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- 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.