few implementations of that one of which is equivalent to the BondDecoratorListScoreState.