Ihm

================
- :class:`ihm.System` now allows for one or more official database IDs to
be associated with the system using the new :class:`ihm.Database` class.
This maps to the mmCIF ``_database_2`` category (135).
- :class:`ihm.location.FileLocation` now allows for an optional file format
to be specified (139).
- The ``util/make-mmcif.py`` script is now included in the installed package,
so can be run if desired with ``python3 -m ihm.util.make_mmcif`` (134).
- Bugfix: allow for file sizes in input mmCIF files to be floating point
values (138).
- Bugfix: the 'Other' content type is now handled correctly when reading
information about external files from an mmCIF file (139).

================
- Support for multi-state schemes (such as kinetic rates and relaxation
times for conversions between states) was added;
see :mod:`ihm.multi_state_scheme`.
- Residue numbering in non-polymer, water, and branched entities should
now be better handled, no longer requiring the various scheme tables
to precede ``atom_site``. If you subclass :class:`ihm.model.Model`, atoms
may need to be renumbered; see :meth:`ihm.model.Model.add_atom` (130).
- Original author-provided numbering can now be provided for waters,
using the ``orig_auth_seq_id_map`` argument to :class:`ihm.WaterAsymUnit`.
- The make-mmcif.py utility script now has basic functionality for
combining multiple input files into one, relabeling chain IDs if necessary.
- An :class:`ihm.Entity` containing just a single sugar is now classified
as a nonpolymer, not branched.

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