First, can everyone please clean up the warnings in your code and docs (do "scons doc > "dev/null"). There are currently quite a few and it is annoying to have to wade through all of them every time I compile to figure out if each is important or not (at least one of the current warnings is pointing out that the wrong function will be called in certain circumstances).

Remember, the only reason that warnings are not counting as errors (that break compilation) is that there were a couple of warnings in boost headers and gcc doesn't offer fine grained control.

Lots of (mosty cosmetic) changes and added functionality.

- IMP::atom::MolecularHierarchy has been renamed to IMP::atom::Hierarchyfile:///flute1/home/drussel/src/IMP/realsvn/doc/html/classIMP_1_1atom_1_1Hierarchy.html. Use

sed -i.old "s#MolecularHierarchy#Hierarchy#g" my_files

- the long-deprecated Name(Decorator) was removed

- The decorator suffix has been removed from decorator names. To update your code do

sed -i.old "s#([a-zA-Z])Decorator#\1#g" **/*.h **/*.cpp **/*.py **/*.i

or

sed -i.old "s#([a-zA-Z])Decorator#\1#g" `find * -name *.h -or -name *.cpp`

(and the various suffixes).

- Unit conventions have been established and documented for distance, energy, force and angle.

- there is a function IMP::atom::create_protein()file:///flute1/home/drussel/src/IMP/realsvn/doc/html/group__unstable.html#gb0c6db2fc2ced9b37dca1587fe310412to create a coarse grained protein. The function is crude so far, but the idea is that we should have standard ways of generating such things so that everyone can benifit from best practices.

- a class IMP::atom::BondGraphfile:///flute1/home/drussel/src/IMP/realsvn/doc/html/classIMP_1_1atom_1_1BondGraph.htmlhas been added so Boost.Graph algorithms can be used with bond graphs

- the IMP-specific doxygen commands have been documented. There is a link from the developers guide page.

- the doxygen commands \unstable{name}, \untested{name}, \unimplemented{name} have been added to doxygen to be used for marking methods and functions as likely to change or not well tested or not yet implemented. Pass the name of the class or method as name.

- bonds can now be added to molecular hierarchies automatically see IMP::atom::add_bonds()file:///flute1/home/drussel/src/IMP/realsvn/doc/html/namespaceIMP_1_1atom.html#69dcb8361d5bb4b68f641a6367e95743