Ihm

================
- 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:`modelcif.CustomTemplate` class allows for custom templates
(that have not been deposited in a database such as PDB) to be referenced,
together with their atomic coordinates (1).
- Model quality scores can now be defined that act on single features or
pairs of features using the :class:`modelcif.qa_metric.Feature` and
:class:`modelcif.qa_metric.FeaturePairwise` classes, respectively.
Features can be defined as groups of atoms, residues, or asyms (38).
- The :class:`modelcif.associated.QAMetricsFile` class should now be used
to reference files that contain model quality scores. The old name
(LocalPairwiseQAScoresFile) is deprecated. This allows for all types of
QA scores, not just local pairwise scores, to be stored in a separate file.
- Sanity checks when writing out a file can now be disabled if desired,
using the new ``check`` argument to :func:`modelcif.dumper.write`.
- :class:`modelcif.reference.TargetReference` now takes an ``is_primary``
argument which can be used to denote the most pertinent sequence
database reference.
- Information on model groups (:class:`modelcif.model.ModelGroup`) is now
written to the new ``ma_model_group`` and ``ma_model_group_link`` mmCIF
tables, instead of ``ma_model_list``, to match the latest ModelCIF
dictionary. Old-style information in ``ma_model_list`` will still be
used when reading a file if these new tables are missing.

================
- Data that have been split over multiple mmCIF or BinaryCIF files can now
be combined into a single :class:`modelcif.System` object using the new
``add_to_system`` argument to :func:`modelcif.reader.read` (10).
- A new example, ``associated.py``, has been added to demonstrate reading
in data that has been split into multiple "associated" mmCIF files using
:class:`modelcif.associated.CIFFile`.