Ihm

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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.

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- More examples have been added to demonstrate interconversion between
mmCIF and BinaryCIF, and to validate mmCIF files.
- A utility script ``util/make-mmcif.py`` has been added which can add
minimal ModelCIF-related tables to an mmCIF file, to add in deposition.
- The reader is now more robust when handling files that are not ModelCIF
compliant (31).
- The ``exptl`` table is no longer written to output mmCIF files, to conform
with wwPDB's recommendation. Instead, the
``struct.pdbx_structure_determination_methodology`` data item denotes
that the model is computational (29).

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- :class:`ihm.ChemComp` now allows for custom chemical components to be
defined in a chemical component dictionary (CCD) outside of the wwPDB CCD,
such as the ModelArchive CCD, or in the file itself using descriptors such
as SMILES or InChI in the :mod:`modelcif.descriptor` module.
- The ``ma_struct_assembly`` category is no longer written out to mmCIF
files, as this is deprecated by ModelCIF (all models are required to
have the same composition).
- Templates can now be described in AlphaFoldDB or PubChem using new
:class:`modelcif.reference.TemplateReference` subclasses.
- HHblits e-values can now be used as alignment scores, using
:class:`modelcif.alignment.HHblitsEValue`.
- Bugfix: :class:`modelcif.associated.CIFFile` now writes local files
(if requested via ``categories`` or ``copy_categories``) even if it
is placed inside a :class:`modelcif.associated.ZipFile` (26).

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- A new class :class:`modelcif.ReferenceDatabase` allows describing
collections of sequences that were used as part of the modeling protocol.
- Lists of ints or floats can now be given as software parameters to the
:class:`modelcif.SoftwareParameter` class.

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- Sequence information for templates is now only written to template-specific
categories in the mmCIF/BinaryCIF, not to the entity, entity_poly etc.
tables, to properly comply with the ModelCIF dictionary.
- :class:`modelcif.Template` now takes a ``entity_id`` argument which can be
used to provide the entity ID (if known) of the template in its own mmCIF
file.
- External files (e.g. alignments, or quality scores) can now be referenced
from the main file (using the :mod:`modelcif.associated` module). Selected
CIF categories can automatically be written to these external files instead
of the main file, in either mmCIF or BinaryCIF format (see
:class:`modelcif.associated.CIFFile`).
- Non-polymer models can now be linked to their template using the
:class:`modelcif.NonPolymerFromTemplate` class.
- Add classes for the PLDDT, PTM, and IpTM quality metrics.
- :class:`modelcif.reference.TargetReference` now supports the version
and CRC64 checksum of the reference sequence.