Tags: ihmwg/python-ihm
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python-ihm 2.6 release - The new :class:`ihm.License` and :class:`ihm.Disclaimer` classes allow describing how the data in the file can be used, and map to the ``pdbx_data_usage`` mmCIF table (#171). - Two :class:`ihm.Assembly` classes are now considered equal if they contain the same set of constituents, even if those constituents are in differing orders or are split differently into domains (#170). - The new :class:`ihm.format.ChangeFuncValueFilter` class allows modifying mmCIF values by passing them through an arbitrary Python function. - Checks for non-canonical atom names no longer use Ligand Expo to obtain CCD info, as it is being retired (#169). - :class:`ihm.metadata.CIFParser` and :class:`ihm.metadata.BinaryCIFParser` now return the same ``entity_source`` mapping that :class:`ihm.metadata.PDBParser` does (#168).
python-ihm 2.5 release - Assemblies are now checked at file-output time to ensure that each asym referenced in an assembly is represented by atoms and/or spheres in at least one model (#165). - ``make_mmcif`` has a new ``--check_atom_names`` option which, if set, will check for any non-canonical atom names (#166). - ``pip install`` should no longer fail to install if the C extension module cannot be built; it will fall back to use the slower pure Python implementation.
python-ihm 2.3 release - The C-accelerated BinaryCIF parser now supports interval quantization encoding and a wider range of data types. - ``make_mmcif`` now has a new ``--histidines`` option to convert any non-standard histidine names to HIS (#164). - Bugfix: don't change name or description of the complete assembly in ``make_mmcif``. - Bugfix: if :class:`ihm.reference.SeqDif` is used to annotate an insertion or deletion, don't erroneously claim the alignment is incorrect.
python-ihm 2.0 release - python-ihm no longer supports Python 2; the latest supported version is now Python 3.6 (#161). - BinaryCIF files are now read in using a C-accelerated parser, which is faster and more memory efficient than the older Python parser (#160). - The tokenizers for mmCIF and BinaryCIF now return data of the correct type (int, float, bool, or string); previously, all values were returned as strings. :class:`ihm.reader.Handler` subclasses now request data of the correct type using Python type annotations. The API of the C-accelerated parsers has changed accordingly (#162). - The new :class:`ihm.metadata.BinaryCIFParser` class can extract metadata such as database IDs and template information from BinaryCIF files, in a similar fashion to the existing :class:`ihm.metadata.CIFParser`. - Information about a deposited structure, such as the deposition date, can now be read from :attr:`System.database_status` (#163). - The new :class:`ihm.format.ReplaceCategoryFilter` class can be used to completely replace or remove an mmCIF category when using :class:`ihm.format.CifTokenReader`.
python-ihm 1.8 release - Support added for datasets containing EPR, X-ray diffraction, footprinting or predicted contacts using the :class:`ihm.dataset.EPRDataset`, :class:`ihm.dataset.XRayDiffractionDataset`, :class:`ihm.dataset.HydroxylRadicalFootprintingDataset`, :class:`ihm.dataset.DNAFootprintingDataset` and :class:`ihm.dataset.PredictedContactsDataset` classes (#157). - Revision information (in the ``pdbx_audit_revision_*`` mmCIF tables) can now be read or written using the new :class:`ihm.Revision` and :class:`ihm.RevisionDetails` classes (#156). - The new :class:`ihm.location.BMRbigLocation` class allows for referencing datasets stored in the BMRbig database. - All references to the old PDB-Dev database are now updated to PDB-IHM.
python-ihm 1.7 release - 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).
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