Releases · ihmwg/python-ihm

A convenience class is added to describe datasets stored in the
ProXL database (:class:ihm.location.ProXLLocation).

Update to match latest FLR dictionary.
Add a simple utility (util/make-mmcif.py) to make a minimal compliant IHM mmCIF file, given an mmCIF file (potentially just coordinates) as input.
Bugfix: the full residue range spanned by a starting model is now reported, rather than just the subset that is mapped to one or more templates (#55).
Bugfix: handle TrEMBL UniProt sequences (#57).

Convenience classes are added to describe hydrogen/deuterium exchange data (ihm.dataset.HDXDataset) and datasets stored in the PDB-Dev database (ihm.location.PDBDevLocation).
Multiple ihm.restraint.CrossLinkPseudoSite objects can now be assigned to a given ihm.restraint.CrossLink.
Bugfix: the ihm.dataset.Dataset base class now has a type of "Other" rather than "unspecified" to conform with the latest IHM dictionary.

ihm.reader.read no longer discards models read from non-IHM mmCIF files; they are instead placed in their own ihm.model.ModelGroup.
Bugfix: both the pure Python and C-accelerated mmCIF readers are now more robust, able to handle files in binary mode (e.g. from opening a URL) and in Unicode (mmCIF files are supposed to be ASCII but python-ihm should handle any encoding Python supports).

ihm.dataset.Dataset objects that derive from another dataset can now record any transformation involved; see ihm.dataset.TransformedDataset.
ihm.metadata.PDBParser now extracts basic metadata from PDB files generated by SWISS-MODEL.
An 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 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).
ihm.restraint.PseudoSiteFeature now references an underlying ihm.restraint.PseudoSite, allowing a single pseudo site to be shared between a feature and a cross-link if desired.
ihm.model.Ensemble now supports describing subsamples from which the ensemble was constructed; see ihm.model.Subsample.
Bugfix: 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.

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 ihm.cross_linkers module.

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

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

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

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