Ihm

=================
- :class:`ihm.dataset.Dataset` objects that derive from another dataset
can now record any transformation involved; see
:class:`ihm.dataset.TransformedDataset`.
- :class:`ihm.metadata.PDBParser` now extracts basic metadata from
PDB files generated by SWISS-MODEL.
- An :class:`ihm.Entity` can now be linked to one or more reference databases
(e.g. UniProt). See the classes in the :mod:`ihm.reference` module.

=================
- A cross-link can now use pseudo sites to represent one or both ends of the
link. The new :class:`ihm.restraint.CrossLinkPseudoSite` object is used
when the end of the cross-link is not represented in the model but its
position is known (e.g. it may have been approximated given the position
of nearby residues).
- :class:`ihm.restraint.PseudoSiteFeature` now references an underlying
:class:`ihm.restraint.PseudoSite`, allowing a single pseudo site to be
shared between a feature and a cross-link if desired.
- :class:`ihm.model.Ensemble` now supports describing subsamples from which
the ensemble was constructed; see :class:`ihm.model.Subsample`.
- Bugfix: :meth:`ihm.Citation.from_pubmed_id` now works correctly when the
journal volume or page range are empty, or the page "range" is just a
single page.

=================
- :func:`ihm.reader.read` has a new optional ``reject_old_file`` argument.
If set, it will raise an exception if asked to read a file that conforms
to too old a version of the IHM extension dictionary.
- Definitions for the DHSO and BMSO cross-linkers are now provided in the
:mod:`ihm.cross_linkers` module.

=================
- :class:`ihm.restraint.ResidueFeature` objects can now act on one or
more :class:`Residue` objects, which act equivalently to
1-residue ranges (:class:`AsymUnitRange` or :class:`EntityRange`).
- The new :class:`ihm.dataset.GeneticInteractionsDataset` class and the
``mic_value`` argument to :class:`ihm.restraint.DerivedDistanceRestraint`
can be used to represent restraints from genetic interactions, such as
point-mutant epistatic miniarray profile (pE-MAP) data.

=================
- :class:`ihm.Assembly` objects can now only contain :class:`AsymUnit`
and :class:`AsymUnitRange` objects (not :class:`Entity` or
:class:`EntityRange`).
- Bugfix: ensembles that don't reference a :class:`ihm.model.ModelGroup`
no longer cause the reader to create bogus empty model groups.

=================
- Features (:class:`ihm.restraint.AtomFeature`,
:class:`ihm.restraint.ResidueFeature`, and
:class:`ihm.restraint.NonPolyFeature`), which previously could select part
or all of an :class:`ihm.AsymUnit`, can now also select parts of an
:class:`Entity`. A restraint acting on an entity-feature is assumed
to apply to all instances of that entity.