Modelcif

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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.

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- 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`.

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- The new class :class:`modelcif.model.NotModeledResidueRange` allows for
the annotation of residue ranges that were explicitly not modeled.
Any residue marked as not-modeled in all models will be excluded from
the ``pdbx_poly_seq_scheme`` table.
- The ``util/make-mmcif.py`` script is now included in the installed package,
so can be run if desired with ``python3 -m modelcif.util.make_mmcif``.
- The ``make_mmcif`` utility script will now automatically add any
missing :class:`modelcif.model.NotModeledResidueRange` objects for
not-modeled residue ranges.

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- Reference information in the ``struct_ref`` mmCIF table is now supported
in addition to the ModelCIF-specific tables such as
``ma_target_ref_db_details``. :class:`modelcif.reference.TargetReference`
now inherits from ``ihm.reference.Sequence`` and allows for the full
database sequence, plus any differences between it and the modeled sequence,
to be recorded. The ``align_begin`` and ``align_end`` arguments are now
deprecated (34).

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- Bugfix: :class:`modelcif.SoftwareGroup` now allows for parameters to
be associated with each piece of software in the group, rather than
with the group as a whole (33).

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- :class:`modelcif.associated.File` now takes an optional ``data``
argument to allow describing any modeling input/output that is stored
in that file.
- RPM packages are now provided for Fedora and RedHat Enterprise Linux.