- Instructions and scripts have been added for building modules and things externally to the \imp build. See the installation guide. Doing this can make the build cycle much faster as you don't have to wait for the scripts to parse all of IMP every time and while scons randomly rebuilds the swig wrappers.
- IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
residue naming to PDB-style, so CHARMM topology files can be used unmodified.
- IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
- IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
- IMP::atom::CHARMMTopology::add_missing_atoms() and
IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
read from a PDB file match the CHARMM topology.
- building of deprecated functionality is now false by default
- the IMP_COMPARISONS(), IMP_COMPARISONS_1(), IMP_COMPARISONS_2() macros now take the name of the class as an additional (first) argument. This avoids the formerly needed, \c This typedef and makes them more consistent with the other macros 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 in modulename/test/SConscript