Ihm

================
- :class:`ihm.format.CifTokenReader` allows for reading an mmCIF file
and breaking it into tokens. This can be used for various housekeeping
tasks directly on an mmCIF file, such as changing chain IDs or renaming
categories or data items, while preserving most other formatting such
as comments and whitespace (141).
- :class:`ihm.restraint.HDXRestraint` adds support for restraints
derived from Hydrogen-Deuterium Exchange experiments (143).
- The ``make_mmcif`` utility script now preserves more "orphan" data from
the input file that is not referenced by other tables (144).

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