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[IMP-dev] recently in IMP

- modules can now be built externally to the \imp svn in addition to applications and biological systems. To do so, create a directory with your module in a subdir containing links to the \imp SConscript file and scons_tools and a config.py that has information needed to run \imp (eg an appropriate \c pythonpath, \c ldpath).

- removed IMP::algebra::GridD::get_index(VectorD) as it wasn't very safe (in that vectors coordinates can get rounded between the IMP::algebra::GridD::get_has_index() and IMP::algebra::GridD::get_index() calls. Use IMP::algebra::GridD::get_nearest_index() or IMP::algebra::GridD::get_extended_index() or IMP::algebra::GridD::operator[]() instead.

- renamed IMP::domino::ParticleStatesTable::get_particles() to IMP::domino::ParticleStatesTable::get_subset() as it is more useful to be able to get the subset containing all the particles.

- rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of \imp.

- renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.

- class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.

- the plural names (eg IMP.Particles()) have been removed from the python side as they are just python lists.

- biological systems can now include internal modules. These provide a conventient place to put application specific C++ and python code. See the example system for more info.

- IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.

- the function IMP::core::Harmonic::k_from_standard_deviation was renamed to IMP::core::Harmonic::get_k_from_standard_deviation() to conform to the standards.

- the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
  means is that they need to be created with \c new in C++ code. It also means that one is
  no longer prohibited from storing them (not that there is much use in doing that).

- the standards tests have been improved to test more useful aspects. Now class and function names are checked some as well as all modules have the checks for show and plural types. The error messages should explain how to fix things.

- IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.

- the transform based methods on referene frame which have been deprecated for a while were removed

- the hierarchy visiting and searching functions have been renamed to better fit the \imp naming scheme as we don't expect they were used outside of the \imp source.

- IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version