Ihm

=================
- :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).

=================
- Strings that start with STAR reserved words such as ``stop_`` are now
quoted to help some readers such as the GEMMI library
(ihmwg/python-modelcif25).
- If an input file defines a chemical descriptor with an empty name
but also defines ``linker_type``, use that to fill in the name (91).
- :class:`ihm.ChemComp` now allows for chemical components to be defined
in a chemical component dictionary (CCD) outside of the wwPDB CCD. This
is not used in python-ihm itself but can be used in python-modelcif.
- Bugfix: if a read mmCIF file defines a complete assembly, do not overwrite
its name and description on output (92).
- Bugfix: only allow clustering methods/features that are supported by
the underlying IHM dictionary for :class:`ihm.model.Ensemble` (94).
- Bugfix: categories such as ``_struct`` that are not typically looped
now support multi-line strings (ihmwg/python-modelcif27).