• IMP::atom::read_pdb() now has some documentation concerning what it
produces, especially in regards to HETATM records. In brief, ligands
are put intoIMP::atom::Residue along with actual residues (amino acids
and nucleotides). The RESIDUE IMP::atom::Hierarchy::Type has been
renamed to AMINOACIDand a type LIGAND has been added. See the
IMP::atom::Hierarchy docs.
• IMP::atom::Mass has been added for decorating particles with mas.
IMP::atom::Atom mass has been changed to use that. Non-atomic
representations of molecules should also use that decorator.
• The way to generate IMP::atom::AtomType strings from non-residue
atoms has now been specified. Code which produces/consumes such atoms
should follow the conventions..
• IMP::atom::get_chain() now returns an IMP::atom::Chain.
IMP::atom::root() was renamed to IMP::atom::get_root() for consistency.
• swig files are now generated from a file called swig.i in the pyext
directory. This file only has to contain module-specific commands such
as lines to wrap headers and instantiate module templates. No more
broiler-plate.
• the contents of bin are moving to tools since the two directories
both contained assorted development tools (not all of which were
executable). For now, bin/imppy.sh will still work, but that will go
away eventually. It really shouldn't be used outside of IMP
development anyway.
• IMP::Decorator::show() now just takes the stream (it used to take a
prefix also, which was often ignored). Anyone who implemented a
decorator will have to delete the second argument of their show
function.
Please make sure any behavior that you depend on of code in IMP is
well documented. Documentation is the only way to tell what is
intended behavior from what just happens to be that way as a result of
how things are implemented. The latter should not be counted on to
stay stable.