Ihm

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- Sanity checks when writing out a file can now be disabled if desired,
using the new ``check`` argument to :func:`ihm.dumper.write` (153).
- Data that have been split over multiple mmCIF or BinaryCIF files can now
be combined into a single :class:`ihm.System` object using the new
``add_to_system`` argument to :func:`ihm.reader.read`.
- Input files that assign multiple :class:`ihm.location.Location` objects
to a single :class:`ihm.dataset.Dataset` can now be read (151).
- Bugfix: multiple :class:`ihm.restraint.EM3DRestraint` and
:class:`ihm.restraint.SASRestraint` objects can now be created for a
single dataset, as long as they act on different assemblies, as allowed
by the dictionary.
- Bugfix: allow for non-standard residues in the ``struct_ref`` table (154).

================
- The new class :class:`ihm.model.NotModeledResidueRange` allows for
the annotation of residue ranges that were explicitly not modeled.
These are written to the ``_ihm_residues_not_modeled`` mmCIF table,
and any residue marked as not-modeled in all models will also be
excluded from the ``pdbx_poly_seq_scheme`` table.
- The ``make_mmcif`` utility script will now automatically add any
missing :class:`ihm.model.NotModeledResidueRange` objects for
not-modeled residue ranges (150).
- Bugfix: the residue range checks introduced in version 1.5 broke the
API used by python-modelcif. They have been reimplemented using the
original API.
- Bugfix: an unknown (?) value for ``pdbx_poly_seq_scheme.auth_seq_num``
is now preserved, not silently removed, when reading an mmCIF file.

================
- Trying to create a :class:`ihm.Residue`, :class:`ihm.EntityRange`, or
:class:`ihm.AsymUnitRange` that references out-of-range residues (i.e.
``seq_id`` less than 1 or beyond the length of the :class:`ihm.Entity`
sequence) will now raise an error.
- Bugfix: :class:`ihm.reference.Reference` objects are no longer given
erroneous duplicate IDs on output (149).

================
- :class:`ihm.metadata.CIFParser` now extracts metadata from mmCIF starting
models from Model Archive or compliant with the ModelCIF dictionary.
- :meth:`ihm.Citation.from_pubmed_id` now takes an ``is_primary`` argument,
to allow denoting the publication as the most pertinent for the modeling.
- Duplicate references, pseudo sites, and features are now pruned on
output (148).
- :class:`ihm.restraint.ResidueFeature` now reports an error if it is
given zero residue ranges (147).
- Bugfix: allow for :class:`ihm.startmodel.Template` ``seq_id_range``
or ``template_seq_id_range`` to be empty.

================
- The new class :class:`ihm.location.ProteomeXchangeLocation` can be used
for datasets stored in the ProteomeXchange database.
- Support is added for changes in the IHMCIF dictionary, specifically
the renaming of "CX-MS data" to "Crosslinking-MS data" and the
``_ihm_ordered_ensemble`` category to ``_ihm_ordered_model``. python-ihm
will output the new names, but for backwards compatibility will read both
old and new names.
- :class:`ihm.protocol.Protocol` can now be given additional text to
describe the protocol.
- :class:`ihm.model.Atom` now takes an ``alt_id`` argument to support
alternate conformations (146).
- Support added for NumPy 2.0.

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