There is now a patch creating a search module which currently has a class to quickly find particles which have a certain values of some given attributes. I wanted to call the module "index" but that stomped on Index.h, so it became "search" instead. The python side of things is kind of a pain as it is too hard for swig to properly parse some of the templates. One could write a cool python wrapper which delegated to the correct C++ structure internally, but I won't.

There are also several other patches in kernel/doc/patch which: - document Particles - add a way to force ScoreStates to update (without having to guess a sequence number to use) - add the posted methods to create atom and residue types - add output to pairs and triplets - remove redundant documentation (although I suspect patches involving moving files are useless, but Ben hasn't responded on this) - clean up the configure scripts to make them more portable and less broken...