python-ihm 2.11 release

• Hydroxyl radical footprinting data is now supported with the new ihm.restraint.HydroxylRadicalFPRestraint class (#193).
• EPR data is now supported using the new ihm.restraint.EPRRestraint and ihm.restraint.Probe classes (#190).
• Interface residues (those identified by experiments to be at the binding interface) can now be used as features using the new ihm.restraint.InterfaceResidueFeature class (#191).
• ihm.restraint.ResidueFeature adds by_residue and rep_atom fields to annotate how residue features are represented.
• make_mmcif will now fall back to ISO-8859-1 encoding if the input mmCIF is not valid UTF-8 (#184).
• make_mmcif now preserves non-IHM data present in the mmCIF struct and struct_asym tables.
• make_mmcif now preserves the original IDs (e.g. for software, datasets) present in the input mmCIF file, rather than reassigning them (#187).
• ihm.Citation now allows specifying the ASTM, CSD, and/or ISSN journal codes, and ihm.Citation.from_pubmed_id will fill in the ISSN code from a PubMed ID.
• An explicit formula weight can now be provided to ChemComp or Entity, which will be used instead of calculating the mass automatically based on the chemical formula and element masses. The latter calculation now takes leaving groups into account and so better estimates the total mass of polypeptides or polynucleotides.
• Bugfix: the chem_comp table no longer includes components that are present only in the reference database sequence (#186).
• Bugfix: better error message for missing features (#185).
• Bugfix: starting model sequence offset is now applied when reading comparative modeling template structures (#188).
• Bugfix: more consistent detection of the complete assembly (#189).

Full Changelog: 2.10...2.11

python-ihm 2.10 release

• The new classes ihm.reference.InsertionSeqDif and ihm.reference.DeletionSeqDif allow for annotating insertions or deletions in the entity sequence relative to the reference database. Files are now checked on output that the entity and reference sequences match with this insertion/deletion information included (#181).
• ihm.LPeptideAlphabet now maps the one-letter code 'O' to pyrrolysine.
• make_mmcif has a new --fix_struct_ref command line flag which if specified will fill in any missing reference database information such as the sequence (in the struct_ref table), by querying UniProt (#182).
• Bugfix: allow the starting model dataset to be empty (#180).

Full Changelog: 2.9...2.10

python-ihm 2.9 release

• If given a file containing non-polymers but missing the pdbx_entity_nonpoly table, make_mmcif will now reconstruct that table using information from the atom_site table (#177).
• If given a file containing an empty assembly (containing zero asyms), make_mmcif will now replace it with an auto-generated assembly containing all of the system's asyms (#178).
• make_mmcif has a new --fix_chem_comp command line flag which if specified will fill in any missing chemical component information (in the chem_comp table) such as type, name, or chemical formula by querying CCD (#179).
• Bugfix: backslash characters in text fields (such as in SMILES strings) no longer erroneously cause a dictionary validation error (#176).

Full Changelog: 2.8...2.9

python-ihm 2.8 release

• The new ihm.System.get_representative_model method returns a single ihm.model.ModelRepresentative that best represents the entire system (#174).
• Bugfix: spurious segments in the ihm_entity_poly_segment table are no longer created for ihm.restraint.ResidueFeature (#175).

Full Changelog: 2.7...2.8

python-ihm 2.7 release

• Representative models for ihm.model.ModelGroup can now be denoted using the ihm.model.ModelRepresentative class (#173).
• Bugfix: fix reference counts of Python bool objects.

Full Changelog: 2.6...2.7

python-ihm 2.6 release

• The new ihm.License and 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 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 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).
• ihm.metadata.CIFParser and ihm.metadata.BinaryCIFParser now return the same entity_source mapping that ihm.metadata.PDBParser does (#168).

Full Changelog: 2.5...2.6

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.

Full Changelog: 2.4...2.5

python-ihm 2.4 release

• Add support for fits of model groups or ensembles to cross-links using the new ihm.restraint.CrossLinkGroupFit class.

Full Changelog: 2.3...2.4

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 ihm.reference.SeqDif is used to annotate an insertion or deletion, don't erroneously claim the alignment is incorrect.

Full Changelog: 2.2...2.3

python-ihm 2.2 release

• The C-accelerated BinaryCIF parser now supports a wider range of data types.

Full Changelog: 2.1...2.2