Ihm

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- The new class :class:`modelcif.model.NotModeledResidueRange` allows for
the annotation of residue ranges that were explicitly not modeled.
Any residue marked as not-modeled in all models will be excluded from
the ``pdbx_poly_seq_scheme`` table.
- The ``util/make-mmcif.py`` script is now included in the installed package,
so can be run if desired with ``python3 -m modelcif.util.make_mmcif``.
- The ``make_mmcif`` utility script will now automatically add any
missing :class:`modelcif.model.NotModeledResidueRange` objects for
not-modeled residue ranges.

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- Reference information in the ``struct_ref`` mmCIF table is now supported
in addition to the ModelCIF-specific tables such as
``ma_target_ref_db_details``. :class:`modelcif.reference.TargetReference`
now inherits from ``ihm.reference.Sequence`` and allows for the full
database sequence, plus any differences between it and the modeled sequence,
to be recorded. The ``align_begin`` and ``align_end`` arguments are now
deprecated (34).

=================
- Branched and polymeric empty entities are now distinguished
based on entity.type in the input file (previously, any empty
entity would always be reported as a polymer) (129).
- Warn rather than reporting an error if the system contains
one or more empty entities (128).
- If an input file contains multiple duplicated datasets, preserve
them as is rather than consolidating into a single dataset (127).
- Allow for multiple branched entities to have the same composition
(they could have different connectivity) (126).

=================
- The :class:`ihm.metadata.CIFParser` class now parses Modeller-specific
CIF categories to add information about software and templates for
Modeller-generated mmCIF starting models.
- Basic support for original author-provided residue numbering is now
provided in the :class:`ihm.AsymUnit` class with a new
``orig_auth_seq_id_map`` argument. This information is read from and
written to the various mmCIF tables such as ``pdbx_poly_seq_scheme``
(124).

=================
- More complete support for oligosaccharides, in particular correct
numbering for atoms in `atom_site`, and the addition of some
data items to the output which are required for full
dictionary compliance.

=================
- 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.