Ihm

=================
- Basic support for oligosaccharides is now provided. New classes are
provided to describe saccharide chemical components
(:class:`ihm.SaccharideChemComp` and subclasses). Unlike polymers and
non-polymers, oligosaccharides can be branched, and a new
:class:`ihm.BranchLink` class allows the linkage between individual
components to be described.
- A summary report of the system can now be produced by calling
:meth:`ihm.System.report`. This can help to reveal errors or
inconsistencies, and will warn about missing data that may not be
technically required for a compliant mmCIF file, but is usually
expected to be present.
- :class:`ihm.metadata.MRCParser` now uses the new EMDB API to extract
version information and details for electron density map datasets.
- RPM packages are now available for recent versions of Fedora and
RedHat Enterprise Linux.

=================
- :class:`ihm.location.DatabaseLocation` no longer accepts a ``db_name``
parameter. Derived classes (such as :class:`ihm.location.PDBLocation`)
should be used instead; the base class should only be used for "other"
databases that are not described in the IHM dictionary (116).
- Bugfix: AlphaFold models in PDB format are no longer categorized by
:class:`ihm.metadata.PDBParser` as being deposited in the PDB database
with an empty accession code.

=================
- Convenience classes are added to describe datasets stored in
the Model Archive, iProX, and AlphaFoldDB repositories
(:class:`ihm.location.ModelArchiveLocation`,
:class:`ihm.location.IProXLocation`, and
:class:`ihm.location.AlphaFoldDBLocation` respectively).
- The new class :class:`ihm.metadata.CIFParser` can be used to extract
metadata from starting models in mmCIF format. It is currently in
development and only supports model metadata from PDB or Model Archive
at this time.
- Line wrapping of output mmCIF files can now be turned if desired using
:func:`ihm.dumper.set_line_wrap` (by default files are wrapped to 80
characters if possible).
- The make-mmcif.py utility script now allows for the name of the output
mmCIF file to be overridden (115).

=================
- Convenience classes are added to describe ensemble FRET datasets
(:class:`ihm.dataset.EnsembleFRETDataset`) and datasets stored in
the jPOSTrepo repository (:class:`ihm.location.JPOSTLocation`).
- Related depositions can now be grouped using the :class:`ihm.Collection`
class (108).
- The :class:`ihm.model.Ensemble` class has a new ``superimposed`` attribute
to indicate whether the grouped models are structurally aligned.

=================
- When reading a file that references external files, preserve any
information on the size of those files (104).
- When reading a file containing models not in a model group, preserve
any information on the number of models deposited (105).
- Bugfix: :func:`ihm.dictionary.read` now correctly handles dictionaries
that define a category after data items in that category (107).

=================
- Author names now use PDB style ("Lastname, A.B.") by default rather
than PubMed style ("Lastname AB") (95).
- Asyms containing multiple water molecules should now be correctly
handled (previously every water molecule in the output ``atom_site``
table was given the same ``auth_seq_id``). Use the new
:class:`ihm.WaterAsymUnit` to create an asym containing waters (98).
- Masses for all elements are now included, so that
``_entity.formula_weight`` can be correctly populated for ligands (99).
- Bugfix: :class:`ihm.analysis.Analysis` objects are now read correctly
from input files when two objects share the same ID but are part
of different protocols (101).