Tags: ihmwg/python-modelcif
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python-modelcif 1.4 release - Revision information and information on how the data in the file can be used are now read from or written to mmCIF or BinaryCIF files. See :attr:`System.revisions` and :attr:`System.data_usage` respectively. - New classes have been added to :mod:`modelcif.alignment`, :mod:`modelcif.qa_metric`, and :mod:`modelcif.protocol` to support all sequence identity denominators (#47), QA metric types (#45), and protocol step types (#44) respectively, as defined in the ModelCIF dictionary. - The new :class:`modelcif.alignment.Local` and :class:`modelcif.alignment.Multiple` classes allow for both local alignments and multiple sequence alignments to be described (#43). - Bugfix: sequence identity and alignment score (``identity`` and ``score`` arguments to :class:`modelcif.alignment.Pair`) are now optional, to match the mmCIF dictionary (#49). - Bugfix: information in ``_ma_template_non_poly.details`` is now read from mmCIF or BinaryCIF files (#48). - Bugfix: files containing empty or missing ``_ma_qa_metric.description`` can now be read (#46).
python-modelcif 1.3 release - 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.
python-modelcif 1.2 release - 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:`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`.
python-modelcif 1.1 release - 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.
python-modelcif 1.0 release - 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).
python-modelcif 0.7 release - 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).
python-modelcif 0.6 release - :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).
python-modelcif 0.5 release - 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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